--- /srv/reproducible-results/rbuild-debian/r-b-build.LIgQFbeB/b1/mia_2.4.7-11_armhf.changes +++ /srv/reproducible-results/rbuild-debian/r-b-build.LIgQFbeB/b2/mia_2.4.7-11_armhf.changes ├── Files │ @@ -1,9 +1,9 @@ │ │ 20b2902fb6121732cd13095f5ea5f92e 89369252 debug optional libmia-2.4-4-dbgsym_2.4.7-11_armhf.deb │ e71f323426d3d35ce802d0e717587230 3980392 libs optional libmia-2.4-4_2.4.7-11_armhf.deb │ 2ff9f6ca3bbd4f90eb4278916426824a 204520 libdevel optional libmia-2.4-dev_2.4.7-11_armhf.deb │ 400c1c26d1199899f46a52dd6058c41a 4768960 doc optional libmia-2.4-doc_2.4.7-11_all.deb │ 9c7486d4c060693bc4439c1adbaf0331 26168 science optional mia-doctools_2.4.7-11_all.deb │ de70b7b99fd1b76d9b5b561fd3a54564 34799600 debug optional mia-tools-dbgsym_2.4.7-11_armhf.deb │ - f433d5da247121801b2623f696eebde1 96268 doc optional mia-tools-doc_2.4.7-11_all.deb │ - 56615341db9d25468906abf9f97ef4be 1696756 science optional mia-tools_2.4.7-11_armhf.deb │ + 8b6e0f131ebef9d2aabb92d715dcb196 96276 doc optional mia-tools-doc_2.4.7-11_all.deb │ + 70f76648439e82bc82407f665d2dee6b 1696508 science optional mia-tools_2.4.7-11_armhf.deb ├── mia-tools-doc_2.4.7-11_all.deb │ ├── file list │ │ @@ -1,3 +1,3 @@ │ │ -rw-r--r-- 0 0 0 4 2022-08-17 13:27:13.000000 debian-binary │ │ --rw-r--r-- 0 0 0 5940 2022-08-17 13:27:13.000000 control.tar.xz │ │ +-rw-r--r-- 0 0 0 5948 2022-08-17 13:27:13.000000 control.tar.xz │ │ -rw-r--r-- 0 0 0 90136 2022-08-17 13:27:13.000000 data.tar.xz │ ├── control.tar.xz │ │ ├── control.tar │ │ │ ├── ./md5sums │ │ │ │ ├── ./md5sums │ │ │ │ │┄ Files differ │ ├── data.tar.xz │ │ ├── data.tar │ │ │ ├── ./usr/share/doc/mia-2.4/userref/SecPlugintype2dimagefilter.html │ │ │ │ @@ -57,15 +57,15 @@ │ │ │ │

│ │ │ │

bandpass

intensity bandpass filter. Supported parameters are:

NameTypeDefaultDescription
maxfloat3.40282e+38maximum of the band
minfloat0minimum of the band

│ │ │ │

│ │ │ │

binarize

image binarize filter. Supported parameters are:

NameTypeDefaultDescription
maxfloat3.40282e+38maximum of accepted range
minfloat0minimum of accepted range

│ │ │ │

│ │ │ │

close

morphological close. Supported parameters are:

NameTypeDefaultDescription
hintsetblacka hint at the main image content Supported values are:(black, white, )
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ │

│ │ │ │ -

combiner

Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run.. Supported parameters are:

NameTypeDefaultDescription
imageio(input,required)second image that is needed in the combiner. For supported file types see Plugin type: 2dimage/io
opfactory(required)Image combiner to be applied to the images. For supported plug-ins see Plugin type: 2dimage/combiner
reversebool0reverse the order in which the images passed to the combiner

│ │ │ │ +

combiner

Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run.. Supported parameters are:

NameTypeDefaultDescription
imageio(required,input)second image that is needed in the combiner. For supported file types see Plugin type: 2dimage/io
opfactory(required)Image combiner to be applied to the images. For supported plug-ins see Plugin type: 2dimage/combiner
reversebool0reverse the order in which the images passed to the combiner

│ │ │ │

│ │ │ │

convert

image pixel format conversion filter. Supported parameters are:

NameTypeDefaultDescription
afloat1linear conversion parameter a
bfloat0linear conversion parameter b
mapdictopt
conversion mapping
copy:copy data when converting
linear:apply linear transformation x -> a*x+b
range:apply linear transformation that maps the input data type range to the output data type range
opt:apply a linear transformation that maps the real input range to the full output range
optstat:apply a linear transform that maps based on input mean and variation to the full output range
repndictubyte
output pixel type
bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined

│ │ │ │

│ │ │ │

crop

Crop a region of an image, the region is always clamped to the original image size.. Supported parameters are:

NameTypeDefaultDescription
endstreamable[[-1,-1]]end of crop region
startstreamable[[0,0]]start of crop region

│ │ │ │

│ │ │ │

dilate

2d image stack dilate filter. Supported parameters are:

NameTypeDefaultDescription
hintsetblacka hint at the main image content Supported values are:(black, white, )
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ │

│ │ │ │ @@ -81,43 +81,43 @@ │ │ │ │

│ │ │ │

invert

intensity invert filter. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │

kmeans

2D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image.. Supported parameters are:

NameTypeDefaultDescription
cint in [2, inf)3number of classes

│ │ │ │

│ │ │ │

label

Label connected components in a binary 2D image.. Supported parameters are:

NameTypeDefaultDescription
nfactory4nNeighborhood mask to describe connectivity.. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ │

│ │ │ │ -

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

NameTypeDefaultDescription
mapstring(input,required)Label mapping file

│ │ │ │ +

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

NameTypeDefaultDescription
mapstring(required,input)Label mapping file

│ │ │ │

│ │ │ │

labelscale

A filter that only creates output voxels that are already created in the input image. Scaling is done by using a voting algorithms that selects the target pixel value based on the highest pixel count of a certain label in the corresponding source region. If the region comprises two labels with the same count, the one with the lower number wins.. Supported parameters are:

NameTypeDefaultDescription
out-size2dbounds(required)target size given as two coma separated values

│ │ │ │

│ │ │ │ -

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

NameTypeDefaultDescription
fileio(input,required)name of the input file to load from.. For supported file types see Plugin type: 2dimage/io

│ │ │ │ +

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

NameTypeDefaultDescription
fileio(required,input)name of the input file to load from.. For supported file types see Plugin type: 2dimage/io

│ │ │ │

│ │ │ │ -

mask

2D masking, one of the two input images must by of type bit.. Supported parameters are:

NameTypeDefaultDescription
filldictmin
fill style for pixels outside of the mask
min:set values outside the mask to the minimum value found in the image.
zero:set the values outside the mask to zero.
max:set values outside the mask to the maximum value found in the image..
inputio(input,required)second input image file name. For supported file types see Plugin type: 2dimage/io
inversebool0set to true to use the inverse of the mask for masking

│ │ │ │ +

mask

2D masking, one of the two input images must by of type bit.. Supported parameters are:

NameTypeDefaultDescription
filldictmin
fill style for pixels outside of the mask
min:set values outside the mask to the minimum value found in the image.
zero:set the values outside the mask to zero.
max:set values outside the mask to the maximum value found in the image..
inputio(required,input)second input image file name. For supported file types see Plugin type: 2dimage/io
inversebool0set to true to use the inverse of the mask for masking

│ │ │ │

│ │ │ │ -

maxflow

This filter implements the uses the max-flow min-cut algorithmfor image segmentation. Supported parameters are:

NameTypeDefaultDescription
sink-flowio(input,required)Image of float type to define the per-pixel flow to the sink. For supported file types see Plugin type: 2dimage/io
source-flowio(input,required)Image of float type to define the per-pixel flow to the source. For supported file types see Plugin type: 2dimage/io

│ │ │ │ +

maxflow

This filter implements the uses the max-flow min-cut algorithmfor image segmentation. Supported parameters are:

NameTypeDefaultDescription
sink-flowio(required,input)Image of float type to define the per-pixel flow to the sink. For supported file types see Plugin type: 2dimage/io
source-flowio(required,input)Image of float type to define the per-pixel flow to the source. For supported file types see Plugin type: 2dimage/io

│ │ │ │

│ │ │ │

mean

2D image mean filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1half filter width

│ │ │ │

│ │ │ │ -

meanvar

Filter that evaluates simultaniously the pixel wise mean and the variance of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output mean and variation are set to zero. The mean intensity image is directly passed as float image to the pipeline, the variation image is saved to a file given with the varfile parameter.. Supported parameters are:

NameTypeDefaultDescription
threshdouble in [0, inf)0Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
varfileio(output,required)name of the output file to save the variation image too.. For supported file types see Plugin type: 2dimage/io
wuint in [1, inf)1filter width parameter

│ │ │ │ +

meanvar

Filter that evaluates simultaniously the pixel wise mean and the variance of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output mean and variation are set to zero. The mean intensity image is directly passed as float image to the pipeline, the variation image is saved to a file given with the varfile parameter.. Supported parameters are:

NameTypeDefaultDescription
threshdouble in [0, inf)0Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
varfileio(required,output)name of the output file to save the variation image too.. For supported file types see Plugin type: 2dimage/io
wuint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │

median

2D image median filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1half filter width

│ │ │ │

│ │ │ │ -

medianmad

Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image.. Supported parameters are:

NameTypeDefaultDescription
madfileio(output,required)name of the output file to save the median absolute deviation image too.. For supported file types see Plugin type: 2dimage/io
threshdouble in [0, inf)0Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
wuint in [1, inf)1filter width parameter

│ │ │ │ +

medianmad

Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image.. Supported parameters are:

NameTypeDefaultDescription
madfileio(required,output)name of the output file to save the median absolute deviation image too.. For supported file types see Plugin type: 2dimage/io
threshdouble in [0, inf)0Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation
wuint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │

mlv

Mean of Least Variance 2D image filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │

ngfnorm

2D image to normalized-gradiend-field-norm filter. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │

noise

2D image noise filter: add additive or modulated noise to an image. Supported parameters are:

NameTypeDefaultDescription
gfactory[gauss:mu=0,sigma=10]noise generator. For supported plug-ins see Plugin type: generator/noise
modbool0additive or modulated noise

│ │ │ │

│ │ │ │

open

morphological open. Supported parameters are:

NameTypeDefaultDescription
hintsetblacka hint at the main image content Supported values are:(black, white, )
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ │

│ │ │ │

pruning

Morphological pruning. Pruning until convergence will erase all pixels but closed loops.. Supported parameters are:

NameTypeDefaultDescription
iterint in [1, 1000000]0Number of iterations to run, 0=until convergence

│ │ │ │

│ │ │ │ -

regiongrow

Region growing startin from a seed until only along increasing gradients. Supported parameters are:

NameTypeDefaultDescription
nfactory8nNeighborhood shape. For supported plug-ins see Plugin type: 2dimage/shape
seedio(input,required)seed image (bit valued). For supported file types see Plugin type: 2dimage/io

│ │ │ │ +

regiongrow

Region growing startin from a seed until only along increasing gradients. Supported parameters are:

NameTypeDefaultDescription
nfactory8nNeighborhood shape. For supported plug-ins see Plugin type: 2dimage/shape
seedio(required,input)seed image (bit valued). For supported file types see Plugin type: 2dimage/io

│ │ │ │

│ │ │ │

sandp

salt and pepper 3d filter. Supported parameters are:

NameTypeDefaultDescription
threshfloat in (0, inf)100thresh value
wint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │

scale

2D image downscale filter. Supported parameters are:

NameTypeDefaultDescription
interpfactory[bspline:d=3]interpolation method to be used . For supported plug-ins see Plugin type: 1d/splinekernel
s2dbounds[[0,0]]target size as 2D vector
sxuint in [0, inf)0target size in x direction, 0: use input size
syuint in [0, inf)0target size in y direction, 0: use input size

│ │ │ │

│ │ │ │

selectbig

2D label select biggest component filter. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │ @@ -125,25 +125,25 @@ │ │ │ │

│ │ │ │

shmean

2D image filter that evaluates the mean over a given neighborhood shape. Supported parameters are:

NameTypeDefaultDescription
shapefactory8nneighborhood shape to evaluate the mean. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ │

│ │ │ │

sobel

The 2D Sobel filter for gradient evaluation. Note that the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable.. Supported parameters are:

NameTypeDefaultDescription
dirdictx
Gradient direction
x:gradient in x-direction
y:gradient in y-direction

│ │ │ │

│ │ │ │

sort-label

This plug-in sorts the labels of a gray-scale image so that the lowest label value corresponts to the lable with themost pixels. The background (0) is not touched. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │ -

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

NameTypeDefaultDescription
gradbool0Interpret the input image as gradient.
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape
seedstring(input,required)seed input image containing the lables for the initial regions

│ │ │ │ +

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

NameTypeDefaultDescription
gradbool0Interpret the input image as gradient.
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape
seedstring(required,input)seed input image containing the lables for the initial regions

│ │ │ │

│ │ │ │ -

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

NameTypeDefaultDescription
fileio(output,required)name of the output file to save the image too.. For supported file types see Plugin type: 2dimage/io

│ │ │ │ +

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

NameTypeDefaultDescription
fileio(required,output)name of the output file to save the image too.. For supported file types see Plugin type: 2dimage/io

│ │ │ │

│ │ │ │

thinning

Morphological thinning. Thinning until convergence will result in a 8-connected skeleton. Supported parameters are:

NameTypeDefaultDescription
iterint in [1, 1000000]0Number of iterations to run, 0=until convergence

│ │ │ │

│ │ │ │

thresh

This filter sets all pixels of an image to zero that fall below a certain threshold and whose neighbours in a given neighborhood shape also fall below a this threshold. Supported parameters are:

NameTypeDefaultDescription
shapefactory4nneighborhood shape to take into account. For supported plug-ins see Plugin type: 2dimage/shape
threshdouble5The threshold value

│ │ │ │

│ │ │ │

tmean

2D image thresholded tmean filter: The output pixel value is zero if the input pixel value is below the given threshold, otherwise the pixels in the evaluation windows are only considered if the input pixel intensity is above the threshold.. Supported parameters are:

NameTypeDefaultDescription
tfloat0Threshold for pixels not to take into account
wint in [1, inf)1half filter width

│ │ │ │

│ │ │ │ -

transform

Transform the input image with the given transformation.. Supported parameters are:

NameTypeDefaultDescription
fileio(input,required)Name of the file containing the transformation.. For supported file types see Plugin type: 2dtransform/io

│ │ │ │ +

transform

Transform the input image with the given transformation.. Supported parameters are:

NameTypeDefaultDescription
fileio(required,input)Name of the file containing the transformation.. For supported file types see Plugin type: 2dtransform/io

│ │ │ │

│ │ │ │

ws

basic watershead segmentation.. Supported parameters are:

NameTypeDefaultDescription
evalgradbool0Set to 1 if the input image does not represent a gradient norm image
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 2dimage/shape
threshfloat in [0, 1)0Relative gradient norm threshold. The actual value threshold value is thresh * (max_grad - min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined

│ │ │ │

Plugin consumers:

│ │ │ │ mia-2dimagefilter │ │ │ │ mia-2dimagefilterstack │ │ │ │ mia-2dsegment-fuzzyw │ │ │ │ mia-2dseries2dordermedian │ │ │ │ ├── html2text {} │ │ │ │ │ @@ -65,15 +65,15 @@ │ │ │ │ │ combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to │ │ │ │ │ false, the first operator is the image passed through the filter pipeline, and │ │ │ │ │ the second image is loaded from the file given with the 'image' parameter the │ │ │ │ │ moment the filter is run.. Supported parameters are: │ │ │ │ │ _____________________________________________________________________________ │ │ │ │ │ |__Name_|__Type_|______Default___|________________________Description_________| │ │ │ │ │ -| image | io |(input,required)|second image that is needed in the combiner.| │ │ │ │ │ +| image | io |(required,input)|second image that is needed in the combiner.| │ │ │ │ │ | | | |For supported file types see Plugin_type: | │ │ │ │ │ |_______|_______|________________|2dimage/io__________________________________| │ │ │ │ │ | op |factory| (required) |Image combiner to be applied to the images. | │ │ │ │ │ | | | |For supported plug-ins see Plugin_type: | │ │ │ │ │ |_______|_______|________________|2dimage/combiner____________________________| │ │ │ │ │ |reverse| bool | 0 |reverse the order in which the images passed| │ │ │ │ │ |_______|_______|________________|to_the_combiner_____________________________| │ │ │ │ │ @@ -174,57 +174,57 @@ │ │ │ │ │ | n |factory| 4n |Neighborhood mask to describe connectivity.. For | │ │ │ │ │ |____|_______|_______|supported_plug-ins_see_Plugin_type:_2dimage/shape| │ │ │ │ │ labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued │ │ │ │ │ intensities/labels.. Supported parameters are: │ │ │ │ │ _______________________________________________ │ │ │ │ │ |Name|_Type_|______Default___|_____Description__| │ │ │ │ │ -|map_|string|(input,required)|Label_mapping_file| │ │ │ │ │ +|map_|string|(required,input)|Label_mapping_file| │ │ │ │ │ labelscale │ │ │ │ │ A filter that only creates output voxels that are already created in the input │ │ │ │ │ image. Scaling is done by using a voting algorithms that selects the target │ │ │ │ │ pixel value based on the highest pixel count of a certain label in the │ │ │ │ │ corresponding source region. If the region comprises two labels with the same │ │ │ │ │ count, the one with the lower number wins.. Supported parameters are: │ │ │ │ │ ___________________________________________________________________________ │ │ │ │ │ |___Name_|___Type_|__Default_|__________________________Description_________| │ │ │ │ │ |out-size|2dbounds|(required)|target_size_given_as_two_coma_separated_values| │ │ │ │ │ load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the │ │ │ │ │ pipeline.. Supported parameters are: │ │ │ │ │ ___________________________________________________________________________ │ │ │ │ │ |Name|Type|______Default___|___________________________Description__________| │ │ │ │ │ -|file| io |(input,required)|name of the input file to load from.. For | │ │ │ │ │ +|file| io |(required,input)|name of the input file to load from.. For | │ │ │ │ │ |____|____|________________|supported_file_types_see_Plugin_type:_2dimage/io| │ │ │ │ │ mask │ │ │ │ │ 2D masking, one of the two input images must by of type bit.. Supported │ │ │ │ │ parameters are: │ │ │ │ │ ____________________________________________________________________________ │ │ │ │ │ |__Name_|Type|______Default___|__________________________Description_________| │ │ │ │ │ | fill |dict| min | _________________________________________ | │ │ │ │ │ | | | ||fill_style_for_pixels_outside_of_the_mask| | │ │ │ │ │ | | | ||min: |set values outside the mask to the | | │ │ │ │ │ | | | ||_____|minimum_value_found_in_the_image.__| | │ │ │ │ │ | | | ||zero:|set the values outside the mask to | | │ │ │ │ │ | | | ||_____|zero.______________________________| | │ │ │ │ │ | | | ||max: |set values outside the mask to the | | │ │ │ │ │ |_______|____|________________||_____|maximum_value_found_in_the_image.._|___| │ │ │ │ │ -| input | io |(input,required)|second input image file name. For supported | │ │ │ │ │ +| input | io |(required,input)|second input image file name. For supported | │ │ │ │ │ |_______|____|________________|file_types_see_Plugin_type:_2dimage/io________| │ │ │ │ │ |inverse|bool| 0 |set to true to use the inverse of the mask for| │ │ │ │ │ |_______|____|________________|masking_______________________________________| │ │ │ │ │ maxflow │ │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image │ │ │ │ │ segmentation. Supported parameters are: │ │ │ │ │ _____________________________________________________________________________ │ │ │ │ │ |_____Name__|Type|______Default___|________________________Description________| │ │ │ │ │ -| sink-flow | io |(input,required)|Image of float type to define the per-pixel| │ │ │ │ │ +| sink-flow | io |(required,input)|Image of float type to define the per-pixel| │ │ │ │ │ | | | |flow to the sink. For supported file types | │ │ │ │ │ |___________|____|________________|see_Plugin_type:_2dimage/io________________| │ │ │ │ │ -|source-flow| io |(input,required)|Image of float type to define the per-pixel| │ │ │ │ │ +|source-flow| io |(required,input)|Image of float type to define the per-pixel| │ │ │ │ │ | | | |flow to the source. For supported file | │ │ │ │ │ |___________|____|________________|types_see_Plugin_type:_2dimage/io__________| │ │ │ │ │ mean │ │ │ │ │ 2D image mean filter. Supported parameters are: │ │ │ │ │ ______________________________________________ │ │ │ │ │ |Name|________Type___|Default|____Description__| │ │ │ │ │ |__w_|int_in_[1,_inf)|____1__|half_filter_width| │ │ │ │ │ @@ -239,15 +239,15 @@ │ │ │ │ │ |__Name_|__________Type____|_______Default___|_______________Description______| │ │ │ │ │ |thresh |double in [0, inf)| 0 |Intensity thresholding | │ │ │ │ │ | | | |parameter: Pixels with | │ │ │ │ │ | | | |intensities below this threshold| │ │ │ │ │ | | | |will be set to zero, and also | │ │ │ │ │ | | | |not used when evaluating mean | │ │ │ │ │ |_______|__________________|_________________|and_variation___________________| │ │ │ │ │ -|varfile| io |(output,required)|name of the output file to save | │ │ │ │ │ +|varfile| io |(required,output)|name of the output file to save | │ │ │ │ │ | | | |the variation image too.. For | │ │ │ │ │ | | | |supported file types see Plugin | │ │ │ │ │ |_______|__________________|_________________|type:_2dimage/io________________| │ │ │ │ │ |____w__|_uint_in_[1,_inf)_|____________1____|filter_width_parameter__________| │ │ │ │ │ median │ │ │ │ │ 2D image median filter. Supported parameters are: │ │ │ │ │ ______________________________________________ │ │ │ │ │ @@ -259,15 +259,15 @@ │ │ │ │ │ the given threshold will be ignored and at their loctions the output median and │ │ │ │ │ MAD are set to zero. The median intensity image is directly passed to the │ │ │ │ │ pipeline, the variation image is saved to a file given with the varfile │ │ │ │ │ parameter. Both output images have the same pixel type like the input image.. │ │ │ │ │ Supported parameters are: │ │ │ │ │ _____________________________________________________________________________ │ │ │ │ │ |__Name_|__________Type____|_______Default___|_______________Description______| │ │ │ │ │ -|madfile| io |(output,required)|name of the output file to save | │ │ │ │ │ +|madfile| io |(required,output)|name of the output file to save | │ │ │ │ │ | | | |the median absolute deviation | │ │ │ │ │ | | | |image too.. For supported file | │ │ │ │ │ | | | |types see Plugin_type:_2dimage/ | │ │ │ │ │ |_______|__________________|_________________|io______________________________| │ │ │ │ │ |thresh |double in [0, inf)| 0 |Intensity thresholding | │ │ │ │ │ | | | |parameter: Pixels with | │ │ │ │ │ | | | |intensities below this threshold| │ │ │ │ │ @@ -309,15 +309,15 @@ │ │ │ │ │ regiongrow │ │ │ │ │ Region growing startin from a seed until only along increasing gradients. │ │ │ │ │ Supported parameters are: │ │ │ │ │ ____________________________________________________________________________ │ │ │ │ │ |Name|__Type_|______Default___|__________________________Description_________| │ │ │ │ │ | n |factory| 8n |Neighborhood shape. For supported plug-ins see| │ │ │ │ │ |____|_______|________________|Plugin_type:_2dimage/shape____________________| │ │ │ │ │ -|seed| io |(input,required)|seed image (bit valued). For supported file | │ │ │ │ │ +|seed| io |(required,input)|seed image (bit valued). For supported file | │ │ │ │ │ |____|_______|________________|types_see_Plugin_type:_2dimage/io_____________| │ │ │ │ │ sandp │ │ │ │ │ salt and pepper 3d filter. Supported parameters are: │ │ │ │ │ _______________________________________________________ │ │ │ │ │ |_Name_|_________Type____|Default|________Description___| │ │ │ │ │ |thresh|float_in_(0,_inf)|___100_|thresh_value__________| │ │ │ │ │ |___w__|_int_in_[1,_inf)_|____1__|filter_width_parameter| │ │ │ │ │ @@ -373,22 +373,22 @@ │ │ │ │ │ |Name|__Type_|______Default___|___________________________Description_________| │ │ │ │ │ |grad|__bool_|___________0____|Interpret_the_input_image_as_gradient._________| │ │ │ │ │ |mark| bool | 0 |Mark the segmented watersheds with a special | │ │ │ │ │ |____|_______|________________|gray_scale_value_______________________________| │ │ │ │ │ | n |factory| [sphere:r=1] |Neighborhood for watershead region growing. For| │ │ │ │ │ | | | |supported plug-ins see Plugin_type:_2dimage/ | │ │ │ │ │ |____|_______|________________|shape__________________________________________| │ │ │ │ │ -|seed|string |(input,required)|seed input image containing the lables for the | │ │ │ │ │ +|seed|string |(required,input)|seed input image containing the lables for the | │ │ │ │ │ |____|_______|________________|initial_regions________________________________| │ │ │ │ │ tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter. │ │ │ │ │ Supported parameters are: │ │ │ │ │ ___________________________________________________________________________ │ │ │ │ │ |Name|Type|_______Default___|___________________________Description_________| │ │ │ │ │ -|file| io |(output,required)|name of the output file to save the image too..| │ │ │ │ │ +|file| io |(required,output)|name of the output file to save the image too..| │ │ │ │ │ | | | |For supported file types see Plugin_type: | │ │ │ │ │ |____|____|_________________|2dimage/io_____________________________________| │ │ │ │ │ thinning │ │ │ │ │ Morphological thinning. Thinning until convergence will result in a 8-connected │ │ │ │ │ skeleton. Supported parameters are: │ │ │ │ │ _____________________________________________________________________ │ │ │ │ │ |Name|___________Type____|Default|__________________Description_______| │ │ │ │ │ @@ -413,15 +413,15 @@ │ │ │ │ │ |__t_|_______float___|____0__|Threshold_for_pixels_not_to_take_into_account| │ │ │ │ │ |__w_|int_in_[1,_inf)|____1__|half_filter_width____________________________| │ │ │ │ │ transform │ │ │ │ │ Transform the input image with the given transformation.. Supported parameters │ │ │ │ │ are: │ │ │ │ │ ___________________________________________________________________________ │ │ │ │ │ |Name|Type|______Default___|___________________________Description__________| │ │ │ │ │ -|file| io |(input,required)|Name of the file containing the transformation..| │ │ │ │ │ +|file| io |(required,input)|Name of the file containing the transformation..| │ │ │ │ │ | | | |For supported file types see Plugin_type: | │ │ │ │ │ |____|____|________________|2dtransform/io__________________________________| │ │ │ │ │ ws │ │ │ │ │ basic watershead segmentation.. Supported parameters are: │ │ │ │ │ ____________________________________________________________________________ │ │ │ │ │ |___Name_|________Type___|___Default__|____________________Description_______| │ │ │ │ │ |evalgrad| bool | 0 |Set to 1 if the input image does not | │ │ │ ├── ./usr/share/doc/mia-2.4/userref/SecPlugintype2dstackfilter.html │ │ │ │ @@ -16,19 +16,19 @@ │ │ │ │

│ │ │ │

dilate

2D Stack morphological filter 'dilate'. Supported parameters are:

NameTypeDefaultDescription
shapefactory6nstructuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │

erode

2D Stack morphological filter 'erode'. Supported parameters are:

NameTypeDefaultDescription
shapefactory6nstructuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │

gauss

Gauss 2D fifo filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter (2*w+1)

│ │ │ │

│ │ │ │ -

label

Stack Label filter. Supported parameters are:

NameTypeDefaultDescription
mapstring(input,required)Mapfile to save label numbers that are joined
nfactory4n2D neighbourhood shape to define connectedness. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ │ +

label

Stack Label filter. Supported parameters are:

NameTypeDefaultDescription
mapstring(required,input)Mapfile to save label numbers that are joined
nfactory4n2D neighbourhood shape to define connectedness. For supported plug-ins see Plugin type: 2dimage/shape

│ │ │ │

│ │ │ │

median

median 2D fifo filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │

mlv

Mean of Least Variance 2D stack image filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │

open

2D Stack morphological filter 'open'. Supported parameters are:

NameTypeDefaultDescription
shapefactory6nstructuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │ -

regiongrow

Run a region-growing filter on a stack of images that comprise a 3D image. The region growing is based on class probabilities obtained from a c-means classification of the pixel intensities. One seed thresh is use to initiate a region, and another (lower) threshold is used to stop the region growing. By holding a number of 3D slices in the working memory to permit the region to grow "backwards " in the stack a Quasi-3D processing is achieved. However, with complex structures the region growing may not properly be segmented.. Supported parameters are:

NameTypeDefaultDescription
classint in [0, inf)2class to be segmented
depthint in [1, inf)10number of slices to keep during processing
lowfloat in (0, 1]0.5low threshold for acceptance probability
mapstring(input,required)seed class map
seedfloat in (0, 1]0.98threshold for seed probability

│ │ │ │ +

regiongrow

Run a region-growing filter on a stack of images that comprise a 3D image. The region growing is based on class probabilities obtained from a c-means classification of the pixel intensities. One seed thresh is use to initiate a region, and another (lower) threshold is used to stop the region growing. By holding a number of 3D slices in the working memory to permit the region to grow "backwards " in the stack a Quasi-3D processing is achieved. However, with complex structures the region growing may not properly be segmented.. Supported parameters are:

NameTypeDefaultDescription
classint in [0, inf)2class to be segmented
depthint in [1, inf)10number of slices to keep during processing
lowfloat in (0, 1]0.5low threshold for acceptance probability
mapstring(required,input)seed class map
seedfloat in (0, 1]0.98threshold for seed probability

│ │ │ │

Plugin consumers:

│ │ │ │ mia-2dstackfilter │ │ │ │

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -42,15 +42,15 @@ │ │ │ │ │ ___________________________________________________________ │ │ │ │ │ |Name|________Type___|Default|______________Description_____| │ │ │ │ │ |__w_|int_in_[1,_inf)|____1__|filter_width_parameter_(2*w+1)| │ │ │ │ │ label │ │ │ │ │ Stack Label filter. Supported parameters are: │ │ │ │ │ _____________________________________________________________________________ │ │ │ │ │ |Name|__Type_|______Default___|___________________________Description_________| │ │ │ │ │ -|map_|string_|(input,required)|Mapfile_to_save_label_numbers_that_are_joined__| │ │ │ │ │ +|map_|string_|(required,input)|Mapfile_to_save_label_numbers_that_are_joined__| │ │ │ │ │ | n |factory| 4n |2D neighbourhood shape to define connectedness.| │ │ │ │ │ | | | |For supported plug-ins see Plugin_type: | │ │ │ │ │ |____|_______|________________|2dimage/shape__________________________________| │ │ │ │ │ median │ │ │ │ │ median 2D fifo filter. Supported parameters are: │ │ │ │ │ ___________________________________________________ │ │ │ │ │ |Name|________Type___|Default|________Description___| │ │ │ │ │ @@ -78,14 +78,14 @@ │ │ │ │ │ ______________________________________________________________________ │ │ │ │ │ |Name_|________Type___|______Default___|_______________Description_____| │ │ │ │ │ |class|int_in_[0,_inf)|___________2____|class_to_be_segmented__________| │ │ │ │ │ |depth|int in [1, inf)| 10 |number of slices to keep during| │ │ │ │ │ |_____|_______________|________________|processing_____________________| │ │ │ │ │ | low |float in (0, 1]| 0.5 |low threshold for acceptance | │ │ │ │ │ |_____|_______________|________________|probability____________________| │ │ │ │ │ -|_map_|______string___|(input,required)|seed_class_map_________________| │ │ │ │ │ +|_map_|______string___|(required,input)|seed_class_map_________________| │ │ │ │ │ |seed_|float_in_(0,_1]|_________0.98___|threshold_for_seed_probability_| │ │ │ │ │ Plugin consumers: │ │ │ │ │ mia-2dstackfilter │ │ │ │ │ =============================================================================== │ │ │ │ │ Prev  Up  Next │ │ │ │ │ Plugin type: 2dimage/transform Home  Plugin type: 2dtransform/io │ │ │ ├── ./usr/share/doc/mia-2.4/userref/SecPlugintype3dimagefilter.html │ │ │ │ @@ -45,15 +45,15 @@ │ │ │ │

│ │ │ │

bandpass

intensity bandpass filter. Supported parameters are:

NameTypeDefaultDescription
maxfloat3.40282e+38maximum of the band
minfloat0minimum of the band

│ │ │ │

│ │ │ │

binarize

image binarize filter. Supported parameters are:

NameTypeDefaultDescription
maxfloat3.40282e+38maximum of accepted range
minfloat0minimum of accepted range

│ │ │ │

│ │ │ │

close

morphological close. Supported parameters are:

NameTypeDefaultDescription
hintstringblacka hint at the main image content (black|white)
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │ -

combiner

Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run.. Supported parameters are:

NameTypeDefaultDescription
imageio(input,required)second image that is needed in the combiner. For supported file types see Plugin type: 3dimage/io
opfactory(required)Image combiner to be applied to the images. For supported plug-ins see Plugin type: 3dimage/combiner
reversebool0reverse the order in which the images passed to the combiner

│ │ │ │ +

combiner

Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run.. Supported parameters are:

NameTypeDefaultDescription
imageio(required,input)second image that is needed in the combiner. For supported file types see Plugin type: 3dimage/io
opfactory(required)Image combiner to be applied to the images. For supported plug-ins see Plugin type: 3dimage/combiner
reversebool0reverse the order in which the images passed to the combiner

│ │ │ │

│ │ │ │

convert

image pixel format conversion filter. Supported parameters are:

NameTypeDefaultDescription
afloat1linear conversion parameter a
bfloat0linear conversion parameter b
mapdictopt
conversion mapping
copy:copy data when converting
linear:apply linear transformation x -> a*x+b
range:apply linear transformation that maps the input data type range to the output data type range
opt:apply a linear transformation that maps the real input range to the full output range
optstat:apply a linear transform that maps based on input mean and variation to the full output range
repndictubyte
output pixel type
bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined

│ │ │ │

│ │ │ │

crop

Crop a region of an image, the region is always clamped to the original image size in the sense that the given range is kept.. Supported parameters are:

NameTypeDefaultDescription
endstreamable[[4294967295,4294967295,4294967295]]end of cropping range, maximum = (-1,-1,-1)
startstreamable[[0,0,0]]begin of cropping range

│ │ │ │

│ │ │ │

dilate

3d image stack dilate filter. Supported parameters are:

NameTypeDefaultDescription
hintstringblacka hint at the main image content (black|white)
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │ @@ -63,33 +63,33 @@ │ │ │ │

│ │ │ │

erode

3d image stack erode filter. Supported parameters are:

NameTypeDefaultDescription
hintstringblacka hint at the main image content (black|white)
shapefactory[sphere:r=2]structuring element. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │

gauss

isotropic 3D gauss filter. Supported parameters are:

NameTypeDefaultDescription
wint in [0, inf)1filter width parameter

│ │ │ │

│ │ │ │

gradnorm

3D image to gradient norm filter. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │ -

growmask

Use an input binary mask and a reference gray scale image to do region growing by adding the neighborhood pixels of an already added pixel if the have a lower intensity that is above the given threshold.. Supported parameters are:

NameTypeDefaultDescription
minfloat1lower threshold for mask growing
refio(input,required)reference image for mask region growing. For supported file types see Plugin type: 3dimage/io
shapefactory6nneighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │ +

growmask

Use an input binary mask and a reference gray scale image to do region growing by adding the neighborhood pixels of an already added pixel if the have a lower intensity that is above the given threshold.. Supported parameters are:

NameTypeDefaultDescription
minfloat1lower threshold for mask growing
refio(required,input)reference image for mask region growing. For supported file types see Plugin type: 3dimage/io
shapefactory6nneighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │

invert

intensity invert filter. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │

isovoxel

This filter scales an image to make the voxel size isometric and its size to correspond to the given value. Supported parameters are:

NameTypeDefaultDescription
interpfactory[bspline:d=3]interpolation kernel to be used . For supported plug-ins see Plugin type: 1d/splinekernel
sizefloat in (0, inf)1isometric target voxel size

│ │ │ │

│ │ │ │

kmeans

3D image k-means filter. In the output image the pixel value represents the class membership and the class centers are stored as attribute in the image.. Supported parameters are:

NameTypeDefaultDescription
cint in [2, inf)3number of classes

│ │ │ │

│ │ │ │

label

A filter to label the connected components of a binary image.. Supported parameters are:

NameTypeDefaultDescription
nfactory6nneighborhood mask. For supported plug-ins see Plugin type: 3dimage/shape

│ │ │ │

│ │ │ │ -

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

NameTypeDefaultDescription
mapstring(input,required)Label mapping file

│ │ │ │ +

labelmap

Image filter to remap label id's. Only applicable to images with integer valued intensities/labels.. Supported parameters are:

NameTypeDefaultDescription
mapstring(required,input)Label mapping file

│ │ │ │

│ │ │ │

labelscale

A filter that only creates output voxels that are already created in the input image. Scaling is done by using a voting algorithms that selects the target pixel value based on the highest pixel count of a certain label in the corresponding source region. If the region comprises two labels with the same count, the one with the lower number wins.. Supported parameters are:

NameTypeDefaultDescription
out-size3dbounds(required)target size given as two coma separated values

│ │ │ │

│ │ │ │ -

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

NameTypeDefaultDescription
fileio(input,required)name of the input file to load from.. For supported file types see Plugin type: 3dimage/io

│ │ │ │ +

load

Load the input image from a file and use it to replace the current image in the pipeline.. Supported parameters are:

NameTypeDefaultDescription
fileio(required,input)name of the input file to load from.. For supported file types see Plugin type: 3dimage/io

│ │ │ │

│ │ │ │

lvdownscale

This is a label voting downscale filter. It adownscales a 3D image by blocks. For each block the (non-zero) label that appears most times in the block is issued as output pixel in the target image. If two labels appear the same number of times, the one with the lower absolute value wins.. Supported parameters are:

NameTypeDefaultDescription
b3dbounds[[1,1,1]]blocksize for the downscaling. Each block will be represented by one pixel in the target image.

│ │ │ │

│ │ │ │ -

mask

Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary.. Supported parameters are:

NameTypeDefaultDescription
inputio(input,required)second input image file name. For supported file types see Plugin type: 3dimage/io

│ │ │ │ +

mask

Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary.. Supported parameters are:

NameTypeDefaultDescription
inputio(required,input)second input image file name. For supported file types see Plugin type: 3dimage/io

│ │ │ │

│ │ │ │

mean

3D image mean filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1half filter width

│ │ │ │

│ │ │ │

median

median 3d filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │

mlv

Mean of Least Variance 3D image filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1filter width parameter

│ │ │ │

│ │ │ │ @@ -109,21 +109,21 @@ │ │ │ │

│ │ │ │

selectbig

A filter that creats a binary mask representing the intensity with the highest pixel count.The pixel value 0 will be ignored, and if two intensities have the same pixel count, then the result is undefined. The input pixel must have an integral pixel type.. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │

sepconv

3D image intensity separaple convolution filter. Supported parameters are:

NameTypeDefaultDescription
kxfactory[gauss:w=1]filter kernel in x-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
kyfactory[gauss:w=1]filter kernel in y-direction. For supported plug-ins see Plugin type: 1d/spacialkernel
kzfactory[gauss:w=1]filter kernel in z-direction. For supported plug-ins see Plugin type: 1d/spacialkernel

│ │ │ │

│ │ │ │

sobel

The 2D Sobel filter for gradient evaluation. Note that the output pixel type of the filtered image is the same as the input pixel type, so converting the input beforehand to a floating point valued image is recommendable.. Supported parameters are:

NameTypeDefaultDescription
dirdictx
Gradient direction
x:gradient in x-direction
y:gradient in y-direction
z:gradient in z-direction

│ │ │ │

│ │ │ │ -

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

NameTypeDefaultDescription
gradbool0Interpret the input image as gradient.
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
seedstring(input,required)seed input image containing the lables for the initial regions

│ │ │ │ +

sws

seeded watershead. The algorithm extracts exactly so many reagions as initial labels are given in the seed image.. Supported parameters are:

NameTypeDefaultDescription
gradbool0Interpret the input image as gradient.
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
seedstring(required,input)seed input image containing the lables for the initial regions

│ │ │ │

│ │ │ │ -

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

NameTypeDefaultDescription
fileio(output,required)name of the output file to save the image too.. For supported file types see Plugin type: 3dimage/io

│ │ │ │ +

tee

Save the input image to a file and also pass it through to the next filter. Supported parameters are:

NameTypeDefaultDescription
fileio(required,output)name of the output file to save the image too.. For supported file types see Plugin type: 3dimage/io

│ │ │ │

│ │ │ │

thinning

3D morphological thinning, based on: Lee and Kashyap, 'Building Skeleton Models via 3-D Medial Surface/Axis Thinning Algorithms', Graphical Models and Image Processing, 56(6):462-478, 1994. This implementation only supports the 26 neighbourhood.. (This plug-in doesn't take parameters)

│ │ │ │

│ │ │ │ -

transform

Transform the input image with the given transformation.. Supported parameters are:

NameTypeDefaultDescription
fileio(input,required)Name of the file containing the transformation.. For supported file types see Plugin type: 3dtransform/io
imgboundaryfactory override image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory override image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

│ │ │ │ +

transform

Transform the input image with the given transformation.. Supported parameters are:

NameTypeDefaultDescription
fileio(required,input)Name of the file containing the transformation.. For supported file types see Plugin type: 3dtransform/io
imgboundaryfactory override image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory override image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

│ │ │ │

│ │ │ │

variance

3D image variance filter. Supported parameters are:

NameTypeDefaultDescription
wint in [1, inf)1half filter width

│ │ │ │

│ │ │ │

ws

basic watershead segmentation.. Supported parameters are:

NameTypeDefaultDescription
evalgradbool0Set to 1 if the input image does not represent a gradient norm image
markbool0Mark the segmented watersheds with a special gray scale value
nfactory[sphere:r=1]Neighborhood for watershead region growing. For supported plug-ins see Plugin type: 3dimage/shape
threshfloat in [0, 1)0Relative gradient norm threshold. The actual value threshold value is thresh * (max_grad - min_grad) + min_grad. Bassins separated by gradients with a lower norm will be joined

│ │ │ │

Plugin consumers:

│ │ │ │ mia-3dcost │ │ │ │ mia-3dimagefilter │ │ │ │ ├── html2text {} │ │ │ │ │ @@ -36,15 +36,15 @@ │ │ │ │ │ combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to │ │ │ │ │ false, the first operator is the image passed through the filter pipeline, and │ │ │ │ │ the second image is loaded from the file given with the 'image' parameter the │ │ │ │ │ moment the filter is run.. Supported parameters are: │ │ │ │ │ _____________________________________________________________________________ │ │ │ │ │ |__Name_|__Type_|______Default___|________________________Description_________| │ │ │ │ │ -| image | io |(input,required)|second image that is needed in the combiner.| │ │ │ │ │ +| image | io |(required,input)|second image that is needed in the combiner.| │ │ │ │ │ | | | |For supported file types see Plugin_type: | │ │ │ │ │ |_______|_______|________________|3dimage/io__________________________________| │ │ │ │ │ | op |factory| (required) |Image combiner to be applied to the images. | │ │ │ │ │ | | | |For supported plug-ins see Plugin_type: | │ │ │ │ │ |_______|_______|________________|3dimage/combiner____________________________| │ │ │ │ │ |reverse| bool | 0 |reverse the order in which the images passed| │ │ │ │ │ |_______|_______|________________|to_the_combiner_____________________________| │ │ │ │ │ @@ -132,15 +132,15 @@ │ │ │ │ │ growmask │ │ │ │ │ Use an input binary mask and a reference gray scale image to do region growing │ │ │ │ │ by adding the neighborhood pixels of an already added pixel if the have a lower │ │ │ │ │ intensity that is above the given threshold.. Supported parameters are: │ │ │ │ │ _____________________________________________________________________________ │ │ │ │ │ |Name_|__Type_|______Default___|__________________________Description_________| │ │ │ │ │ |_min_|_float_|___________1____|lower_threshold_for_mask_growing______________| │ │ │ │ │ -| ref | io |(input,required)|reference image for mask region growing. For | │ │ │ │ │ +| ref | io |(required,input)|reference image for mask region growing. For | │ │ │ │ │ | | | |supported file types see Plugin_type:_3dimage/| │ │ │ │ │ |_____|_______|________________|io____________________________________________| │ │ │ │ │ |shape|factory| 6n |neighborhood mask. For supported plug-ins see | │ │ │ │ │ |_____|_______|________________|Plugin_type:_3dimage/shape____________________| │ │ │ │ │ invert │ │ │ │ │ intensity invert filter. (This plug-in doesn't take parameters) │ │ │ │ │ isovoxel │ │ │ │ │ @@ -167,30 +167,30 @@ │ │ │ │ │ | n |factory| 6n |neighborhood mask. For supported plug-ins see Plugin| │ │ │ │ │ |____|_______|_______|type:_3dimage/shape_________________________________| │ │ │ │ │ labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued │ │ │ │ │ intensities/labels.. Supported parameters are: │ │ │ │ │ _______________________________________________ │ │ │ │ │ |Name|_Type_|______Default___|_____Description__| │ │ │ │ │ -|map_|string|(input,required)|Label_mapping_file| │ │ │ │ │ +|map_|string|(required,input)|Label_mapping_file| │ │ │ │ │ labelscale │ │ │ │ │ A filter that only creates output voxels that are already created in the input │ │ │ │ │ image. Scaling is done by using a voting algorithms that selects the target │ │ │ │ │ pixel value based on the highest pixel count of a certain label in the │ │ │ │ │ corresponding source region. If the region comprises two labels with the same │ │ │ │ │ count, the one with the lower number wins.. Supported parameters are: │ │ │ │ │ ___________________________________________________________________________ │ │ │ │ │ |___Name_|___Type_|__Default_|__________________________Description_________| │ │ │ │ │ |out-size|3dbounds|(required)|target_size_given_as_two_coma_separated_values| │ │ │ │ │ load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the │ │ │ │ │ pipeline.. Supported parameters are: │ │ │ │ │ ___________________________________________________________________________ │ │ │ │ │ |Name|Type|______Default___|___________________________Description__________| │ │ │ │ │ -|file| io |(input,required)|name of the input file to load from.. For | │ │ │ │ │ +|file| io |(required,input)|name of the input file to load from.. For | │ │ │ │ │ |____|____|________________|supported_file_types_see_Plugin_type:_3dimage/io| │ │ │ │ │ lvdownscale │ │ │ │ │ This is a label voting downscale filter. It adownscales a 3D image by blocks. │ │ │ │ │ For each block the (non-zero) label that appears most times in the block is │ │ │ │ │ issued as output pixel in the target image. If two labels appear the same │ │ │ │ │ number of times, the one with the lower absolute value wins.. Supported │ │ │ │ │ parameters are: │ │ │ │ │ @@ -202,15 +202,15 @@ │ │ │ │ │ Mask an image, one image is taken from the parameters list and the other from │ │ │ │ │ the normal filter input. Both images must be of the same dimensions and one │ │ │ │ │ must be binary. The attributes of the image coming through the filter pipeline │ │ │ │ │ are preserved. The output pixel type corresponds to the input image that is not │ │ │ │ │ binary.. Supported parameters are: │ │ │ │ │ ____________________________________________________________________________ │ │ │ │ │ |Name_|Type|______Default___|___________________________Description__________| │ │ │ │ │ -|input| io |(input,required)|second input image file name. For supported file| │ │ │ │ │ +|input| io |(required,input)|second input image file name. For supported file| │ │ │ │ │ |_____|____|________________|types_see_Plugin_type:_3dimage/io_______________| │ │ │ │ │ mean │ │ │ │ │ 3D image mean filter. Supported parameters are: │ │ │ │ │ ______________________________________________ │ │ │ │ │ |Name|________Type___|Default|____Description__| │ │ │ │ │ |__w_|int_in_[1,_inf)|____1__|half_filter_width| │ │ │ │ │ median │ │ │ │ │ @@ -330,35 +330,35 @@ │ │ │ │ │ |Name|__Type_|______Default___|___________________________Description_________| │ │ │ │ │ |grad|__bool_|___________0____|Interpret_the_input_image_as_gradient._________| │ │ │ │ │ |mark| bool | 0 |Mark the segmented watersheds with a special | │ │ │ │ │ |____|_______|________________|gray_scale_value_______________________________| │ │ │ │ │ | n |factory| [sphere:r=1] |Neighborhood for watershead region growing. For| │ │ │ │ │ | | | |supported plug-ins see Plugin_type:_3dimage/ | │ │ │ │ │ |____|_______|________________|shape__________________________________________| │ │ │ │ │ -|seed|string |(input,required)|seed input image containing the lables for the | │ │ │ │ │ +|seed|string |(required,input)|seed input image containing the lables for the | │ │ │ │ │ |____|_______|________________|initial_regions________________________________| │ │ │ │ │ tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter. │ │ │ │ │ Supported parameters are: │ │ │ │ │ ___________________________________________________________________________ │ │ │ │ │ |Name|Type|_______Default___|___________________________Description_________| │ │ │ │ │ -|file| io |(output,required)|name of the output file to save the image too..| │ │ │ │ │ +|file| io |(required,output)|name of the output file to save the image too..| │ │ │ │ │ | | | |For supported file types see Plugin_type: | │ │ │ │ │ |____|____|_________________|3dimage/io_____________________________________| │ │ │ │ │ thinning │ │ │ │ │ 3D morphological thinning, based on: Lee and Kashyap, 'Building Skeleton Models │ │ │ │ │ via 3-D Medial Surface/Axis Thinning Algorithms', Graphical Models and Image │ │ │ │ │ Processing, 56(6):462-478, 1994. This implementation only supports the 26 │ │ │ │ │ neighbourhood.. (This plug-in doesn't take parameters) │ │ │ │ │ transform │ │ │ │ │ Transform the input image with the given transformation.. Supported parameters │ │ │ │ │ are: │ │ │ │ │ ____________________________________________________________________________ │ │ │ │ │ |_____Name__|__Type_|______Default___|_____________________Description_______| │ │ │ │ │ -| file | io |(input,required)|Name of the file containing the | │ │ │ │ │ +| file | io |(required,input)|Name of the file containing the | │ │ │ │ │ | | | |transformation.. For supported file | │ │ │ │ │ |___________|_______|________________|types_see_Plugin_type:_3dtransform/io__| │ │ │ │ │ |imgboundary|factory|   |override image interpolation boundary | │ │ │ │ │ | | | |conditions. For supported plug-ins see | │ │ │ │ │ |___________|_______|________________|Plugin_type:_1d/splinebc_______________| │ │ │ │ │ | imgkernel |factory|   |override image interpolator kernel. For| │ │ │ │ │ | | | |supported plug-ins see Plugin_type:_1d/| │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2davgmasked.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-2davgmasked

mia-2davgmasked

Sysnopis:

mia-2davgmasked {-i io} {-m io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Evaluate average intensities of an image seriesThis program is used to evaluate the average intensity and its variation of a series of images in a given masked region.

Options:

-i, --in-files=(input, required); io

input image(s). For supported file types see Plugin type: 2dimage/io

-m, --mask-file=(input, required); io

mask image, must be of type byte. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

Evaluate average intensities of an image seriesThis program is used to evaluate the average intensity and its variation of a series of images in a given masked region.

Options:

-i, --in-files=(required, input); io

input image(s). For supported file types see Plugin type: 2dimage/io

-m, --mask-file=(required, input); io

mask image, must be of type byte. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-2davgmasked 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,17 +5,17 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2davgmasked {-i io} {-m io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Evaluate average intensities of an image seriesThis program is used to evaluate │ │ │ │ │ the average intensity and its variation of a series of images in a given masked │ │ │ │ │ region. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-files=(input, required); io │ │ │ │ │ + -i, --in-files=(required, input); io │ │ │ │ │ input image(s). For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -m, --mask-file=(input, required); io │ │ │ │ │ + -m, --mask-file=(required, input); io │ │ │ │ │ mask image, must be of type byte. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dbinarycombine.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dbinarycombine

mia-2dbinarycombine

Sysnopis:

mia-2dbinarycombine {-1 io} {-2 io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(input, required); io

input mask image 1. For supported file types see Plugin type: 2dimage/io

-2, --file2=(input, required); io

input mask image 2. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output mask image. For supported file types see Plugin type: 2dimage/io

-p, --operation=nor; dict

Operation to be applied

or:logocal or
nor:logocal nor
and:logocal and
nand:logocal nand
xor:logocal xor
nxor:logocal nxor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-2dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(required, input); io

input mask image 1. For supported file types see Plugin type: 2dimage/io

-2, --file2=(required, input); io

input mask image 2. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output mask image. For supported file types see Plugin type: 2dimage/io

-p, --operation=nor; dict

Operation to be applied

or:logocal or
nor:logocal nor
and:logocal and
nand:logocal nand
xor:logocal xor
nxor:logocal nxor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-2dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,19 +3,19 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dbinarycombine │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dbinarycombine {-1 io} {-2 io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to combine two binary images by some kind of operation. │ │ │ │ │ Options: │ │ │ │ │ - -1, --file1=(input, required); io │ │ │ │ │ + -1, --file1=(required, input); io │ │ │ │ │ input mask image 1. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -2, --file2=(input, required); io │ │ │ │ │ + -2, --file2=(required, input); io │ │ │ │ │ input mask image 2. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output mask image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -p, --operation=nor; dict │ │ │ │ │ Operation to be applied │ │ │ │ │ or: logocal or │ │ │ │ │ nor: logocal nor │ │ │ │ │ and: logocal and │ │ │ │ │ nand: logocal nand │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2ddeform.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2ddeform

mia-2ddeform

Sysnopis:

mia-2ddeform {-i io} {-o io} {-t io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to deform a 2D image using a deformation vector field. Input image and deformation field must be of the same size. The transformation formula is 'x -> x - v(x)'

Options:

-i, --in-file=(input, required); io

input image. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

transformed image. For supported file types see Plugin type: 2dimage/io

-t, --transformation=(input, required); io

transformation vector field. For supported file types see Plugin type: 2dvf/io

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Deform image input.png by using the transformation given in transform.v and store the result in deformed.png using linear interpolation

mia-2ddeform -i input.png -t transform.v -o deformed.png -p bspline:d=1

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to deform a 2D image using a deformation vector field. Input image and deformation field must be of the same size. The transformation formula is 'x -> x - v(x)'

Options:

-i, --in-file=(required, input); io

input image. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

transformed image. For supported file types see Plugin type: 2dimage/io

-t, --transformation=(required, input); io

transformation vector field. For supported file types see Plugin type: 2dvf/io

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Deform image input.png by using the transformation given in transform.v and store the result in deformed.png using linear interpolation

mia-2ddeform -i input.png -t transform.v -o deformed.png -p bspline:d=1

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,19 +5,19 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2ddeform {-i io} {-o io} {-t io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to deform a 2D image using a deformation vector field. │ │ │ │ │ Input image and deformation field must be of the same size. The transformation │ │ │ │ │ formula is 'x -> x - v(x)' │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ transformed image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation vector field. For supported file types see Plugin_type: │ │ │ │ │ 2dvf/io │ │ │ │ │ -p, --interpolator=bspline:d=3; factory │ │ │ │ │ image interpolator kernel. For supported plug-ins see Plugin_type:_1d/ │ │ │ │ │ splinekernel │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2ddistance.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2ddistance

mia-2ddistance

Sysnopis:

mia-2ddistance {-i io} {-d io} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program evaluate the average or maximum distance of a mask given by a binary image to an image representing a distance map and prints the result to stdout. The distance map can be obtained by running the filter 'diatance' on a binary image.

Options:

-i, --in-file=(input, required); io

input image. For supported file types see Plugin type: 2dimage/io

-d, --distance-file=(input, required); io

distance field image (floating point). For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); string

output file, '-': write to stdout

-s, --scale=1; float

distance scaling factor

-m, --method=avg; dict

distance measuring method

avg:use average
max:use maximum
raw:collect raw values as vector

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the maximum distance of mask m.v by using the distance field distance.v and scale by factor 2.0. The result is written to stdout

mia-2ddistance -i m.v -d distance.v -s 2.0 -m max

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program evaluate the average or maximum distance of a mask given by a binary image to an image representing a distance map and prints the result to stdout. The distance map can be obtained by running the filter 'diatance' on a binary image.

Options:

-i, --in-file=(required, input); io

input image. For supported file types see Plugin type: 2dimage/io

-d, --distance-file=(required, input); io

distance field image (floating point). For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); string

output file, '-': write to stdout

-s, --scale=1; float

distance scaling factor

-m, --method=avg; dict

distance measuring method

avg:use average
max:use maximum
raw:collect raw values as vector

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the maximum distance of mask m.v by using the distance field distance.v and scale by factor 2.0. The result is written to stdout

mia-2ddistance -i m.v -d distance.v -s 2.0 -m max

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,20 +6,20 @@ │ │ │ │ │ mia-2ddistance {-i io} {-d io} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program evaluate the average or maximum distance of a mask given by a │ │ │ │ │ binary image to an image representing a distance map and prints the result to │ │ │ │ │ stdout. The distance map can be obtained by running the filter 'diatance' on a │ │ │ │ │ binary image. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -d, --distance-file=(input, required); io │ │ │ │ │ + -d, --distance-file=(required, input); io │ │ │ │ │ distance field image (floating point). For supported file types see │ │ │ │ │ Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output file, '-': write to stdout │ │ │ │ │ -s, --scale=1; float │ │ │ │ │ distance scaling factor │ │ │ │ │ -m, --method=avg; dict │ │ │ │ │ distance measuring method │ │ │ │ │ avg: use average │ │ │ │ │ max: use maximum │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2devaltransformquantity.html │ │ │ │ @@ -14,9 +14,9 @@ │ │ │ │ style=sparse #storage style (sparse|grid) │ │ │ │ repn=float32 #representation of values │ │ │ │ size=1000 1000 #grid size of the transformation │ │ │ │ endian=low #endianess of binary data (low|big) │ │ │ │ } │ │ │ │ │ │ │ │ This example header has to be interpreted like follows: two-dimensional data, each entry consists of 7 values the values etry consists of a 2D vector, a scalar, and a 2x2 matrix (saved in row-major format).The data records represent strain tensors, and only a sparse set of points is given. The values are given as single floating point (32 bit). The original transformation field corresponds to images of 1000x1000 pixels and the binary data is stored in low endian format.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.

-o, --out-file=(output, required); string

output strains file, for a format description see above.

-t, --transformation=(input, required); io

transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 2dtransform/io

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.

-o, --out-file=(required, output); string

output strains file, for a format description see above.

-t, --transformation=(required, input); io

transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 2dtransform/io

│ │ │ │ Parameters

-q, --quantity=strain; dict

Specify the quantity to be evaluated at the given points

derivative:Evaluate the transformation derivative at the given points
strain:Evaluate the strain tensor at the given points

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Derivative of the transformation change.v2df for each point given in input.csv are evaluated and written to output.s.

mia-2deval-transformquantity -i input.csv -o output.s --transformation change.v2df

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -20,21 +20,21 @@ │ │ │ │ │ of a 2D vector, a scalar, and a 2x2 matrix (saved in row-major format).The data │ │ │ │ │ records represent strain tensors, and only a sparse set of points is given. The │ │ │ │ │ values are given as single floating point (32 bit). The original transformation │ │ │ │ │ field corresponds to images of 1000x1000 pixels and the binary data is stored │ │ │ │ │ in low endian format. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input point set, if this parameter is given a sparse evaluation of the │ │ │ │ │ quantity will be done, otherwise the quantity is evaluated for each grid │ │ │ │ │ point of the transformation range. │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output strains file, for a format description see above. │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation of which the quantity will be evaluated.. For supported │ │ │ │ │ file types see Plugin_type:_2dtransform/io │ │ │ │ │ Parameters │ │ │ │ │ -q, --quantity=strain; dict │ │ │ │ │ Specify the quantity to be evaluated at the given points │ │ │ │ │ derivative: Evaluate the transformation derivative at the given points │ │ │ │ │ strain: Evaluate the strain tensor at the given points │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dfluid.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dfluid

mia-2dfluid

Sysnopis:

mia-2dfluid {-i io} {-r io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used for non-rigid registration based on fluid dynamics. For reference see

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(input, required); io

input (test) image to be registered. For supported file types see Plugin type: 2dimage/io

-r, --ref-image=(input, required); io

reference image. For supported file types see Plugin type: 2dimage/io

-o, --out-transformation=(output); io

output transformation comprising the registration. For supported file types see Plugin type: 2dvf/io

-d, --out-image=(output); io

output image deformed according to the transformation. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

-m, --mgstart=16; uint

multigrid start size

-e, --epsilon=0.001; float

optimization breaking condition

--mu=1; float

elasticity parameter

--lambda=1; float

elasticity parameter

--elastic

use elastic registration

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-2dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used for non-rigid registration based on fluid dynamics. For reference see

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(required, input); io

input (test) image to be registered. For supported file types see Plugin type: 2dimage/io

-r, --ref-image=(required, input); io

reference image. For supported file types see Plugin type: 2dimage/io

-o, --out-transformation=(output); io

output transformation comprising the registration. For supported file types see Plugin type: 2dvf/io

-d, --out-image=(output); io

output image deformed according to the transformation. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

-m, --mgstart=16; uint

multigrid start size

-e, --epsilon=0.001; float

optimization breaking condition

--mu=1; float

elasticity parameter

--lambda=1; float

elasticity parameter

--elastic

use elastic registration

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-2dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -9,18 +9,18 @@ │ │ │ │ │ reference see │ │ │ │ │ Wollny,_G._and_Kruggel,_F.,_'Computational_cost_of_non-rigid_registration │ │ │ │ │ algorithms_based_on_fluid_dynamics',_IEEE_Transactions_on_Medical_Imaging,_11 │ │ │ │ │ (8),_pp._946-952,_2002. │ │ │ │ │ It uses SSD as the sole registration criterion. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ input (test) image to be registered. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ - -r, --ref-image=(input, required); io │ │ │ │ │ + -r, --ref-image=(required, input); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -o, --out-transformation=(output); io │ │ │ │ │ output transformation comprising the registration. For supported file │ │ │ │ │ types see Plugin_type:_2dvf/io │ │ │ │ │ -d, --out-image=(output); io │ │ │ │ │ output image deformed according to the transformation. For supported file │ │ │ │ │ types see Plugin_type:_2dimage/io │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dfluidsynregistration.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dfluid-syn-registration

mia-2dfluid-syn-registration

Sysnopis:

mia-2dfluid-syn-registration {-i io} {-r io} {-o io} {-O io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements the registration of two gray scale 2D images. The transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently, this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have the same voxel spacing, and any intensity range normalization or equalization should also be done before calling this program.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(input, required); io

test image. For supported file types see Plugin type: 2dimage/io

-r, --ref-image=(input, required); io

reference image. For supported file types see Plugin type: 2dimage/io

-o, --transform=(output, required); io

output transformation. For supported file types see Plugin type: 2dtransform/io

-O, --inverse-transform=(output, required); io

inverse output transformation. For supported file types see Plugin type: 2dtransform/io

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint

Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.

-S, --step=0.25; float in (0, 0.5]

Initial step size for all levels

-c, --cost=ssd; factory

Image similarity function to be minimized. For supported plug-ins see Plugin type: 2dimage/cost

-R, --regularizer=sor:kernel=fluid,maxiter=50; factory

Regularization for the force to transformation update. For supported plug-ins see Plugin type: 2dvf/regularizer

-T, --conv-test-interval= in [4, 40]

Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-D, --stop-decline-rate= in [0, inf)

Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-C, --stop-cost=

Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-I, --iter= in [4, inf)

Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-2dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements the registration of two gray scale 2D images. The transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently, this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have the same voxel spacing, and any intensity range normalization or equalization should also be done before calling this program.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(required, input); io

test image. For supported file types see Plugin type: 2dimage/io

-r, --ref-image=(required, input); io

reference image. For supported file types see Plugin type: 2dimage/io

-o, --transform=(required, output); io

output transformation. For supported file types see Plugin type: 2dtransform/io

-O, --inverse-transform=(required, output); io

inverse output transformation. For supported file types see Plugin type: 2dtransform/io

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint

Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.

-S, --step=0.25; float in (0, 0.5]

Initial step size for all levels

-c, --cost=ssd; factory

Image similarity function to be minimized. For supported plug-ins see Plugin type: 2dimage/cost

-R, --regularizer=sor:kernel=fluid,maxiter=50; factory

Regularization for the force to transformation update. For supported plug-ins see Plugin type: 2dvf/regularizer

-T, --conv-test-interval= in [4, 40]

Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-D, --stop-decline-rate= in [0, inf)

Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-C, --stop-cost=

Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-I, --iter= in [4, inf)

Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-2dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -29,22 +29,22 @@ │ │ │ │ │ -h, --help=(); bool │ │ │ │ │ print this help │ │ │ │ │ -?, --usage=(); bool │ │ │ │ │ print a short help │ │ │ │ │ --version=(); bool │ │ │ │ │ print the version number and exit │ │ │ │ │ IO │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ test image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -r, --ref-image=(input, required); io │ │ │ │ │ + -r, --ref-image=(required, input); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --transform=(output, required); io │ │ │ │ │ + -o, --transform=(required, output); io │ │ │ │ │ output transformation. For supported file types see Plugin_type: │ │ │ │ │ 2dtransform/io │ │ │ │ │ - -O, --inverse-transform=(output, required); io │ │ │ │ │ + -O, --inverse-transform=(required, output); io │ │ │ │ │ inverse output transformation. For supported file types see Plugin_type: │ │ │ │ │ 2dtransform/io │ │ │ │ │ Processing │ │ │ │ │ --threads=-1; int │ │ │ │ │ Maxiumum number of threads to use for processing,This number should be │ │ │ │ │ lower or equal to the number of logical processor cores in the machine. │ │ │ │ │ (-1: automatic estimation). │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dforce.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dforce

mia-2dforce

Sysnopis:

mia-2dforce {-i io} {-r io} {-o io} {-c string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This image evaluate the force field between two images based on a given cost function.

Options:

-i, --src-file=(input, required); io

input image. For supported file types see Plugin type: 2dimage/io

-r, --ref-file=(input, required); io

reference image. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output force norm image. For supported file types see Plugin type: 2dimage/io

-c, --cost=(required); string

cost function to use

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force between test.v and reference.v by using SSD ans save the norm of the force to forcenorm.v

mia-2dforce -i test.v -r reference.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This image evaluate the force field between two images based on a given cost function.

Options:

-i, --src-file=(required, input); io

input image. For supported file types see Plugin type: 2dimage/io

-r, --ref-file=(required, input); io

reference image. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output force norm image. For supported file types see Plugin type: 2dimage/io

-c, --cost=(required); string

cost function to use

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force between test.v and reference.v by using SSD ans save the norm of the force to forcenorm.v

mia-2dforce -i test.v -r reference.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,19 +4,19 @@ │ │ │ │ │ mia-2dforce │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dforce {-i io} {-r io} {-o io} {-c string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This image evaluate the force field between two images based on a given cost │ │ │ │ │ function. │ │ │ │ │ Options: │ │ │ │ │ - -i, --src-file=(input, required); io │ │ │ │ │ + -i, --src-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -r, --ref-file=(input, required); io │ │ │ │ │ + -r, --ref-file=(required, input); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output force norm image. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -c, --cost=(required); string │ │ │ │ │ cost function to use │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dfuzzysegment.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dfuzzysegment

mia-2dfuzzysegment

Sysnopis:

mia-2dfuzzysegment {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a fuzzy segmentation of 2D image. cf D.L. Pham and J.L.Prince, "An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities", Pat. Rec. Let., 20:57-68,1999

Options:

File-IO

-i, --in-file=(input, required); io

input image(s) to be segmenetd. For supported file types see Plugin type: 2dimage/io

-c, --cls-file=(output); io

output class probability images (floating point values and multi-image). For supported file types see Plugin type: 2dimage/io

-o, --b0-file=(output); io

image corrected for intensity non-uniformity. For supported file types see Plugin type: 2dimage/io

-g, --gain-file=(output); io

gain field (floating point valued). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int

number of classes

-r, --residuum=0.1; float

relative residuum

--l1=200000; float

Penalize magnitude of intensity inhomogeinity correction

--l2=2e+06; float

Smoothness of intensity inhomogeinity correction

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-2dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a fuzzy segmentation of 2D image. cf D.L. Pham and J.L.Prince, "An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities", Pat. Rec. Let., 20:57-68,1999

Options:

File-IO

-i, --in-file=(required, input); io

input image(s) to be segmenetd. For supported file types see Plugin type: 2dimage/io

-c, --cls-file=(output); io

output class probability images (floating point values and multi-image). For supported file types see Plugin type: 2dimage/io

-o, --b0-file=(output); io

image corrected for intensity non-uniformity. For supported file types see Plugin type: 2dimage/io

-g, --gain-file=(output); io

gain field (floating point valued). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int

number of classes

-r, --residuum=0.1; float

relative residuum

--l1=200000; float

Penalize magnitude of intensity inhomogeinity correction

--l2=2e+06; float

Smoothness of intensity inhomogeinity correction

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-2dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ │ Description: │ │ │ │ │ This program runs a combined fuzzy c-means clustering and B-field correction to │ │ │ │ │ facilitate a fuzzy segmentation of 2D image. cf D.L. Pham and J.L.Prince, "An │ │ │ │ │ adaptive fuzzy C-means algorithm for image segmentation in the presence of │ │ │ │ │ intensity inhomogeneities", Pat. Rec. Let., 20:57-68,1999 │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be segmenetd. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -c, --cls-file=(output); io │ │ │ │ │ output class probability images (floating point values and multi-image). │ │ │ │ │ For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -o, --b0-file=(output); io │ │ │ │ │ image corrected for intensity non-uniformity. For supported file types │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dgrayimagecombinetorgb.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dgrayimage-combine-to-rgb

mia-2dgrayimage-combine-to-rgb

Sysnopis:

mia-2dgrayimage-combine-to-rgb {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program combines up to three gray scale image to a three channel RGB image with eight bit per color channel. The input images must be gray scale of eight bit colordepth. If at input one channel is not given, it will be set to zero. at least one input channel must be given.

Options:

-b, --blue=(input); io

input image for blue channel. For supported file types see Plugin type: 2dimage/io

-g, --green=(input); io

input image for green channel. For supported file types see Plugin type: 2dimage/io

-r, --red=(input); io

input image for red channel. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

combined output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the images red.png, blue.tiff, and green.bmp to the output image rgb.jpg.

mia-2dgrayimage-combine-to-rgb -r red.png -b blue.tiff -g green.bmp -o rgb.jpg

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program combines up to three gray scale image to a three channel RGB image with eight bit per color channel. The input images must be gray scale of eight bit colordepth. If at input one channel is not given, it will be set to zero. at least one input channel must be given.

Options:

-b, --blue=(input); io

input image for blue channel. For supported file types see Plugin type: 2dimage/io

-g, --green=(input); io

input image for green channel. For supported file types see Plugin type: 2dimage/io

-r, --red=(input); io

input image for red channel. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

combined output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the images red.png, blue.tiff, and green.bmp to the output image rgb.jpg.

mia-2dgrayimage-combine-to-rgb -r red.png -b blue.tiff -g green.bmp -o rgb.jpg

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -15,15 +15,15 @@ │ │ │ │ │ 2dimage/io │ │ │ │ │ -g, --green=(input); io │ │ │ │ │ input image for green channel. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -r, --red=(input); io │ │ │ │ │ input image for red channel. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ combined output image. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dgroundtruthreg.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dgroundtruthreg

mia-2dgroundtruthreg

Sysnopis:

mia-2dgroundtruthreg {-i string} {-o string} {-A double} {-B double} {-R double} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images as described in

Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009.

Note that for this nonlinear motion correction a preceding linear registration step is usually required.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered files

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered files

│ │ │ │ Preconditions

-s, --skip=2; uint

skip images at beginning of series

-P, --passes=4; uint

number of registration passes

│ │ │ │ Pseudo-Ground-Thruth

-A, --alpha=(required); double

spacial neighborhood penalty weight

-B, --beta=(required); double

temporal second derivative penalty weight

-R, --rho_thresh=(required); double

correlation threshold for neighborhood analysis

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

-l, --mr-levels=3; uint

multi-resolution levels

-d, --divcurl=20; double

divcurl regularization weight

--divcurl-divider=4; double

divcurl weight scaling with each new pass

-a, --start-c-rate=32; uint

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4; double

cofficient rate divider for each pass

-w, --imageweight=1; double

image cost weight

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given by images imageXXXX.exr by using Pseudo Ground Truth estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result images to 'regXXXX.exr'.

mia-2dgroundtruthreg -i imageXXXX.exr -o regXXXX.exr -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -12,17 +12,17 @@ │ │ │ │ │ Chao_Li_and_Ying_Sun,_'Nonrigid_Registration_of_Myocardial_Perfusion_MRI_Using │ │ │ │ │ Pseudo_Ground_Truth'_,_In_Proc._Medical_Image_Computing_and_Computer-Assisted │ │ │ │ │ Intervention_MICCAI_2009,_165-172,_2009. │ │ │ │ │ Note that for this nonlinear motion correction a preceding linear registration │ │ │ │ │ step is usually required. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=reg; stringSTRING │ │ │ │ │ file name base for registered files │ │ │ │ │ Preconditions │ │ │ │ │ -s, --skip=2; uint │ │ │ │ │ skip images at beginning of series │ │ │ │ │ -P, --passes=4; uint │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagecombinedice.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dimagecombine-dice

mia-2dimagecombine-dice

Sysnopis:

mia-2dimagecombine-dice {-1 io} {-2 io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program evaluate the dice index of two binary masks given as binary images. The result is written to stdout.

Options:

-1, --in-file-1=(input, required); io

input image 1. For supported file types see Plugin type: 2dimage/io

-2, --in-file-2=(input, required); io

input image 2. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of maks1.png and mask2.png

mia-2dimagecombine-dice -1 mask1.png -2 mask2.png

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program evaluate the dice index of two binary masks given as binary images. The result is written to stdout.

Options:

-1, --in-file-1=(required, input); io

input image 1. For supported file types see Plugin type: 2dimage/io

-2, --in-file-2=(required, input); io

input image 2. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of maks1.png and mask2.png

mia-2dimagecombine-dice -1 mask1.png -2 mask2.png

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-2dimagecombine-dice │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dimagecombine-dice {-1 io} {-2 io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program evaluate the dice index of two binary masks given as binary │ │ │ │ │ images. The result is written to stdout. │ │ │ │ │ Options: │ │ │ │ │ - -1, --in-file-1=(input, required); io │ │ │ │ │ + -1, --in-file-1=(required, input); io │ │ │ │ │ input image 1. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -2, --in-file-2=(input, required); io │ │ │ │ │ + -2, --in-file-2=(required, input); io │ │ │ │ │ input image 2. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagecombiner.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dimagecombiner

mia-2dimagecombiner

Sysnopis:

mia-2dimagecombiner {-1 io} {-2 io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Combine two image by a given operation.

Options:

-1, --in-file-1=(input, required); io

first input image to be combined. For supported file types see Plugin type: 2dimage/io

-2, --in-file-2=(input, required); io

second input image to be combined. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io

-p, --operation=absdiff; factory

operation to be applied. For supported plug-ins see Plugin type: 2dimage/combiner

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine image A.exr and image B.exr by adding the intensity values and save the output to sum.exr.

mia-2dimagecombiner -i A.exr -r B.exr -o sum.exr -p add

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Combine two image by a given operation.

Options:

-1, --in-file-1=(required, input); io

first input image to be combined. For supported file types see Plugin type: 2dimage/io

-2, --in-file-2=(required, input); io

second input image to be combined. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io

-p, --operation=absdiff; factory

operation to be applied. For supported plug-ins see Plugin type: 2dimage/combiner

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine image A.exr and image B.exr by adding the intensity values and save the output to sum.exr.

mia-2dimagecombiner -i A.exr -r B.exr -o sum.exr -p add

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,21 +3,21 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dimagecombiner │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dimagecombiner {-1 io} {-2 io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Combine two image by a given operation. │ │ │ │ │ Options: │ │ │ │ │ - -1, --in-file-1=(input, required); io │ │ │ │ │ + -1, --in-file-1=(required, input); io │ │ │ │ │ first input image to be combined. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ - -2, --in-file-2=(input, required); io │ │ │ │ │ + -2, --in-file-2=(required, input); io │ │ │ │ │ second input image to be combined. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image(s) that have been filtered. For supported file types see │ │ │ │ │ Plugin_type:_2dimage/io │ │ │ │ │ -p, --operation=absdiff; factory │ │ │ │ │ operation to be applied. For supported plug-ins see Plugin_type:_2dimage/ │ │ │ │ │ combiner │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagecreator.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dimagecreator

mia-2dimagecreator

Sysnopis:

mia-2dimagecreator {-o io} {-j factory} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to create test images.

Options:

-o, --out-file=(output, required); io

output file for create object. For supported file types see Plugin type: 2dimage/io

-s, --size=[128,128]; 2dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-j, --object=(required); factory

object to be created. For supported plug-ins see Plugin type: 2dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a 2D image containing a lattic with standard parameters of size <64,128> and pixel type 'float' and save the result to lattic.v

mia-2dimagecreator -o lattic.v -s '<64,128>' -r float -j lattic

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to create test images.

Options:

-o, --out-file=(required, output); io

output file for create object. For supported file types see Plugin type: 2dimage/io

-s, --size=[128,128]; 2dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-j, --object=(required); factory

object to be created. For supported plug-ins see Plugin type: 2dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a 2D image containing a lattic with standard parameters of size <64,128> and pixel type 'float' and save the result to lattic.v

mia-2dimagecreator -o lattic.v -s '<64,128>' -r float -j lattic

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,15 +3,15 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dimagecreator │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dimagecreator {-o io} {-j factory} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to create test images. │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file for create object. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -s, --size=[128,128]; 2dbounds │ │ │ │ │ size of the object │ │ │ │ │ -r, --repn=ubyte; dict │ │ │ │ │ input pixel type │ │ │ │ │ bit: binary data │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagefilter.html │ │ │ │ @@ -2,8 +2,8 @@ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ │ │ ...]

Description:

This program runs a series filters on a given input image. The filters are given as extra parameters on the command line and Ware run in the order in which they are given. To obtain a list of available filters you may run │ │ │ │ 'mia-plugin-help filter/2dimage' │ │ │ │ -from the command line

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a kmeans classification of 5 classes on input.png and then a binarization of the 4th class and store the result in result.png

mia-2dimagefilter -i input.png -o result.png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

│ │ │ │ +from the command line

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output image(s) that have been filtered. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a kmeans classification of 5 classes on input.png and then a binarization of the 4th class and store the result in result.png

mia-2dimagefilter -i input.png -o result.png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ │ ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs a series filters on a given input image. The filters are │ │ │ │ │ given as extra parameters on the command line and Ware run in the order in │ │ │ │ │ which they are given. To obtain a list of available filters you may run 'mia- │ │ │ │ │ plugin-help filter/2dimage' from the command line │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image(s) that have been filtered. For supported file types see │ │ │ │ │ Plugin_type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagefilterstack.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dimagefilterstack

mia-2dimagefilterstack

Sysnopis:

mia-2dimagefilterstack {-i io} {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ │ │ - ...]

Description:

This program runs a series filters on a series of consecutive numbered input image. The filters are given as extra parameters on the command line and are run in the order in which they are given.

Options:

File IO

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output file name base, the file type is set accurding to the 'type' option. For supported file types see Plugin type: 2dimage/io

-t, --type=

output file type, if not given the input type is used Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Processing1

-s, --start=0; uint

first possible number of file number range to be filtered

-e, --end=2147483647; uint

last possible number of file number range to be filtered

Example:

Run a kmeans classification of 5 classes on images inputXXXX.png (X being digits) and then a binarization of the 4th class and store the result in resultXXXX.png

mia-2dimagefilterstack -i input0000.png -o result -t png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs a series filters on a series of consecutive numbered input image. The filters are given as extra parameters on the command line and are run in the order in which they are given.

Options:

File IO

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output file name base, the file type is set accurding to the 'type' option. For supported file types see Plugin type: 2dimage/io

-t, --type=

output file type, if not given the input type is used Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Processing1

-s, --start=0; uint

first possible number of file number range to be filtered

-e, --end=2147483647; uint

last possible number of file number range to be filtered

Example:

Run a kmeans classification of 5 classes on images inputXXXX.png (X being digits) and then a binarization of the 4th class and store the result in resultXXXX.png

mia-2dimagefilterstack -i input0000.png -o result -t png kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

│ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagefullstats.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dimagefullstats

mia-2dimagefullstats

Sysnopis:

mia-2dimagefullstats {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, Min and Max of the intensity values.

Options:

-i, --in-file=(input, required); io

input image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png

mia-2dimagefullstats -i input.png

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, Min and Max of the intensity values.

Options:

-i, --in-file=(required, input); io

input image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png

mia-2dimagefullstats -i input.png

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-2dimagefullstats │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dimagefullstats {-i io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This progranm is used to evaluate some statistics of an image. Output is Mean, │ │ │ │ │ Variation, Median, Min and Max of the intensity values. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimageregistration.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dimageregistration

mia-2dimageregistration

Sysnopis:

mia-2dimageregistration {-i io} {-r io} {-t io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ │ │ - ...]

Description:

This program runs registration of two images optimizing a transformation of the given transformation model by optimizing certain cost measures that are given as free parameters.

Options:

File-IO

-i, --in-image=(input, required); io

test image to be registered. For supported file types see Plugin type: 2dimage/io

-r, --ref-image=(input, required); io

reference image to be registered to. For supported file types see Plugin type: 2dimage/io

-o, --out-image=(output); io

registered output image. For supported file types see Plugin type: 2dimage/io

-t, --transformation=(output, required); io

output transformation comprising the registration. For supported file types see Plugin type: 2dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-R, --refiner=

optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image 'moving.png' to the image 'reference.png' by using a rigid transformation model and ssd as cost function. Write the result to output.png

mia-2dimageregistration   -i moving.png -r reference.png -o output.png -f rigid image:cost=ssd

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs registration of two images optimizing a transformation of the given transformation model by optimizing certain cost measures that are given as free parameters.

Options:

File-IO

-i, --in-image=(required, input); io

test image to be registered. For supported file types see Plugin type: 2dimage/io

-r, --ref-image=(required, input); io

reference image to be registered to. For supported file types see Plugin type: 2dimage/io

-o, --out-image=(output); io

registered output image. For supported file types see Plugin type: 2dimage/io

-t, --transformation=(required, output); io

output transformation comprising the registration. For supported file types see Plugin type: 2dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-R, --refiner=

optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image 'moving.png' to the image 'reference.png' by using a rigid transformation model and ssd as cost function. Write the result to output.png

mia-2dimageregistration   -i moving.png -r reference.png -o output.png -f rigid image:cost=ssd

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,24 +7,24 @@ │ │ │ │ │ 2dimage/fullcost ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs registration of two images optimizing a transformation of the │ │ │ │ │ given transformation model by optimizing certain cost measures that are given │ │ │ │ │ as free parameters. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ test image to be registered. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -r, --ref-image=(input, required); io │ │ │ │ │ + -r, --ref-image=(required, input); io │ │ │ │ │ reference image to be registered to. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ -o, --out-image=(output); io │ │ │ │ │ registered output image. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -t, --transformation=(output, required); io │ │ │ │ │ + -t, --transformation=(required, output); io │ │ │ │ │ output transformation comprising the registration. For supported file │ │ │ │ │ types see Plugin_type:_2dtransform/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimageselect.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dimageselect

mia-2dimageselect

Sysnopis:

mia-2dimageselect {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to select one 2D images from a multi-image file.

Options:

-i, --in-file=(input, required); io

input images. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output image. For supported file types see Plugin type: 2dimage/io

-n, --number=0; uint

image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-2dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to select one 2D images from a multi-image file.

Options:

-i, --in-file=(required, input); io

input images. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output image. For supported file types see Plugin type: 2dimage/io

-n, --number=0; uint

image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-2dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,17 +3,17 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dimageselect │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dimageselect {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to select one 2D images from a multi-image file. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input images. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -n, --number=0; uint │ │ │ │ │ image number to be selected │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimageseriesmaximumintensityprojection.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-2dimageseries-maximum-intensity-projection

mia-2dimageseries-maximum-intensity-projection

Sysnopis:

mia-2dimageseries-maximum-intensity-projection {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to evaluate the per-pixel maximum intensity of an image series.

Options:

-o, --out-file=(output, required); io

output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

This program is used to evaluate the per-pixel maximum intensity of an image series.

Options:

-o, --out-file=(required, output); io

output image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-2dimageseries-maximum-intensity-projection 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-2dimageseries-maximum-intensity-projection │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dimageseries-maximum-intensity-projection {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to evaluate the per-pixel maximum intensity of an image │ │ │ │ │ series. │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagestackcmeans.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dimagestack-cmeans

mia-2dimagestack-cmeans

Sysnopis:

mia-2dimagestack-cmeans {-i io} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram and then writes the probability mapping for thr original intensity values

Options:

File-IO

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-probmap=(output, required); string

Save probability map to this file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]

Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.

-C, --classes=kmeans:nc=3; factory

C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 5% bins (if available), run cmeans with three classes on the non-zero pixels.

mia-2dimagestack-cmeans -i image0000.png -o cmeans,txt --histogram-tresh=5 --classes 3

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram and then writes the probability mapping for thr original intensity values

Options:

File-IO

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-probmap=(required, output); string

Save probability map to this file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]

Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.

-C, --classes=kmeans:nc=3; factory

C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 5% bins (if available), run cmeans with three classes on the non-zero pixels.

mia-2dimagestack-cmeans -i image0000.png -o cmeans,txt --histogram-tresh=5 --classes 3

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ mia-2dimagestack-cmeans {-i io} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program first evaluates a sparse histogram of an input image series, then │ │ │ │ │ runs a c-means classification over the histogram and then writes the │ │ │ │ │ probability mapping for thr original intensity values │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -o, --out-probmap=(output, required); string │ │ │ │ │ + -o, --out-probmap=(required, output); string │ │ │ │ │ Save probability map to this file │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dimagestats.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dimagestats

mia-2dimagestats

Sysnopis:

mia-2dimagestats {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, and Median Average Distance of the intensity values. The program allows one to set a lower threshold and to cut off a percentage of the high intensity pixels

Options:

-i, --in-file=(input, required); io

input image to be analyzed. For supported file types see Plugin type: 2dimage/io

-t, --thresh=10; float

intensity thresh to ignore

-g, --high-thresh=0.05; float

upper histogram percentage to ignore

--use-histogram

Use a histogram to accumulate statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png. Don't include the upper 1% of intensities in the statistics. The result is written to stdout

mia-2dimagestats -i input.png -g 1

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, and Median Average Distance of the intensity values. The program allows one to set a lower threshold and to cut off a percentage of the high intensity pixels

Options:

-i, --in-file=(required, input); io

input image to be analyzed. For supported file types see Plugin type: 2dimage/io

-t, --thresh=10; float

intensity thresh to ignore

-g, --high-thresh=0.05; float

upper histogram percentage to ignore

--use-histogram

Use a histogram to accumulate statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.png. Don't include the upper 1% of intensities in the statistics. The result is written to stdout

mia-2dimagestats -i input.png -g 1

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ mia-2dimagestats {-i io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This progranm is used to evaluate some statistics of an image. Output is Mean, │ │ │ │ │ Variation, Median, and Median Average Distance of the intensity values. The │ │ │ │ │ program allows one to set a lower threshold and to cut off a percentage of the │ │ │ │ │ high intensity pixels │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image to be analyzed. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -t, --thresh=10; float │ │ │ │ │ intensity thresh to ignore │ │ │ │ │ -g, --high-thresh=0.05; float │ │ │ │ │ upper histogram percentage to ignore │ │ │ │ │ --use-histogram │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dlerp.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dlerp

mia-2dlerp

Sysnopis:

mia-2dlerp {-1 io} {-2 io} {-o io} {-p vfloat} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Merge two images by pixel-wise linearly combining their intensities.

Options:

-1, --first=(input, required); io

first input image . For supported file types see Plugin type: 2dimage/io

-2, --second=(input, required); io

second input image . For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output vector field. For supported file types see Plugin type: 2dimage/io

-p, --positions=(required); vfloat

image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(

run a self test of the program

Example:

Combine image inputA.v and inputB.v by using position coordinates 4, 7, and 9. This means the output pixel values will be evaluated according to │ │ │ │ + ...]

Description:

Merge two images by pixel-wise linearly combining their intensities.

Options:

-1, --first=(required, input); io

first input image . For supported file types see Plugin type: 2dimage/io

-2, --second=(required, input); io

second input image . For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output vector field. For supported file types see Plugin type: 2dimage/io

-p, --positions=(required); vfloat

image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(

run a self test of the program

Example:

Combine image inputA.v and inputB.v by using position coordinates 4, 7, and 9. This means the output pixel values will be evaluated according to │ │ │ │ │ │ │ │ (9-7)/(9-4) * A + (7-4)/(9-4) * B │ │ │ │ │ │ │ │ The result image will be written to output.v

mia-2dlerp -1 inputA.v -2 inputB.v -p 4,7,9 -o output.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,19 +3,19 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dlerp │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dlerp {-1 io} {-2 io} {-o io} {-p vfloat} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Merge two images by pixel-wise linearly combining their intensities. │ │ │ │ │ Options: │ │ │ │ │ - -1, --first=(input, required); io │ │ │ │ │ + -1, --first=(required, input); io │ │ │ │ │ first input image . For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -2, --second=(input, required); io │ │ │ │ │ + -2, --second=(required, input); io │ │ │ │ │ second input image . For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output vector field. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -p, --positions=(required); vfloat │ │ │ │ │ image series positions (first, target, second) │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmany2onenonrigid.html │ │ │ │ @@ -1,9 +1,9 @@ │ │ │ │ mia-2dmany2one-nonrigid

mia-2dmany2one-nonrigid

Sysnopis:

mia-2dmany2one-nonrigid {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ │ │ ...]

Description:

This program registers all images of a conscutively numbered set of images to one common user defined reference.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

file name for registered images, numbering and pattern are deducted from the input data

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

file name for registered images, numbering and pattern are deducted from the input data

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING

Optimizer used for minimization

-l, --mg-levels=3; uint

multi-resolution levels

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

-r, --ref=-1; int

reference frame (-1 == use image in the middle)

-k, --skip=0; int

skip registration of these images at the beginning of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image series given by images 'inputXXXX.png' to reference image 30. Skip two images at the beginning and using mutual information as cost function, and penalize the transformation by divcurl with weight 5. Store the result in 'registeredXXXX.png'.

mia-2dmany2one-nonrigid   -i input0000.png -o registered%04d.png -k 2 -r 30 image:cost=mi divcurl:weight=5

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,17 +6,17 @@ │ │ │ │ │ mia-2dmany2one-nonrigid {-i string} {-o string} [ options ...] [ Plugin_type: │ │ │ │ │ 2dimage/fullcost ...] │ │ │ │ │ Description: │ │ │ │ │ This program registers all images of a conscutively numbered set of images to │ │ │ │ │ one common user defined reference. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ file name for registered images, numbering and pattern are deducted from │ │ │ │ │ the input data │ │ │ │ │ Registration │ │ │ │ │ -O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING │ │ │ │ │ Optimizer used for minimization │ │ │ │ │ -l, --mg-levels=3; uint │ │ │ │ │ multi-resolution levels │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiforce.html │ │ │ │ @@ -1,9 +1,9 @@ │ │ │ │ mia-2dmulti-force

mia-2dmulti-force

Sysnopis:

mia-2dmulti-force {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ │ │ - ...]

Description:

This program evaluates the 2D image cost force norm image of a given cost function set. The input images must be of the same dimensions and gray scale (whatever bit-depth).

Options:

-o, --out-file=(output, required); io

output norm image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force normimage weighted sum of costs SSD and NGF of image1.v and image2.v. and store the result to force.v.

mia-2dmulti-force -o force.v 
│ │ │ │ +        ...]

Description:

This program evaluates the 2D image cost force norm image of a given cost function set. The input images must be of the same dimensions and gray scale (whatever bit-depth).

Options:

-o, --out-file=(required, output); io

output norm image. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the force normimage weighted sum of costs SSD and NGF of image1.v and image2.v. and store the result to force.v.

mia-2dmulti-force -o force.v 
│ │ │ │   image:cost=ssd,src=image1.v,ref=image2.v,weight=0.1
│ │ │ │   image:cost=ngf,src=image1.v,ref=image2.v,weight=2.0

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dmulti-force {-o io} [ options ...] [ Plugin_type:_2dimage/fullcost ...] │ │ │ │ │ Description: │ │ │ │ │ This program evaluates the 2D image cost force norm image of a given cost │ │ │ │ │ function set. The input images must be of the same dimensions and gray scale │ │ │ │ │ (whatever bit-depth). │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output norm image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiimageregistration.html │ │ │ │ @@ -1,9 +1,9 @@ │ │ │ │ mia-2dmultiimageregistration

mia-2dmultiimageregistration

Sysnopis:

mia-2dmultiimageregistration {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ │ │ - ...]

Description:

This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-2dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels)

Options:

-o, --out-transform=(output, required); io

output transformation. For supported file types see Plugin type: 2dtransform/io

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline:rate=10,penalty=divcurl; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v by using a spline transformation with a coefficient rate of 5 and write the registered image to reg.v. Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 as transformation smoothness penalty. The resulting transformation is saved in reg.vf.

mia-2dmultiimageregistration -o reg.vf -l 2
│ │ │ │ +        ...]

Description:

This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-2dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels)

Options:

-o, --out-transform=(required, output); io

output transformation. For supported file types see Plugin type: 2dtransform/io

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline:rate=10,penalty=divcurl; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v by using a spline transformation with a coefficient rate of 5 and write the registered image to reg.v. Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 as transformation smoothness penalty. The resulting transformation is saved in reg.vf.

mia-2dmultiimageregistration -o reg.vf -l 2
│ │ │ │   -f spline:rate=3,penalty=divcurl
│ │ │ │   image:cost=ssd,src=test.v,ref=ref.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ │ a given transformation model. Other than mia-2dnonrigidreg it doesn't support │ │ │ │ │ specific command line parameters to provide the images. Instead the images are │ │ │ │ │ specified dirctly when defining the cost function. Hence, image registrations │ │ │ │ │ can be executed that optimize the aligmnet of more than one image pair at the │ │ │ │ │ same time. Note, however, that all input images must be of the same dimension │ │ │ │ │ (in pixels) │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-transform=(output, required); io │ │ │ │ │ + -o, --out-transform=(required, output); io │ │ │ │ │ output transformation. For supported file types see Plugin_type: │ │ │ │ │ 2dtransform/io │ │ │ │ │ -l, --levels=3; uint │ │ │ │ │ multi-resolution levels │ │ │ │ │ -O, --optimizer=gsl:opt=gd,step=0.1; factory │ │ │ │ │ Optimizer used for minimization. For supported plug-ins see Plugin_type: │ │ │ │ │ minimizer/singlecost │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiimageto3d.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmultiimageto3d

mia-2dmultiimageto3d

Sysnopis:

mia-2dmultiimageto3d {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to convert a 2D multi-image file to a 3D image.

Options:

-i, --in-file=(input, required); io

input images. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert an series of images stored in a 2D image container multiimage2d.v to a 3D image image3d.v.

mia-2dmultiimageto3d -i multiimage2d.v -o image3d.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to convert a 2D multi-image file to a 3D image.

Options:

-i, --in-file=(required, input); io

input images. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert an series of images stored in a 2D image container multiimage2d.v to a 3D image image3d.v.

mia-2dmultiimageto3d -i multiimage2d.v -o image3d.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,17 +3,17 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dmultiimageto3d │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dmultiimageto3d {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to convert a 2D multi-image file to a 3D image. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input images. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmultiimagevar.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dmultiimagevar

mia-2dmultiimagevar

Sysnopis:

mia-2dmultiimagevar {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/io │ │ │ │ │ │ │ │ - ...]

Description:

This program evaluates the pixel-wise accumulated intensity variation of a set of image given on the command line. If the input image files contain more then one image all images are used. All images must be of the same size.

Options:

-o, --out-file=(output, required); io

output image . For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the pixel-vise intensity variation of images i1.png, i2.png, i3.png, and i4.png and store the result to var.v.

mia-2dmultiimagevar -o var.v i1.png i2.png i3.png i4.png

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program evaluates the pixel-wise accumulated intensity variation of a set of image given on the command line. If the input image files contain more then one image all images are used. All images must be of the same size.

Options:

-o, --out-file=(required, output); io

output image . For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the pixel-vise intensity variation of images i1.png, i2.png, i3.png, and i4.png and store the result to var.v.

mia-2dmultiimagevar -o var.v i1.png i2.png i3.png i4.png

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dmultiimagevar {-o io} [ options ...] [ Plugin_type:_2dimage/io ...] │ │ │ │ │ Description: │ │ │ │ │ This program evaluates the pixel-wise accumulated intensity variation of a set │ │ │ │ │ of image given on the command line. If the input image files contain more then │ │ │ │ │ one image all images are used. All images must be of the same size. │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image . For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyocardica.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-2dmyocard-ica

mia-2dmyocard-ica

Sysnopis:

mia-2dmyocard-ica {-i io} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program is used to run a ICA on a series of myocardial perfusion images to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better to create a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a segmentation set, then on can also use mia-2dmyocard-icaseries. │ │ │ │ -This program is essentially used to test different options on how to run the ICA forreference image creation.

Options:

-i, --in-base=(input, required); io

input file name ofolloing pattern nameXXXX.ext X=numbers. For supported file types see Plugin type: 2dimage/io

--coefs=STRING

output mixing coefficients to this file

-o, --out-base=(output); string

output file name base

-t, --type=exr; set

output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

-k, --skip=2; uint

skip images at beginning of series

-e, --end=60; uint

last image in series

-C, --components=0; uint

nr. of components, 0=estimate automatically

-m, --strip-mean

strip mean image from series

-f, --save-features=STRING

save feature image

-p, --strip-periodic

strip only periodic component

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-x, --max-ica-iterations=0; int

max ICA solver iterations

-n, --ica-normalize

ica_normalize feature images

--all-features=STRING

save all feature images to

-L, --LV-crop-amp=0; float

LV crop mask amplification, 0.0 = don't crop

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the synthetic references from images imageXXXX.exr and save them to refXXXX.exr by using five independend components, mean stripping, normalizing, and skipping 2 images.

mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n

Author(s):

Gert Wollny

│ │ │ │ +This program is essentially used to test different options on how to run the ICA forreference image creation.

Options:

-i, --in-base=(required, input); io

input file name ofolloing pattern nameXXXX.ext X=numbers. For supported file types see Plugin type: 2dimage/io

--coefs=STRING

output mixing coefficients to this file

-o, --out-base=(output); string

output file name base

-t, --type=exr; set

output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

-k, --skip=2; uint

skip images at beginning of series

-e, --end=60; uint

last image in series

-C, --components=0; uint

nr. of components, 0=estimate automatically

-m, --strip-mean

strip mean image from series

-f, --save-features=STRING

save feature image

-p, --strip-periodic

strip only periodic component

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-x, --max-ica-iterations=0; int

max ICA solver iterations

-n, --ica-normalize

ica_normalize feature images

--all-features=STRING

save all feature images to

-L, --LV-crop-amp=0; float

LV crop mask amplification, 0.0 = don't crop

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the synthetic references from images imageXXXX.exr and save them to refXXXX.exr by using five independend components, mean stripping, normalizing, and skipping 2 images.

mia-2dmyocard-ica -i imageXXXX.exr -o ref -k 2 -C 5 -m -n

Author(s):

Gert Wollny

│ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyocardicaseries.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmyocard-icaseries

mia-2dmyocard-icaseries

Sysnopis:

mia-2dmyocard-icaseries {-i string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to run a ICA on a series of myocardial perfusion images given in a segmentation set in order to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better run mia-2dmyoica-nonrigid, since this program is essentially the same without the registration bits.

Options:

File-IO

-i, --in-file=(input, required); string

input perfusion data set

-r, --references=(output); string

File name base for the reference images. Image type and numbering scheme are taken from the input images.

-c, --save-cropped=(output); string

save cropped set of the original set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the synthetic references from set segment.set and save them to refXXXX.??? by using five independend components, and skipping 2 images. Per default a bounding box around the LV will be segmented and scaled by 1.4 and the cropped images will be saved to cropXXXX.??? and a segmentation set cropped.set is created. The image file type ??? is deducted from the input images in segment.set.

mia-2dmyocard-icaseries -i segment.set -r ref -o ref -k 2 -C 5

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to run a ICA on a series of myocardial perfusion images given in a segmentation set in order to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better run mia-2dmyoica-nonrigid, since this program is essentially the same without the registration bits.

Options:

File-IO

-i, --in-file=(required, input); string

input perfusion data set

-r, --references=(output); string

File name base for the reference images. Image type and numbering scheme are taken from the input images.

-c, --save-cropped=(output); string

save cropped set of the original set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the synthetic references from set segment.set and save them to refXXXX.??? by using five independend components, and skipping 2 images. Per default a bounding box around the LV will be segmented and scaled by 1.4 and the cropped images will be saved to cropXXXX.??? and a segmentation set cropped.set is created. The image file type ??? is deducted from the input images in segment.set.

mia-2dmyocard-icaseries -i segment.set -r ref -o ref -k 2 -C 5

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ This program is used to run a ICA on a series of myocardial perfusion images │ │ │ │ │ given in a segmentation set in order to create sythetic references that can be │ │ │ │ │ used for motion correction by image registration. If the aim is to run a full │ │ │ │ │ motion compensation then it is better run mia-2dmyoica-nonrigid, since this │ │ │ │ │ program is essentially the same without the registration bits. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ -r, --references=(output); string │ │ │ │ │ File name base for the reference images. Image type and numbering scheme │ │ │ │ │ are taken from the input images. │ │ │ │ │ -c, --save-cropped=(output); string │ │ │ │ │ save cropped set of the original set to this file, the image files will │ │ │ │ │ use the stem of the name as file name base │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyocardsegment.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmyocard-segment

mia-2dmyocard-segment

Sysnopis:

mia-2dmyocard-segment {-i string} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is work in progress

Options:

File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); io

output myocardial mask. For supported file types see Plugin type: 2dimage/io

-f, --save-features=(output); string

save ICA features to files with this name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation testing 4 and 5

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-k, --skip=2; uint

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Example

mia-2dmyocard-segment Example

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is work in progress

Options:

File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); io

output myocardial mask. For supported file types see Plugin type: 2dimage/io

-f, --save-features=(output); string

save ICA features to files with this name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation testing 4 and 5

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-k, --skip=2; uint

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Example

mia-2dmyocard-segment Example

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-2dmyocard-segment │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dmyocard-segment {-i string} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is work in progress │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output myocardial mask. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -f, --save-features=(output); string │ │ │ │ │ save ICA features to files with this name base │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicafull.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmyoica-full

mia-2dmyoica-full

Sysnopis:

mia-2dmyoica-full {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012.

The software may first run a linear registration and then a non-linear registration or just one of the two.This version of the program can run all registrations in parallel.

Options:

File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=STRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test. A value 0.0 forces the series to be identified as acquired with initial breath hold.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

--linear-transform=affine; factory

linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform

-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

-R, --reference=-1; int

Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-p, --linear-passes=3; uint

linear registration passes (0 to disable)

-P, --nonlinear-passes=3; uint

non-linear registration passes (0 to disable)

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-full   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012.

The software may first run a linear registration and then a non-linear registration or just one of the two.This version of the program can run all registrations in parallel.

Options:

File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=STRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test. A value 0.0 forces the series to be identified as acquired with initial breath hold.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

--linear-transform=affine; factory

linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform

-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

-R, --reference=-1; int

Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-p, --linear-passes=3; uint

linear registration passes (0 to disable)

-P, --nonlinear-passes=3; uint

non-linear registration passes (0 to disable)

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-full   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -11,17 +11,17 @@ │ │ │ │ │ Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using │ │ │ │ │ Independent_Component_Analysis",_Medical_Image_Analysis,_2012. │ │ │ │ │ The software may first run a linear registration and then a non-linear │ │ │ │ │ registration or just one of the two.This version of the program can run all │ │ │ │ │ registrations in parallel. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=STRING │ │ │ │ │ File name base for the registered images. Image type and numbering scheme │ │ │ │ │ are taken from the input images as given in the input data set. │ │ │ │ │ --save-cropped=(output); string │ │ │ │ │ save cropped set to this file, the image files will use the stem of the │ │ │ │ │ name as file name base │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicanonrigid.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmyoica-nonrigid

mia-2dmyoica-nonrigid

Sysnopis:

mia-2dmyoica-nonrigid {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012.

Options:

File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered fiels

--save-cropped=STRING

save cropped set to this file

--save-feature=STRING

save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

--save-refs=STRING

save synthetic reference images

--save-regs=STRING

save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-R, --refiner=

optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=2; double

cofficient rate divider for each pass

-d, --start-divcurl=10; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=2; double

divcurl weight scaling with each new pass

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=5; uint

registration passes

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-nonrigid   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012.

Options:

File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered fiels

--save-cropped=STRING

save cropped set to this file

--save-feature=STRING

save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

--save-refs=STRING

save synthetic reference images

--save-regs=STRING

save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-R, --refiner=

optimizer used for refinement after the main optimizer was called. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=2; double

cofficient rate divider for each pass

-d, --start-divcurl=10; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=2; double

divcurl weight scaling with each new pass

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=5; uint

registration passes

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-nonrigid   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,17 +7,17 @@ │ │ │ │ │ Description: │ │ │ │ │ This program implements the motion compensation algorithm described in │ │ │ │ │ Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion │ │ │ │ │ Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using │ │ │ │ │ Independent_Component_Analysis"_Medical_Image_Analysis,_2012. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=reg; stringSTRING │ │ │ │ │ file name base for registered fiels │ │ │ │ │ --save-cropped=STRING │ │ │ │ │ save cropped set to this file │ │ │ │ │ --save-feature=STRING │ │ │ │ │ save the features images resulting from the ICA and some intermediate │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicanonrigid2.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dmyoica-nonrigid2

mia-2dmyoica-nonrigid2

Sysnopis:

mia-2dmyoica-nonrigid2 {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program runs the non-rigid registration of an perfusion image series.In each pass, first an ICA analysis is run to estimate and eliminate the periodic movement and create reference images with intensities similar to the corresponding original image. Then non-rigid registration is run using the an "ssd + divcurl" cost model. The B-spline c-rate and the divcurl cost weight are changed in each pass according to given parameters.In the first pass a bounding box around the LV myocardium may be extractedto speed up computation │ │ │ │ Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered fiels

--save-cropped=STRING

save cropped set to this file

--save-feature=STRING

save segmentation feature images and initial ICA mixing matrix

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered fiels

--save-cropped=STRING

save cropped set to this file

--save-feature=STRING

save segmentation feature images and initial ICA mixing matrix

│ │ │ │ ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

don't normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=32; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4; double

cofficient rate divider for each pass

-d, --start-divcurl=20; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4; double

divcurl weight scaling with each new pass

-w, --imageweight=1; double

image cost weight

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=3; uint

registration passes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-nonrigid2   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -12,17 +12,17 @@ │ │ │ │ │ "ssd + divcurl" cost model. The B-spline c-rate and the divcurl cost weight are │ │ │ │ │ changed in each pass according to given parameters.In the first pass a bounding │ │ │ │ │ box around the LV myocardium may be extractedto speed up computation Special │ │ │ │ │ note to this implemnentation: the registration is always run from the original │ │ │ │ │ images to avoid the accumulation of interpolation errors. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=reg; stringSTRING │ │ │ │ │ file name base for registered fiels │ │ │ │ │ --save-cropped=STRING │ │ │ │ │ save cropped set to this file │ │ │ │ │ --save-feature=STRING │ │ │ │ │ save segmentation feature images and initial ICA mixing matrix │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicanonrigidparallel.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmyoica-nonrigid-parallel

mia-2dmyoica-nonrigid-parallel

Sysnopis:

mia-2dmyoica-nonrigid-parallel {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012.

This version of the program runs all registrations in parallel.

Options:

File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=3; uint

registration passes

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-nonrigid-parallel   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements the 2D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012.

This version of the program runs all registrations in parallel.

Options:

File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=reg; stringSTRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=3; uint

registration passes

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoica-nonrigid-parallel   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -9,17 +9,17 @@ │ │ │ │ │ described in │ │ │ │ │ Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion │ │ │ │ │ Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using │ │ │ │ │ Independent_Component_Analysis"_Medical_Image_Analysis,_2012. │ │ │ │ │ This version of the program runs all registrations in parallel. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=reg; stringSTRING │ │ │ │ │ File name base for the registered images. Image type and numbering scheme │ │ │ │ │ are taken from the input images as given in the input data set. │ │ │ │ │ --save-cropped=(output); string │ │ │ │ │ save cropped set to this file, the image files will use the stem of the │ │ │ │ │ name as file name base │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoicapgt.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-2dmyoicapgt

mia-2dmyoicapgt

Sysnopis:

mia-2dmyoicapgt {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program implements a two passs motion compensation algorithm. First a linear registration is run based on a variation of

Gupta et~al. "Fully automatic registration and segmentation of first-pass myocardial perfusion MR image sequences", Academic Radiology 17, 1375-1385

as described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis", Medical Image Analysis, 2012,

followed by a non-linear registration based

Chao Li and Ying Sun, "Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth", In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009.

Note that for this nonlinear motion correction a preceding linear registration step is usually required. This version of the program may run all registrations in parallel.

Options:

│ │ │ │ -Pseudo Ground Thruth estimation

-A, --alpha=0.1; double

spacial neighborhood penalty weight

-B, --beta=4; double

temporal second derivative penalty weight

-T, --rho-thresh=0.85; double

correlation threshold for neighborhood analysis

File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=STRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test. A value 0.0 forces the series to be identified as acquired with initial breath hold.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

--linear-transform=affine; factory

linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform

-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

-R, --reference=-1; int

Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-p, --linear-passes=3; uint

linear registration passes (0 to disable)

-P, --nonlinear-passes=3; uint

non-linear registration passes (0 to disable)

Example:

Register the perfusion series given in 'segment.set' by first using automatic ICA estimation to run the linear registration and then the PGT registration. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoicapgt   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ +Pseudo Ground Thruth estimation
-A, --alpha=0.1; double

spacial neighborhood penalty weight

-B, --beta=4; double

temporal second derivative penalty weight

-T, --rho-thresh=0.85; double

correlation threshold for neighborhood analysis

File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=STRING

File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set.

--save-cropped=(output); string

save cropped set to this file, the image files will use the stem of the name as file name base

--save-feature=(output); string

save segmentation feature images and initial ICA mixing matrix

--save-refs=(output); string

for each registration pass save the reference images to files with the given name base

--save-regs=(output); string

for each registration pass save intermediate registered images

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-s, --segscale=0; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images
-b, --min-breathing-frequency=-1; float

minimal mean frequency a mixing curve can have to be considered to stem from brething. A healthy rest breating rate is 12 per minute. A negative value disables the test. A value 0.0 forces the series to be identified as acquired with initial breath hold.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-L, --linear-optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization of the linear registration The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

--linear-transform=affine; factory

linear transform to be used The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/transform

-O, --non-linear-optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization in the non-linear registration. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=16; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass.

--c-rate-divider=2; double

Cofficient rate divider for each pass.

-d, --start-divcurl=10000; double

Start divcurl weight, gets divided by --divcurl-divider with every pass.

--divcurl-divider=2; double

Divcurl weight scaling with each new pass.

-R, --reference=-1; int

Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement

-w, --imagecost=image:weight=1,cost=ssd; factory

image cost, do not specify the src and ref parameters, these will be set by the program. The string value will be used to construct a plug-in.. For supported plug-ins see Plugin type: 2dimage/fullcost

-l, --mg-levels=3; uint

multi-resolution levels

-p, --linear-passes=3; uint

linear registration passes (0 to disable)

-P, --nonlinear-passes=3; uint

non-linear registration passes (0 to disable)

Example:

Register the perfusion series given in 'segment.set' by first using automatic ICA estimation to run the linear registration and then the PGT registration. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyoicapgt   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -25,17 +25,17 @@ │ │ │ │ │ -A, --alpha=0.1; double │ │ │ │ │ spacial neighborhood penalty weight │ │ │ │ │ -B, --beta=4; double │ │ │ │ │ temporal second derivative penalty weight │ │ │ │ │ -T, --rho-thresh=0.85; double │ │ │ │ │ correlation threshold for neighborhood analysis │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=STRING │ │ │ │ │ File name base for the registered images. Image type and numbering scheme │ │ │ │ │ are taken from the input images as given in the input data set. │ │ │ │ │ --save-cropped=(output); string │ │ │ │ │ save cropped set to this file, the image files will use the stem of the │ │ │ │ │ name as file name base │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyomilles.html │ │ │ │ @@ -1,5 +1,5 @@ │ │ │ │ mia-2dmyomilles

mia-2dmyomilles

Sysnopis:

mia-2dmyomilles {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program is use to run a modified version of the ICA based registration approach described in

Milles et al. 'Fully Automated Motion Correction in First-Pass Myocardial Perfusion MR Image Sequences', Trans. Med. Imaging., 27(11), 1611-1621, 2008.

Changes include the extraction of the quasi-periodic movement in free breathingly acquired data sets and the option to run affine or rigid registration instead of the optimization of translations only. │ │ │ │ -

Options:

File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=STRING

file name base for registered files

--save-references=STRING

save synthetic reference images to this file base

--save-cropped=STRING

save cropped image set to this file

--save-feature=STRING

save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-g, --guess

use initial guess for myocardial perfusion

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-c, --cost=ssd; stringSTRING

registration criterion

-O, --optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=rigid; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

-l, --mg-levels=3; uint

multi-resolution levels

-R, --reference=-1; int

Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement

-P, --passes=2; uint

registration passes

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'. │ │ │ │ +

Options:

File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=STRING

file name base for registered files

--save-references=STRING

save synthetic reference images to this file base

--save-cropped=STRING

save cropped image set to this file

--save-feature=STRING

save the features images resulting from the ICA and some intermediate images used for the RV-LV segmentation with the given file name base to PNG files. Also save the coefficients of the initial best and the final IC mixing matrix.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--normalize

normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-g, --guess

use initial guess for myocardial perfusion

-s, --segscale=1.4; float

segment and scale the crop box around the LV (0=no segmentation)

-k, --skip=0; uint

skip images at the beginning of the series as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

-E, --segmethod=features; dict

Segmentation method

delta-feature:difference of the feature images
delta-peak:difference of the peak enhancement images
features:feature images

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-c, --cost=ssd; stringSTRING

registration criterion

-O, --optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=rigid; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

-l, --mg-levels=3; uint

multi-resolution levels

-R, --reference=-1; int

Global reference all image should be aligned to. If set to a non-negative value, the images will be aligned to this references, and the cropped output image date will be injected into the original images. Leave at -1 if you don't care. In this case all images with be registered to a mean position of the movement

-P, --passes=2; uint

registration passes

Example:

Register the perfusion series given in 'segment.set' by using automatic ICA estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'. │ │ │ │

mia-2dmyomilles   -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -10,17 +10,17 @@ │ │ │ │ │ Milles_et_al._'Fully_Automated_Motion_Correction_in_First-Pass_Myocardial │ │ │ │ │ Perfusion_MR_Image_Sequences',_Trans._Med._Imaging.,_27(11),_1611-1621,_2008. │ │ │ │ │ Changes include the extraction of the quasi-periodic movement in free │ │ │ │ │ breathingly acquired data sets and the option to run affine or rigid │ │ │ │ │ registration instead of the optimization of translations only. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=STRING │ │ │ │ │ file name base for registered files │ │ │ │ │ --save-references=STRING │ │ │ │ │ save synthetic reference images to this file base │ │ │ │ │ --save-cropped=STRING │ │ │ │ │ save cropped image set to this file │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoperiodicnonrigid.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dmyoperiodic-nonrigid

mia-2dmyoperiodic-nonrigid

Sysnopis:

mia-2dmyoperiodic-nonrigid {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program runs the non-rigid registration of an perfusion image series preferable acquired letting the patient breath freely. The registration algorithm implementes

G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered fiels

--save-references

Save synthetic references to files refXXXX.v

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered fiels

--save-references

Save synthetic references to files refXXXX.v

│ │ │ │ Preconditions

-k, --skip=0; uint

Skip images at the begin of the series

--max-candidates=20; uint

maximum number of candidates for global reference image

-S, --cost-series=image:cost=[ngf:eval=ds]; factory

Const function to use for the analysis of the series. For supported plug-ins see Plugin type: 2dimage/fullcost

--ref-idx=STRING

save reference index number to this file

-R, --global-reference=-1; int

save reference index number to this file

-D, --max-subset-delta=0; uint

Maximum delta between two elements of the prealigned subset

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.01; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

--refiner=

optimizer used for additional minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-l, --mr-levels=3; uint

multi-resolution levels

-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

-1, --cost-subset=image:cost=[ngf:eval=ds]; factory

Cost function for registration during the subset registration. For supported plug-ins see Plugin type: 2dimage/fullcost

-2, --cost-final=image:cost=ssd; factory

Cost function for registration during the final registration. For supported plug-ins see Plugin type: 2dimage/fullcost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in 'segment.set'. Skip two images at the beginning, usa spline transformation of a knot rate 16 pixels, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'. │ │ │ │

mia-2dmyoperiodic-nonrigid   -i segment.set -o registered.set -k 2 -d 5 -f spline:rate=16,penalty=[divcurl:weight=5]

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -9,17 +9,17 @@ │ │ │ │ │ preferable acquired letting the patient breath freely. The registration │ │ │ │ │ algorithm implementes │ │ │ │ │ G._Wollny,_M-J_Ledesma-Cabryo,_P.Kellman,_and_A.Santos,_"Exploiting │ │ │ │ │ Quasiperiodicity_in_Motion_Correction_of_Free-Breathing,"_IEEE_Transactions_on │ │ │ │ │ Medical_Imaging,_29(8),_2010. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=reg; stringSTRING │ │ │ │ │ file name base for registered fiels │ │ │ │ │ --save-references │ │ │ │ │ Save synthetic references to files refXXXX.v │ │ │ │ │ Preconditions │ │ │ │ │ -k, --skip=0; uint │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyopgtnonrigid.html │ │ │ │ @@ -1,6 +1,6 @@ │ │ │ │ mia-2dmyopgt-nonrigid

mia-2dmyopgt-nonrigid

Sysnopis:

mia-2dmyopgt-nonrigid {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program implements the non-linear registration based on Pseudo Ground Thruth for motion compensation of series of myocardial perfusion images given as a data set as described in

Chao Li and Ying Sun, 'Nonrigid Registration of Myocardial Perfusion MRI Using Pseudo Ground Truth' , In Proc. Medical Image Computing and Computer-Assisted Intervention MICCAI 2009, 165-172, 2009

. Note that for this nonlinear motion correction a preceding linear registration step is usually required.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered files, the image file type is the same as given in the input data set

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-r, --registered=reg; stringSTRING

file name base for registered files, the image file type is the same as given in the input data set

│ │ │ │ Pseudo Ground Thruth estimation

-A, --alpha=1; double

spacial neighborhood penalty weight

-B, --beta=1; double

temporal second derivative penalty weight

-R, --rho-thresh=0.85; double

correlation threshold for neighborhood analysis

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-a, --start-c-rate=32; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4; double

cofficient rate divider for each pass

-d, --start-divcurl=20; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4; double

divcurl weight scaling with each new pass

-w, --imageweight=1; double

image cost weight

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=4; uint

registration passes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in 'segment.set' by using Pseudo Ground Truth estimation. Skip two images at the beginning and otherwiese use the default parameters. Store the result in 'registered.set'.

mia-2dmyopgt-nonrigid -i segment.set -o registered.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -11,17 +11,17 @@ │ │ │ │ │ Chao_Li_and_Ying_Sun,_'Nonrigid_Registration_of_Myocardial_Perfusion_MRI_Using │ │ │ │ │ Pseudo_Ground_Truth'_,_In_Proc._Medical_Image_Computing_and_Computer-Assisted │ │ │ │ │ Intervention_MICCAI_2009,_165-172,_2009 │ │ │ │ │ . Note that for this nonlinear motion correction a preceding linear │ │ │ │ │ registration step is usually required. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -r, --registered=reg; stringSTRING │ │ │ │ │ file name base for registered files, the image file type is the same as │ │ │ │ │ given in the input data set │ │ │ │ │ Pseudo Ground Thruth estimation │ │ │ │ │ -A, --alpha=1; double │ │ │ │ │ spacial neighborhood penalty weight │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoserialnonrigid.html │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ mia-2dmyoserial-nonrigid

mia-2dmyoserial-nonrigid

Sysnopis:

mia-2dmyoserial-nonrigid {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ │ │ ...]

Description:

This program runs the non-rigid motion compensation registration of an perfusion image series. The registration is run in a serial manner, this is, only images in temporal succession are registered, and the obtained transformations are applied accumulated to reach full registration. See:

Wollny, G., Ledesma-Carbayo, M.J., Kellman, P., Santos, A. "A New Similarity Measure for Non-Rigid Breathing Motion Compensation of Myocardial Perfusion MRI ". Proc 30th Annual International IEEE EMBS Conference, pp. 3389-3392. Vancouver, Aug. 2008.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

-R, --registered=reg; stringSTRING

file name base for registered fiels

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

-R, --registered=reg; stringSTRING

file name base for registered fiels

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-l, --mg-levels=3; uint

multi-resolution levels

-f, --transForm=spline:rate=16,penalty=[divcurl:weight=0.01]; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

-r, --ref=-1; int

reference frame (-1 == use image in the middle)

-k, --skip=0; int

skip registration of these images at the beginning of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in 'segment.set' to reference image 30. Skip two images at the beginning and using mutual information as cost function, and penalize the transformation by divcurl with weight 5. Store the result in 'registered.set'. │ │ │ │

mia-2dmyoserial-nonrigid   -i segment.set -o registered.set -k 2  -r 30 image:cost=mi -f spline:rate=5,penalty=[divcurl:weight=5]

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -12,17 +12,17 @@ │ │ │ │ │ transformations are applied accumulated to reach full registration. See: │ │ │ │ │ Wollny,_G.,_Ledesma-Carbayo,_M.J.,_Kellman,_P.,_Santos,_A._"A_New_Similarity │ │ │ │ │ Measure_for_Non-Rigid_Breathing_Motion_Compensation_of_Myocardial_Perfusion_MRI │ │ │ │ │ "._Proc_30th_Annual_International_IEEE_EMBS_Conference,_pp._3389-3392. │ │ │ │ │ Vancouver,_Aug._2008. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ -R, --registered=reg; stringSTRING │ │ │ │ │ file name base for registered fiels │ │ │ │ │ Registration │ │ │ │ │ -O, --optimizer=gsl:opt=gd,step=0.1; factory │ │ │ │ │ Optimizer used for minimization. For supported plug-ins see Plugin_type: │ │ │ │ │ minimizer/singlecost │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoseriescompdice.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmyoseries-compdice

mia-2dmyoseries-compdice

Sysnopis:

mia-2dmyoseries-compdice {-1 string} {-2 string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of two image series

Options:

-1, --first=(input, required); string

first segmentation set

-2, --second=(input, required); string

second segmentation set

-k, --skip=2; uint

images to skip atthe begin of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame dice index of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dmyoseries-compdice -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of two image series

Options:

-1, --first=(required, input); string

first segmentation set

-2, --second=(required, input); string

second segmentation set

-k, --skip=2; uint

images to skip atthe begin of the series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame dice index of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dmyoseries-compdice -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-2dmyoseries-compdice │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dmyoseries-compdice {-1 string} {-2 string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to evaluate the per-frame dice index of segmented regions │ │ │ │ │ of two image series │ │ │ │ │ Options: │ │ │ │ │ - -1, --first=(input, required); string │ │ │ │ │ + -1, --first=(required, input); string │ │ │ │ │ first segmentation set │ │ │ │ │ - -2, --second=(input, required); string │ │ │ │ │ + -2, --second=(required, input); string │ │ │ │ │ second segmentation set │ │ │ │ │ -k, --skip=2; uint │ │ │ │ │ images to skip atthe begin of the series │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyoseriesdice.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dmyoseries-dice

mia-2dmyoseries-dice

Sysnopis:

mia-2dmyoseries-dice {-i string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of an image with respect to the segmentation of a reference frame from the same series.

Options:

-i, --input=(input, required); string

original segmentation set

-k, --skip=2; int

images to skip atthe bgin of the series

-r, --reference=20; uint

reference image

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of segmentation set segment.set with reference 30 and skipping the first two frames.

mia-2dmyoseries-dice -i segment.set -r 30 -k 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to evaluate the per-frame dice index of segmented regions of an image with respect to the segmentation of a reference frame from the same series.

Options:

-i, --input=(required, input); string

original segmentation set

-k, --skip=2; int

images to skip atthe bgin of the series

-r, --reference=20; uint

reference image

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the dice index of segmentation set segment.set with reference 30 and skipping the first two frames.

mia-2dmyoseries-dice -i segment.set -r 30 -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dmyoseries-dice {-i string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to evaluate the per-frame dice index of segmented regions │ │ │ │ │ of an image with respect to the segmentation of a reference frame from the same │ │ │ │ │ series. │ │ │ │ │ Options: │ │ │ │ │ - -i, --input=(input, required); string │ │ │ │ │ + -i, --input=(required, input); string │ │ │ │ │ original segmentation set │ │ │ │ │ -k, --skip=2; int │ │ │ │ │ images to skip atthe bgin of the series │ │ │ │ │ -r, --reference=20; uint │ │ │ │ │ reference image │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dmyosetall2onenonrigid.html │ │ │ │ @@ -1,10 +1,10 @@ │ │ │ │ mia-2dmyoset-all2one-nonrigid

mia-2dmyoset-all2one-nonrigid

Sysnopis:

mia-2dmyoset-all2one-nonrigid {-i string} {-o string} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/fullcost │ │ │ │ │ │ │ │ ...]

Description:

This program runs non-rigid registration of a series of images given in an image set. All images are registered to one user defined reference image.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output, required); string

output perfusion data set

--out-filebase=reg; stringSTRING

file name basae for registered files, file type is deducted from the image file type in the input data set.

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(required, output); string

output perfusion data set

--out-filebase=reg; stringSTRING

file name basae for registered files, file type is deducted from the image file type in the input data set.

│ │ │ │ Registration

-k, --skip=0; int

Skip images at the beginning of the series

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING

Optimizer used for minimization

-l, --mg-levels=3; uint

multi-resolution levels

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 2dimage/transform

-r, --ref=-1; int

reference frame (-1 == use image in the middle)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the perfusion series given in segment.set by optimizing a spline based transformation with a coefficient rate of 16 pixel using Mutual Information and penalize the transformation by using divcurl with aweight of 2.0.

mia-2dmyoset-all2one-nonrigid -i segment.set -o registered.set 
│ │ │ │      -f spline:rate=16,penalty=[divcurl:weight=2.0] image:cost=mi,weight=2.0

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,17 +6,17 @@ │ │ │ │ │ mia-2dmyoset-all2one-nonrigid {-i string} {-o string} [ options ...] [ Plugin │ │ │ │ │ type:_2dimage/fullcost ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs non-rigid registration of a series of images given in an │ │ │ │ │ image set. All images are registered to one user defined reference image. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output perfusion data set │ │ │ │ │ --out-filebase=reg; stringSTRING │ │ │ │ │ file name basae for registered files, file type is deducted from the │ │ │ │ │ image file type in the input data set. │ │ │ │ │ Registration │ │ │ │ │ -k, --skip=0; int │ │ │ │ │ Skip images at the beginning of the series │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegcompare.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegcompare

mia-2dsegcompare

Sysnopis:

mia-2dsegcompare {-i string} {-r string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to evaluate the Hausdorff distance between each frame of a perfusion time series of the input set to the corresponding frame of the reference set and prints the result to stdout.

Options:

-i, --in-file=(input, required); string

input segmentation set

-r, --ref-file=(input, required); string

reference segmentation set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-slice Hausdorff distance of input.set and reference.set.

mia-2dsegcompare -i input.set -r reference.set

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to evaluate the Hausdorff distance between each frame of a perfusion time series of the input set to the corresponding frame of the reference set and prints the result to stdout.

Options:

-i, --in-file=(required, input); string

input segmentation set

-r, --ref-file=(required, input); string

reference segmentation set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-slice Hausdorff distance of input.set and reference.set.

mia-2dsegcompare -i input.set -r reference.set

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,17 +5,17 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dsegcompare {-i string} {-r string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to evaluate the Hausdorff distance between each frame of a │ │ │ │ │ perfusion time series of the input set to the corresponding frame of the │ │ │ │ │ reference set and prints the result to stdout. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -r, --ref-file=(input, required); string │ │ │ │ │ + -r, --ref-file=(required, input); string │ │ │ │ │ reference segmentation set │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseghausdorff.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dseghausdorff

mia-2dseghausdorff

Sysnopis:

mia-2dseghausdorff {-i string} {-r uint} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference frame and print it to stdout.

Options:

-i, --in-file=(input, required); string

input segmentation set

-r, --ref-frame=(required); uint

reference frame

-k, --skip=0; int

skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Hausdorff distance of the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseghausdorff  -i segment.set -r 20

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference frame and print it to stdout.

Options:

-i, --in-file=(required, input); string

input segmentation set

-r, --ref-frame=(required); uint

reference frame

-k, --skip=0; int

skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Hausdorff distance of the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseghausdorff  -i segment.set -r 20

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-2dseghausdorff │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dseghausdorff {-i string} {-r uint} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Get the per-slice Hausdorff distance of a segmentation with respect to a given │ │ │ │ │ reference frame and print it to stdout. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ -r, --ref-frame=(required); uint │ │ │ │ │ reference frame │ │ │ │ │ -k, --skip=0; int │ │ │ │ │ skip frames at the beginning │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentahmed.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegment-ahmed

mia-2dsegment-ahmed

Sysnopis:

mia-2dsegment-ahmed {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

-i, --in-file=(input, required); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io

-a, --no-of-classes=3; int

number of classes

-b, --bias-correct

apply bias field correction

-c, --class-centres=

initial class centers

-s, --spread=64; float

spread parameter describing the strength of mattar distinction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-2dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

-i, --in-file=(required, input); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io

-a, --no-of-classes=3; int

number of classes

-b, --bias-correct

apply bias field correction

-c, --class-centres=

initial class centers

-s, --spread=64; float

spread parameter describing the strength of mattar distinction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-2dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ │ Description: │ │ │ │ │ This program implements a variation of the paper: │ │ │ │ │ Mohamed_N._Ahmed_et._al,_"A_Modified_Fuzzy_C-Means_Algorithm_for_Bias_Field │ │ │ │ │ estimation_and_Segmentation_of_MRI_Data",_IEEE_Trans._on_Medical_Imaging,_Vol. │ │ │ │ │ 21,_No._3,_March_2002, │ │ │ │ │ changes are: p=2, and exp │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ image to be segmented. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ class probability images, the image type must support multiple images and │ │ │ │ │ floating point values. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ -a, --no-of-classes=3; int │ │ │ │ │ number of classes │ │ │ │ │ -b, --bias-correct │ │ │ │ │ apply bias field correction │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentcropbox.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegmentcropbox

mia-2dsegmentcropbox

Sysnopis:

mia-2dsegmentcropbox {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined.

Options:

-i, --in-file=(input, required); string

input segmentation set

-p, --override-imagepath

Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory

-o, --out-file=(output, required); string

output segmentation set

-c, --cropped-base=crop; stringSTRING

Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering.

-e, --enlarge=5; float

Enlarge the area around the obtained sbounding box by this number of pixels in each direction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3 pixels. Store the resulting set in the file cropped.set.

mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined.

Options:

-i, --in-file=(required, input); string

input segmentation set

-p, --override-imagepath

Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory

-o, --out-file=(required, output); string

output segmentation set

-c, --cropped-base=crop; stringSTRING

Base name for the cropped image files, the file type and numbering will be based on the input image file type and numbering.

-e, --enlarge=5; float

Enlarge the area around the obtained sbounding box by this number of pixels in each direction

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the optimal cropping for a segmentation set segment.set and enlarge it by 3 pixels. Store the resulting set in the file cropped.set.

mia-2dsegmentcropbox -i segment.set -o cropped.set -e 3

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -8,20 +8,20 @@ │ │ │ │ │ This program is used on a segmentation set and evaluates a bounding box that │ │ │ │ │ encloses the segmentation in all slices. This bounding box is then used to crop │ │ │ │ │ the original images, correct the segmentation and store a new segmentation set │ │ │ │ │ with the cropped images. The cropped images will be of the same type as the │ │ │ │ │ original images. If no segmentation is given in the set, the result is │ │ │ │ │ undefined. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ -p, --override-imagepath │ │ │ │ │ Instead of using the path of the image files as given in the segmentation │ │ │ │ │ set, assume the files are located in the current directory │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output segmentation set │ │ │ │ │ -c, --cropped-base=crop; stringSTRING │ │ │ │ │ Base name for the cropped image files, the file type and numbering will │ │ │ │ │ be based on the input image file type and numbering. │ │ │ │ │ -e, --enlarge=5; float │ │ │ │ │ Enlarge the area around the obtained sbounding box by this number of │ │ │ │ │ pixels in each direction │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentfuzzyw.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegment-fuzzyw

mia-2dsegment-fuzzyw

Sysnopis:

mia-2dsegment-fuzzyw {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is a implementation of a fuzzy c-means segmentation algorithm

Options:

File I/O

-i, --in-file=(input, required); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-c, --cls-file=(output); io

class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output); io

B-field corrected image. For supported file types see Plugin type: 2dimage/io

-g, --gain-log-file=(output); io

Logarithmic gain field, the image type must support floating point values. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Segmentation parameters

-n, --no-of-classes=3; uint

number of classes to segment

-C, --class-centres=

initial class centers

-N, --neighborhood=shmean:shape=8n; factory

neighborhood filter for B-field correction. For supported plug-ins see Plugin type: 2dimage/filter

-a, --alpha=0.7; float

weight of neighborhood filter for B-field correction

-p, --fuzziness=2; float

parameter describing the fuzzyness of mattar distinction

-e, --epsilon=0.01; float

Stopping criterion for class center estimation.

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v.

mia-2dsegment-fuzzyw -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is a implementation of a fuzzy c-means segmentation algorithm

Options:

File I/O

-i, --in-file=(required, input); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-c, --cls-file=(output); io

class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output); io

B-field corrected image. For supported file types see Plugin type: 2dimage/io

-g, --gain-log-file=(output); io

Logarithmic gain field, the image type must support floating point values. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Segmentation parameters

-n, --no-of-classes=3; uint

number of classes to segment

-C, --class-centres=

initial class centers

-N, --neighborhood=shmean:shape=8n; factory

neighborhood filter for B-field correction. For supported plug-ins see Plugin type: 2dimage/filter

-a, --alpha=0.7; float

weight of neighborhood filter for B-field correction

-p, --fuzziness=2; float

parameter describing the fuzzyness of mattar distinction

-e, --epsilon=0.01; float

Stopping criterion for class center estimation.

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v.

mia-2dsegment-fuzzyw -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-2dsegment-fuzzyw │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dsegment-fuzzyw {-i io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is a implementation of a fuzzy c-means segmentation algorithm │ │ │ │ │ Options: │ │ │ │ │ File I/O │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ image to be segmented. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ -c, --cls-file=(output); io │ │ │ │ │ class probability images, the image type must support multiple images and │ │ │ │ │ floating point values. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ -o, --out-file=(output); io │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentlocalcmeans.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegment-local-cmeans

mia-2dsegment-local-cmeans

Sysnopis:

mia-2dsegment-local-cmeans {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs the segmentation of a 2D image by applying a localized c-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global c-means clustering, and then separates the image into overlapping regions where more c-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. This program implements a 2D prototype of the algorithm described in:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(input, required); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output); io

class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

-G, --out-global-crisp=(output); io

class label image based on global segmentation. For supported file types see Plugin type: 2dimage/io

-C, --class-prob=(output); io

class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf)

Spacing of the grid used to modulate the intensity inhomogeneities

-c, --cmeans=kmeans:nc=3; factory

c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans

-e, --c-means-epsilon=0.0001; float in (0, inf)

c-means breaking condition for update tolerance

-t, --relative-cluster-threshold=0.02; double in [0, 1)

threshhold to ignore classes when initializing the local cmeans from the global one.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs the segmentation of a 2D image by applying a localized c-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global c-means clustering, and then separates the image into overlapping regions where more c-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. This program implements a 2D prototype of the algorithm described in:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(required, input); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output); io

class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

-G, --out-global-crisp=(output); io

class label image based on global segmentation. For supported file types see Plugin type: 2dimage/io

-C, --class-prob=(output); io

class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf)

Spacing of the grid used to modulate the intensity inhomogeneities

-c, --cmeans=kmeans:nc=3; factory

c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans

-e, --c-means-epsilon=0.0001; float in (0, inf)

c-means breaking condition for update tolerance

-t, --relative-cluster-threshold=0.02; double in [0, 1)

threshhold to ignore classes when initializing the local cmeans from the global one.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -12,15 +12,15 @@ │ │ │ │ │ including the locally present classes, i.e. the classes that relatively contain │ │ │ │ │ more pixels than a given threshold. This program implements a 2D prototype of │ │ │ │ │ the algorithm described in: │ │ │ │ │ Dunmore_CJ,_Wollny_G,_Skinner_MM._(2018)_MIA-Clustering:_a_novel_method_for │ │ │ │ │ segmentation_of_paleontological_material._PeerJ_6:e4374. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ image to be segmented. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ -o, --out-file=(output); io │ │ │ │ │ class label image based on merging local labels. For supported file types │ │ │ │ │ see Plugin_type:_2dimage/io │ │ │ │ │ -G, --out-global-crisp=(output); io │ │ │ │ │ class label image based on global segmentation. For supported file types │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentlocalkmeans.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegment-local-kmeans

mia-2dsegment-local-kmeans

Sysnopis:

mia-2dsegment-local-kmeans {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold.

Options:

File-IO

-i, --in-file=(input, required); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output); io

class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

-O, --out-file2=(output); io

class label image based on classifying by using the interpolated class centers . For supported file types see Plugin type: 2dimage/io

-D, --debug-centers=(output); io

Save the class center images to a debug file (type is double). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=20; int in [3, inf)

Spacing of the grid used to modulate the intensity inhomogeneities

-n, --nclasses=3; uint in [2, 127]

Number of intensity classes to segment

-t, --relative-cluster-threshold=0.0001; double in [0, 1)

Number of intensity classes to segment

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold.

Options:

File-IO

-i, --in-file=(required, input); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output); io

class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

-O, --out-file2=(output); io

class label image based on classifying by using the interpolated class centers . For supported file types see Plugin type: 2dimage/io

-D, --debug-centers=(output); io

Save the class center images to a debug file (type is double). For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=20; int in [3, inf)

Spacing of the grid used to modulate the intensity inhomogeneities

-n, --nclasses=3; uint in [2, 127]

Number of intensity classes to segment

-t, --relative-cluster-threshold=0.0001; double in [0, 1)

Number of intensity classes to segment

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-local-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ │ means approach that helps to overcome intensity inhomogeneities in the image. │ │ │ │ │ The approach evaluates a global k-means clustering, and then separates the │ │ │ │ │ image into overlapping regions where more k-means iterations are run only │ │ │ │ │ including the locally present classes, i.e. the classes that relatively contain │ │ │ │ │ more pixels than a given threshold. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ image to be segmented. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ -o, --out-file=(output); io │ │ │ │ │ class label image based on merging local labels. For supported file types │ │ │ │ │ see Plugin_type:_2dimage/io │ │ │ │ │ -O, --out-file2=(output); io │ │ │ │ │ class label image based on classifying by using the interpolated class │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegmentperpixelkmeans.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegment-per-pixel-kmeans

mia-2dsegment-per-pixel-kmeans

Sysnopis:

mia-2dsegment-per-pixel-kmeans {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold.

Options:

File-IO

-i, --in-file=(input, required); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-w, --window=20; int in [3, inf)

Window size around the pixel to be analyzed

-n, --nclasses=3; uint in [2, 127]

Number of intensity classes to segment

-t, --relative-cluster-threshold=0.0001; double in [0, 1)

Number of intensity classes to segment

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-per-pixel-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs the segmentation of a 2D image by applying a localized k-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global k-means clustering, and then separates the image into overlapping regions where more k-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold.

Options:

File-IO

-i, --in-file=(required, input); io

image to be segmented. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

class label image based on merging local labels. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-w, --window=20; int in [3, inf)

Window size around the pixel to be analyzed

-n, --nclasses=3; uint in [2, 127]

Number of intensity classes to segment

-t, --relative-cluster-threshold=0.0001; double in [0, 1)

Number of intensity classes to segment

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-2dsegment-per-pixel-kmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -9,18 +9,18 @@ │ │ │ │ │ means approach that helps to overcome intensity inhomogeneities in the image. │ │ │ │ │ The approach evaluates a global k-means clustering, and then separates the │ │ │ │ │ image into overlapping regions where more k-means iterations are run only │ │ │ │ │ including the locally present classes, i.e. the classes that relatively contain │ │ │ │ │ more pixels than a given threshold. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ image to be segmented. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ class label image based on merging local labels. For supported file types │ │ │ │ │ see Plugin_type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegseriesstats.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dsegseriesstats

mia-2dsegseriesstats

Sysnopis:

mia-2dsegseriesstats {-o string} {-g string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used evaluate various time-intensity curves over a series of images given by a segmentation set. Specifically, the program is taylored to evaluate average intensities and variations of sections the left ventricle myocardium. The segmentation set must contain the segmentations for all slices that will be accessed during evaluation.

Options:

-o, --original=(input, required); string

original segmentation set

-g, --registered=(input, required); string

registered segmentation set

-k, --skip=2; int

images to skip at the begin of the series, if (k < 0) use RV peak of the registered set if set

-r, --reference=-1; int

reference frame for automatic curve extraction. Negative values can be used to indicate specific values (if given in the segmentation set): │ │ │ │ + ...]

Description:

This program is used evaluate various time-intensity curves over a series of images given by a segmentation set. Specifically, the program is taylored to evaluate average intensities and variations of sections the left ventricle myocardium. The segmentation set must contain the segmentations for all slices that will be accessed during evaluation.

Options:

-o, --original=(required, input); string

original segmentation set

-g, --registered=(required, input); string

registered segmentation set

-k, --skip=2; int

images to skip at the begin of the series, if (k < 0) use RV peak of the registered set if set

-r, --reference=-1; int

reference frame for automatic curve extraction. Negative values can be used to indicate specific values (if given in the segmentation set): │ │ │ │ -3: Middle of the series │ │ │ │ -2: prefererred reference │ │ │ │ -1: LV peak │ │ │ │ if any of the above is not available or the value is < -3, use the last frame of the series.

-c, --curves=(output); string

region average value curves, The output files each comprises a table in plain-text format that contains three columns for each section of the LV myocardium: The first column contains the values obtained by using the original segmentation of the reference on all images of the original series, the second column contains the values obtained by the registered segmentation of the reference on all images of the registered series, and the third column contains the values obtained by using the segmentations of each slice on the original images.

-v, --varcurves=(output); string

region variation values, same formt as described above.

-n, --nsections=0; uint

number of sections to use, 0=use as segmented, otherwise Otherwise, the LV myocardium is divided into n sections that enclose equal angles starting at the right ventricle insertion point moving clock-wise using the LV center as angular point.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the two curve typed for 12 sections from segemntation sets orig.set and reg.set skipping the first 2 frames. The output will be written to curves.txt and varcurves.txt respectively.

mia-2dsegseriesstats -i org.set -g reg.set -c curves.txt -v varcurves.txt -n 12 -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,17 +7,17 @@ │ │ │ │ │ Description: │ │ │ │ │ This program is used evaluate various time-intensity curves over a series of │ │ │ │ │ images given by a segmentation set. Specifically, the program is taylored to │ │ │ │ │ evaluate average intensities and variations of sections the left ventricle │ │ │ │ │ myocardium. The segmentation set must contain the segmentations for all slices │ │ │ │ │ that will be accessed during evaluation. │ │ │ │ │ Options: │ │ │ │ │ - -o, --original=(input, required); string │ │ │ │ │ + -o, --original=(required, input); string │ │ │ │ │ original segmentation set │ │ │ │ │ - -g, --registered=(input, required); string │ │ │ │ │ + -g, --registered=(required, input); string │ │ │ │ │ registered segmentation set │ │ │ │ │ -k, --skip=2; int │ │ │ │ │ images to skip at the begin of the series, if (k < 0) use RV peak of the │ │ │ │ │ registered set if set │ │ │ │ │ -r, --reference=-1; int │ │ │ │ │ reference frame for automatic curve extraction. Negative values can be │ │ │ │ │ used to indicate specific values (if given in the segmentation set): -3: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegshift.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegshift

mia-2dsegshift

Sysnopis:

mia-2dsegshift {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped.

Options:

-i, --in-file=(input, required); io

input segmentation set. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

input segmentation set. For supported file types see Plugin type: 2dimage/io

-g, --image-file=crop; stringSTRING

output image filename base

-S, --shift=[0,0]; 2dfvector

shift of segmentation

-k, --skip=2; uint

skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Shift the segmentations of a set segement.set by -20 pixels in horizontal direction and -30 pixels in vertical direction (as if the images where cropped starting at (20,30) and store it in translate.set. The shiftes files are named translatedXXXX.png

mia-2dsegshift -i segment.set -o translate.set -g translated -S "<20,30>"

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped.

Options:

-i, --in-file=(required, input); io

input segmentation set. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

input segmentation set. For supported file types see Plugin type: 2dimage/io

-g, --image-file=crop; stringSTRING

output image filename base

-S, --shift=[0,0]; 2dfvector

shift of segmentation

-k, --skip=2; uint

skip frames at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Shift the segmentations of a set segement.set by -20 pixels in horizontal direction and -30 pixels in vertical direction (as if the images where cropped starting at (20,30) and store it in translate.set. The shiftes files are named translatedXXXX.png

mia-2dsegshift -i segment.set -o translate.set -g translated -S "<20,30>"

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ mia-2dsegshift {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program move the segmentation(s) of an image series by using a shift that │ │ │ │ │ is equal for all slices. The program also may remove images from the begin of │ │ │ │ │ the series. The program can be used to correct the segmentation of the images │ │ │ │ │ if the images where cropped. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input segmentation set. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ input segmentation set. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -g, --image-file=crop; stringSTRING │ │ │ │ │ output image filename base │ │ │ │ │ -S, --shift=[0,0]; 2dfvector │ │ │ │ │ shift of segmentation │ │ │ │ │ -k, --skip=2; uint │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dsegshiftperslice.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dsegshiftperslice

mia-2dsegshiftperslice

Sysnopis:

mia-2dsegshiftperslice {-i string} {-o string} {-S string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program move the segmentation(s) of an image series by using a shift that is given on a per-slice base. The program can be used to correct the segmentation of the images if a linear registration was executed that only applies a translation and does not correct the segmentation automatically.

Options:

-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(output, required); string

output segmentation set

-g, --image-file=crop; stringSTRING

output image filename base

-S, --shift=(required); string

shift of segmentation - base name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Shirt the segmentation given in set segment.set by files shiftXXXX.txt and store the result in shifted.set. Note, the numbering of the shiftXXXX.txx files must coincide.

mia-2dsegshiftperslice -i segment.set -o shifted.set -g shifted -S shift

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program move the segmentation(s) of an image series by using a shift that is given on a per-slice base. The program can be used to correct the segmentation of the images if a linear registration was executed that only applies a translation and does not correct the segmentation automatically.

Options:

-i, --in-file=(required, input); string

input segmentation set

-o, --out-file=(required, output); string

output segmentation set

-g, --image-file=crop; stringSTRING

output image filename base

-S, --shift=(required); string

shift of segmentation - base name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Shirt the segmentation given in set segment.set by files shiftXXXX.txt and store the result in shifted.set. Note, the numbering of the shiftXXXX.txx files must coincide.

mia-2dsegshiftperslice -i segment.set -o shifted.set -g shifted -S shift

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,17 +6,17 @@ │ │ │ │ │ mia-2dsegshiftperslice {-i string} {-o string} {-S string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program move the segmentation(s) of an image series by using a shift that │ │ │ │ │ is given on a per-slice base. The program can be used to correct the │ │ │ │ │ segmentation of the images if a linear registration was executed that only │ │ │ │ │ applies a translation and does not correct the segmentation automatically. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output segmentation set │ │ │ │ │ -g, --image-file=crop; stringSTRING │ │ │ │ │ output image filename base │ │ │ │ │ -S, --shift=(required); string │ │ │ │ │ shift of segmentation - base name │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseries2dordermedian.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dseries2dordermedian

mia-2dseries2dordermedian

Sysnopis:

mia-2dseries2dordermedian {-i string} {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ │ │ - ...]

Description:

This program evaluates the pixel-wise median of the absolute values of the gauss filtered 2nd order temporal derivative of a series of images. In addition, it can be used to output the time-intensity curve of a given pixel.The program supports slice-wise spacial pre-filtering by giving additional filters as free parameters (filter/2dimage).

Options:

-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(output, required); io

output image name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

-g, --gauss=1; uint

gauss filter width for moothing the gradient

--itc-file=STRING

intensity time curve output file

--itc-loc=[0,0]; 2dbounds

intensity time curve output pixel coordinates

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the median of the 2nd order derivative of the series given in segmentation set segment.set after filtering with a Gaussian of width 3. In addition write the time intensity curve of pixel <128,64> to curve.txt.

mia-2dseries2dordermedian -i segment.set -o gradmedian.exr -g 1 --itc-file curve.txt --itc-loc "<128,64>"

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program evaluates the pixel-wise median of the absolute values of the gauss filtered 2nd order temporal derivative of a series of images. In addition, it can be used to output the time-intensity curve of a given pixel.The program supports slice-wise spacial pre-filtering by giving additional filters as free parameters (filter/2dimage).

Options:

-i, --in-file=(required, input); string

input segmentation set

-o, --out-file=(required, output); io

output image name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

-g, --gauss=1; uint

gauss filter width for moothing the gradient

--itc-file=STRING

intensity time curve output file

--itc-loc=[0,0]; 2dbounds

intensity time curve output pixel coordinates

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the median of the 2nd order derivative of the series given in segmentation set segment.set after filtering with a Gaussian of width 3. In addition write the time intensity curve of pixel <128,64> to curve.txt.

mia-2dseries2dordermedian -i segment.set -o gradmedian.exr -g 1 --itc-file curve.txt --itc-loc "<128,64>"

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -8,17 +8,17 @@ │ │ │ │ │ Description: │ │ │ │ │ This program evaluates the pixel-wise median of the absolute values of the │ │ │ │ │ gauss filtered 2nd order temporal derivative of a series of images. In │ │ │ │ │ addition, it can be used to output the time-intensity curve of a given │ │ │ │ │ pixel.The program supports slice-wise spacial pre-filtering by giving │ │ │ │ │ additional filters as free parameters (filter/2dimage). │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image name. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -k, --skip=0; uint │ │ │ │ │ Skip files at the beginning │ │ │ │ │ -e, --enlarge-boundary=5; uint │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ │ -c, --crop │ │ │ │ │ crop image before running statistics │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseries2sets.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dseries2sets

mia-2dseries2sets

Sysnopis:

mia-2dseries2sets {-o string} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/io │ │ │ │ │ │ │ │ - ...]

Description:

This program takes all image files that are given as free parameters on the command line and creates segmentation sets based on information found in the images. Used information is the z-location of the slice and the acquisition number. The code is taylored to used the according descriptors defined in the DICOM standard. All images with the same slice location will be grouped together in one segmentation set and ordered according to their acquisition number. Slice locations are rounded to three digits accuracy to make proper comparison of floating point values feasible.

Options:

-o, --out-directory=(output, required); string

output directory (needs to exist and be writable)

--no-copy

don't copy image files to output directory

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the segmentation sets from a series of DICOM images and copy the files to the output directory (copying is the default).

mia-2dseries2sets -o /home/user/series /net/dicoms/patient1/series1/*.dcm

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program takes all image files that are given as free parameters on the command line and creates segmentation sets based on information found in the images. Used information is the z-location of the slice and the acquisition number. The code is taylored to used the according descriptors defined in the DICOM standard. All images with the same slice location will be grouped together in one segmentation set and ordered according to their acquisition number. Slice locations are rounded to three digits accuracy to make proper comparison of floating point values feasible.

Options:

-o, --out-directory=(required, output); string

output directory (needs to exist and be writable)

--no-copy

don't copy image files to output directory

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the segmentation sets from a series of DICOM images and copy the files to the output directory (copying is the default).

mia-2dseries2sets -o /home/user/series /net/dicoms/patient1/series1/*.dcm

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ │ images. Used information is the z-location of the slice and the acquisition │ │ │ │ │ number. The code is taylored to used the according descriptors defined in the │ │ │ │ │ DICOM standard. All images with the same slice location will be grouped │ │ │ │ │ together in one segmentation set and ordered according to their acquisition │ │ │ │ │ number. Slice locations are rounded to three digits accuracy to make proper │ │ │ │ │ comparison of floating point values feasible. │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-directory=(output, required); string │ │ │ │ │ + -o, --out-directory=(required, output); string │ │ │ │ │ output directory (needs to exist and be writable) │ │ │ │ │ --no-copy │ │ │ │ │ don't copy image files to output directory │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriescorr.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dseriescorr

mia-2dseriescorr

Sysnopis:

mia-2dseriescorr {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Given a set of images of temporal sucession, evaluates images that represent the time-intensity correlation in horizontal and vertical direction as well as average correlation of each pixel with its neighbors. All input images must be of the same pixel type and size.

Options:

-i, --in-base=(input, required); io

input file name base. For supported file types see Plugin type: 2dimage/io

-o, --outname=(output, required); io

output file name to save the avarage per-pixel correlation. For supported file types see Plugin type: 2dimage/io

-z, --horizontal=(output); io

horiZontal correlation output file name. For supported file types see Plugin type: 2dimage/io

-t, --vertical=(output); io

verTical correlation output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=2; uint

skip images at beginning of series

-e, --end=60; uint

last image in series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the time-intensity correaltions for an image series imageXXXX.png starting at image 2 and stop at image 30. Store the results in horizontal.exr, and vertical.exr.

mia-2dseriescorr -i image0000.png -k 2 -e 30 -z horizontal.exr -t vertical.exr

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Given a set of images of temporal sucession, evaluates images that represent the time-intensity correlation in horizontal and vertical direction as well as average correlation of each pixel with its neighbors. All input images must be of the same pixel type and size.

Options:

-i, --in-base=(required, input); io

input file name base. For supported file types see Plugin type: 2dimage/io

-o, --outname=(required, output); io

output file name to save the avarage per-pixel correlation. For supported file types see Plugin type: 2dimage/io

-z, --horizontal=(output); io

horiZontal correlation output file name. For supported file types see Plugin type: 2dimage/io

-t, --vertical=(output); io

verTical correlation output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=2; uint

skip images at beginning of series

-e, --end=60; uint

last image in series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the time-intensity correaltions for an image series imageXXXX.png starting at image 2 and stop at image 30. Store the results in horizontal.exr, and vertical.exr.

mia-2dseriescorr -i image0000.png -k 2 -e 30 -z horizontal.exr -t vertical.exr

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ mia-2dseriescorr {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Given a set of images of temporal sucession, evaluates images that represent │ │ │ │ │ the time-intensity correlation in horizontal and vertical direction as well as │ │ │ │ │ average correlation of each pixel with its neighbors. All input images must be │ │ │ │ │ of the same pixel type and size. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-base=(input, required); io │ │ │ │ │ + -i, --in-base=(required, input); io │ │ │ │ │ input file name base. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ - -o, --outname=(output, required); io │ │ │ │ │ + -o, --outname=(required, output); io │ │ │ │ │ output file name to save the avarage per-pixel correlation. For supported │ │ │ │ │ file types see Plugin_type:_2dimage/io │ │ │ │ │ -z, --horizontal=(output); io │ │ │ │ │ horiZontal correlation output file name. For supported file types see │ │ │ │ │ Plugin_type:_2dimage/io │ │ │ │ │ -t, --vertical=(output); io │ │ │ │ │ verTical correlation output file name. For supported file types see │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriesgradMAD.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dseriesgradMAD

mia-2dseriesgradMAD

Sysnopis:

mia-2dseriesgradMAD {-i string} {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ │ │ - ...]

Description:

Given a set of images of temporal sucession, evaluates the pixel-wise temporal gradient and then its median average distance (MAD) and stores the result in an image. Spacial pre-filtering may be applied as given additional plugin(s) (filter/2dimage).

Options:

-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the MAD-image of the bounding box surrounding the segmentation from a series segment.set. No spacial filtering will be applied. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriesgradMAD  -i segment.set -o mad.exr -c -e 3

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Given a set of images of temporal sucession, evaluates the pixel-wise temporal gradient and then its median average distance (MAD) and stores the result in an image. Spacial pre-filtering may be applied as given additional plugin(s) (filter/2dimage).

Options:

-i, --in-file=(required, input); string

input segmentation set

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the MAD-image of the bounding box surrounding the segmentation from a series segment.set. No spacial filtering will be applied. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriesgradMAD  -i segment.set -o mad.exr -c -e 3

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,17 +7,17 @@ │ │ │ │ │ filter ...] │ │ │ │ │ Description: │ │ │ │ │ Given a set of images of temporal sucession, evaluates the pixel-wise temporal │ │ │ │ │ gradient and then its median average distance (MAD) and stores the result in an │ │ │ │ │ image. Spacial pre-filtering may be applied as given additional plugin(s) │ │ │ │ │ (filter/2dimage). │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file name. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -k, --skip=0; uint │ │ │ │ │ Skip files at the beginning │ │ │ │ │ -e, --enlarge-boundary=5; uint │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ │ -c, --crop │ │ │ │ │ crop image before running statistics │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriesgradvariation.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dseriesgradvariation

mia-2dseriesgradvariation

Sysnopis:

mia-2dseriesgradvariation {-i string} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Given a set of images of temporal sucession, this program evaluates the gradient variation of the pixel-wise time-intensity curves of this series. If the input image set provides a segmentation, then this segmentation can be used to create a bounding box and restrict evaluation to this box.

Options:

-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the gradient-variation image of the bounding box surrounding the segmentation from a series 'segment.set'. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriesgradvariation  -i segment.set -o gradvar.exr -c -e 3

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Given a set of images of temporal sucession, this program evaluates the gradient variation of the pixel-wise time-intensity curves of this series. If the input image set provides a segmentation, then this segmentation can be used to create a bounding box and restrict evaluation to this box.

Options:

-i, --in-file=(required, input); string

input segmentation set

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the gradient-variation image of the bounding box surrounding the segmentation from a series 'segment.set'. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriesgradvariation  -i segment.set -o gradvar.exr -c -e 3

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,17 +6,17 @@ │ │ │ │ │ mia-2dseriesgradvariation {-i string} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Given a set of images of temporal sucession, this program evaluates the │ │ │ │ │ gradient variation of the pixel-wise time-intensity curves of this series. If │ │ │ │ │ the input image set provides a segmentation, then this segmentation can be used │ │ │ │ │ to create a bounding box and restrict evaluation to this box. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file name. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -k, --skip=0; uint │ │ │ │ │ Skip files at the beginning │ │ │ │ │ -e, --enlarge-boundary=5; uint │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ │ -c, --crop │ │ │ │ │ crop image before running statistics │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dserieshausdorff.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dserieshausdorff

mia-2dserieshausdorff

Sysnopis:

mia-2dserieshausdorff {-i string} {-r string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set.

Options:

-i, --in-file=(input, required); string

input segmentation set

-r, --ref-file=(input, required); string

reference segmentation set

-k, --skip=0; int

skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame Hausdorff distance of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dserieshausdorff  -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set.

Options:

-i, --in-file=(required, input); string

input segmentation set

-r, --ref-file=(required, input); string

reference segmentation set

-k, --skip=0; int

skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the per-frame Hausdorff distance of the segmentations of set segment.set with respect to the segmentation set reference.set skipping two images at the beginning.

mia-2dserieshausdorff  -i segment.set -r reference.set -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-2dserieshausdorff │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dserieshausdorff {-i string} {-r string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Get the per-slice Hausdorff distance of a segmentation with respect to a given │ │ │ │ │ reference segmentation set. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -r, --ref-file=(input, required); string │ │ │ │ │ + -r, --ref-file=(required, input); string │ │ │ │ │ reference segmentation set │ │ │ │ │ -k, --skip=0; int │ │ │ │ │ skip images at the beginning │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriesmincorr.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dseries-mincorr

mia-2dseries-mincorr

Sysnopis:

mia-2dseries-mincorr {-i string} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Given a set of images of temporal sucession, this program evaluates the minimal correlation of the time-intensity curve between neighboring pixels.

Options:

-i, --in-set=(input, required); string

input segmentation set

-o, --out-set=(output, required); io

output image of minimal correlation. For supported file types see Plugin type: 2dimage/io

-k, --skip=2; uint

skip images at beginning of series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the minimal correlation image of a series givemn in segment.set and store the image in OpenEXR format. Skip two images at the beginning of the series.

mia-2dseries-mincorr -i segment.set -o mincorr.exr -k 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Given a set of images of temporal sucession, this program evaluates the minimal correlation of the time-intensity curve between neighboring pixels.

Options:

-i, --in-set=(required, input); string

input segmentation set

-o, --out-set=(required, output); io

output image of minimal correlation. For supported file types see Plugin type: 2dimage/io

-k, --skip=2; uint

skip images at beginning of series

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the minimal correlation image of a series givemn in segment.set and store the image in OpenEXR format. Skip two images at the beginning of the series.

mia-2dseries-mincorr -i segment.set -o mincorr.exr -k 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-2dseries-mincorr │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dseries-mincorr {-i string} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Given a set of images of temporal sucession, this program evaluates the minimal │ │ │ │ │ correlation of the time-intensity curve between neighboring pixels. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-set=(input, required); string │ │ │ │ │ + -i, --in-set=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-set=(output, required); io │ │ │ │ │ + -o, --out-set=(required, output); io │ │ │ │ │ output image of minimal correlation. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ -k, --skip=2; uint │ │ │ │ │ skip images at beginning of series │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriessectionmask.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dseries-sectionmask

mia-2dseries-sectionmask

Sysnopis:

mia-2dseries-sectionmask {-i string} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Evaluate the masks for the sections of a segmented frame.

Options:

-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(output, required); io

output image containing the mask. For supported file types see Plugin type: 2dimage/io

-f, --frame=0; uint

Frame number for which to extract the mask

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mask image from the segmentation of image 20 in segment.set and store it to mask20.png:

mia-2dseries-sectionmask -i segment.set -f 20 -o mask20.png

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Evaluate the masks for the sections of a segmented frame.

Options:

-i, --in-file=(required, input); string

input segmentation set

-o, --out-file=(required, output); io

output image containing the mask. For supported file types see Plugin type: 2dimage/io

-f, --frame=0; uint

Frame number for which to extract the mask

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mask image from the segmentation of image 20 in segment.set and store it to mask20.png:

mia-2dseries-sectionmask -i segment.set -f 20 -o mask20.png

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,17 +3,17 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dseries-sectionmask │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dseries-sectionmask {-i string} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Evaluate the masks for the sections of a segmented frame. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image containing the mask. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ -f, --frame=0; uint │ │ │ │ │ Frame number for which to extract the mask │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriessegdistance.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dseries-segdistance

mia-2dseries-segdistance

Sysnopis:

mia-2dseries-segdistance {-i string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Get the mean distance of a segmentation boundary to the reference boundary.

Options:

-i, --in-file=(input, required); string

input segmentation set

-r, --reference=20; uint

reference frame

-k, --skip=0; int

skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mean absolute border distanceof the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseries-segdistance  -i segment.set -r 20

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Get the mean distance of a segmentation boundary to the reference boundary.

Options:

-i, --in-file=(required, input); string

input segmentation set

-r, --reference=20; uint

reference frame

-k, --skip=0; int

skip images at the beginning

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the mean absolute border distanceof the segmentations of set segment.set with respect to the segmentation given in frame 20.

mia-2dseries-segdistance  -i segment.set -r 20

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,15 +3,15 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dseries-segdistance │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dseries-segdistance {-i string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Get the mean distance of a segmentation boundary to the reference boundary. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ -r, --reference=20; uint │ │ │ │ │ reference frame │ │ │ │ │ -k, --skip=0; int │ │ │ │ │ skip images at the beginning │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriessmoothgradMAD.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dseriessmoothgradMAD

mia-2dseriessmoothgradMAD

Sysnopis:

mia-2dseriessmoothgradMAD {-i string} {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/filter │ │ │ │ │ │ │ │ - ...]

Description:

Given a set of images of temporal sucession, evaluate the temporal pixel-wise gaussian and evaluate pixel-wise its MAD.A spacial pre-filtering may be applied by specifying additional plugins (filter/2dimage)

Options:

-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

-g, --gauss=1; uint

gauss filter width for moothing the gradient

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the MAD-image of the bounding box surrounding the segmentation from a series segment.set after applying a temporal Gaussian filter of width 5. No spacial filtering will be applied. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriessmoothgradMAD -i segment.set -o mad.exr -g 2 -c -e 3

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Given a set of images of temporal sucession, evaluate the temporal pixel-wise gaussian and evaluate pixel-wise its MAD.A spacial pre-filtering may be applied by specifying additional plugins (filter/2dimage)

Options:

-i, --in-file=(required, input); string

input segmentation set

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 2dimage/io

-k, --skip=0; uint

Skip files at the beginning

-e, --enlarge-boundary=5; uint

Enlarge cropbox by number of pixels

-c, --crop

crop image before running statistics

-g, --gauss=1; uint

gauss filter width for moothing the gradient

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the MAD-image of the bounding box surrounding the segmentation from a series segment.set after applying a temporal Gaussian filter of width 5. No spacial filtering will be applied. The bounding box will be enlarged by 3 pixels in all directions. Store the image in OpenEXR format.

mia-2dseriessmoothgradMAD -i segment.set -o mad.exr -g 2 -c -e 3

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,17 +6,17 @@ │ │ │ │ │ mia-2dseriessmoothgradMAD {-i string} {-o io} [ options ...] [ Plugin_type: │ │ │ │ │ 2dimage/filter ...] │ │ │ │ │ Description: │ │ │ │ │ Given a set of images of temporal sucession, evaluate the temporal pixel-wise │ │ │ │ │ gaussian and evaluate pixel-wise its MAD.A spacial pre-filtering may be applied │ │ │ │ │ by specifying additional plugins (filter/2dimage) │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file name. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -k, --skip=0; uint │ │ │ │ │ Skip files at the beginning │ │ │ │ │ -e, --enlarge-boundary=5; uint │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ │ -c, --crop │ │ │ │ │ crop image before running statistics │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dseriestovolume.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dseriestovolume

mia-2dseriestovolume

Sysnopis:

mia-2dseriestovolume {-i string} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Obtaines a 3D volume image by combining the images of the segmentation set.

Options:

-i, --in-file=(input, required); string

input segmentation set

-o, --out-file=(output, required); io

output 3D image . For supported file types see Plugin type: 3dimage/io

-k, --skip=0; uint

number of frames to skip at the beginning of the series.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the volume volume.v from the series series.set but skip the first two images.

mia-2dseriestovolume -i series.set -k 2 -o volume.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Obtaines a 3D volume image by combining the images of the segmentation set.

Options:

-i, --in-file=(required, input); string

input segmentation set

-o, --out-file=(required, output); io

output 3D image . For supported file types see Plugin type: 3dimage/io

-k, --skip=0; uint

number of frames to skip at the beginning of the series.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create the volume volume.v from the series series.set but skip the first two images.

mia-2dseriestovolume -i series.set -k 2 -o volume.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,17 +3,17 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dseriestovolume │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dseriestovolume {-i string} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Obtaines a 3D volume image by combining the images of the segmentation set. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input segmentation set │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output 3D image . For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ -k, --skip=0; uint │ │ │ │ │ number of frames to skip at the beginning of the series. │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dstackcmeanspresegment.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dstack-cmeans-presegment

mia-2dstack-cmeans-presegment

Sysnopis:

mia-2dstack-cmeans-presegment {-i io} {-o string} {-L int} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram, and then estimates the mask for one (given) class based on class probabilities. This program accepts only images of eight or 16 bit integer pixels.

Options:

File-IO

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-p, --out-probmap=(output); string

Save probability map to this file

-t, --type=png; stringSTRING

output file name type

-o, --out-mask=(output, required); string

output file name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]

Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.

-C, --classes=kmeans:nc=3; factory

C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans

-S, --seed-threshold=0.95; float in (0, 1)

Probability threshold value to consider a pixel as seed pixel.

-L, --label=(required); int in [0, 10]

Class label to create the mask from

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 30% bins (if available), run cmeans with two classes on the non-zero pixels and then create the mask for class 1 as foregroundXXXX.png.

mia-2dstack-cmeans-presegment -i imageXXXX.png -o foreground -t png --histogram-tresh=30 --classes 2 --label 1

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram, and then estimates the mask for one (given) class based on class probabilities. This program accepts only images of eight or 16 bit integer pixels.

Options:

File-IO

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-p, --out-probmap=(output); string

Save probability map to this file

-t, --type=png; stringSTRING

output file name type

-o, --out-mask=(required, output); string

output file name base

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-T, --histogram-thresh=5; float in [0, 50]

Percent of the extrem parts of the histogram to be collapsed into the respective last histogram bin.

-C, --classes=kmeans:nc=3; factory

C-means class initializer. For supported plug-ins see Plugin type: 1d/cmeans

-S, --seed-threshold=0.95; float in (0, 1)

Probability threshold value to consider a pixel as seed pixel.

-L, --label=(required); int in [0, 10]

Class label to create the mask from

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the program over images imageXXXX.png with the sparse histogram, threshold the lower 30% bins (if available), run cmeans with two classes on the non-zero pixels and then create the mask for class 1 as foregroundXXXX.png.

mia-2dstack-cmeans-presegment -i imageXXXX.png -o foreground -t png --histogram-tresh=30 --classes 2 --label 1

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,22 +7,22 @@ │ │ │ │ │ Description: │ │ │ │ │ This program first evaluates a sparse histogram of an input image series, then │ │ │ │ │ runs a c-means classification over the histogram, and then estimates the mask │ │ │ │ │ for one (given) class based on class probabilities. This program accepts only │ │ │ │ │ images of eight or 16 bit integer pixels. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ -p, --out-probmap=(output); string │ │ │ │ │ Save probability map to this file │ │ │ │ │ -t, --type=png; stringSTRING │ │ │ │ │ output file name type │ │ │ │ │ - -o, --out-mask=(output, required); string │ │ │ │ │ + -o, --out-mask=(required, output); string │ │ │ │ │ output file name base │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dstackfilter.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dstackfilter

mia-2dstackfilter

Sysnopis:

mia-2dstackfilter {-i io} {-o io} {-t set} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dstack/filter │ │ │ │ │ │ │ │ - ...]

Description:

This program is used to filter and convert a series of 2D gray scale images in a 3D fashion by running filters (filter/2dimage) as given on the command line.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output file name base, the actual names is created by adding the file number based on output order and the extension bysed on the 'type' parameter. For supported file types see Plugin type: 2dimage/io

-t, --type=(required); set

output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.exr and store the output in images filteredXXXX.exr

mia-2dstackfilter -i image0000.exr -o filtered -t exr mlv:w=2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to filter and convert a series of 2D gray scale images in a 3D fashion by running filters (filter/2dimage) as given on the command line.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output file name base, the actual names is created by adding the file number based on output order and the extension bysed on the 'type' parameter. For supported file types see Plugin type: 2dimage/io

-t, --type=(required); set

output file type Supported values are:(-, @, BMP, DCM, EXR, JPEG, JPG, PNG, RAW, TIF, TIFF, V, VISTA, bmp, dcm, exr, jpeg, jpg, png, raw, tif, tiff, v, vista, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.exr and store the output in images filteredXXXX.exr

mia-2dstackfilter -i image0000.exr -o filtered -t exr mlv:w=2

Author(s):

Gert Wollny

│ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dto3dimage.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dto3dimage

mia-2dto3dimage

Sysnopis:

mia-2dto3dimage {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to combine a series of 2D images of equal size and type images following a certain numbering scheme to a 3D image.

Options:

-i, --in-file=(input, required); io

input image(s) to be combined. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimage -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to combine a series of 2D images of equal size and type images following a certain numbering scheme to a 3D image.

Options:

-i, --in-file=(required, input); io

input image(s) to be combined. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimage -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,18 +4,18 @@ │ │ │ │ │ mia-2dto3dimage │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dto3dimage {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to combine a series of 2D images of equal size and type │ │ │ │ │ images following a certain numbering scheme to a 3D image. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be combined. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file name. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dto3dimageb.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-2dto3dimageb

mia-2dto3dimageb

Sysnopis:

mia-2dto3dimageb {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 2dimage/io │ │ │ │ │ │ │ │ - ...]

Description:

This program is used to convert a series 2D images into a 3D image. The 2D images are read as additional command line parameters and the slice ordering corresponds to the ordering of the file names on the commend line.

Options:

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimageb -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to convert a series 2D images into a 3D image. The 2D images are read as additional command line parameters and the slice ordering corresponds to the ordering of the file names on the commend line.

Options:

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a series of images imageXXXX.png to a 3D image 3d.v

mia-2dto3dimageb -i imageXXXX.png -o 3d.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dto3dimageb {-o io} [ options ...] [ Plugin_type:_2dimage/io ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to convert a series 2D images into a 3D image. The 2D │ │ │ │ │ images are read as additional command line parameters and the slice ordering │ │ │ │ │ corresponds to the ordering of the file names on the commend line. │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file name. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dtrackpixelmovement.html │ │ │ │ @@ -1,8 +1,8 @@ │ │ │ │ mia-2dtrackpixelmovement

mia-2dtrackpixelmovement

Sysnopis:

mia-2dtrackpixelmovement {-i string} {-o string} {-t io} [ │ │ │ │ options │ │ │ │ ...]

Description:

Track the position of a pixel by means of a transformation obtained by using image registration. The pixel data is given in CSV format │ │ │ │ id;time;x;y;z;reserved │ │ │ │ │ │ │ │ The fields 'time', 'x', 'y', and 'z' are updated, and the fields 'id' and 'reserved' are preserved, empty lines are ignored.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input point set

-o, --out-file=(output, required); string

output point set

-t, --transformation=(input, required); io

transformation describing the monitored change. For supported file types see Plugin type: 2dtransform/io

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input point set

-o, --out-file=(required, output); string

output point set

-t, --transformation=(required, input); io

transformation describing the monitored change. For supported file types see Plugin type: 2dtransform/io

│ │ │ │ Parameters

-T, --time-step=1; float

time step to use for the position update

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

This program evaluated the changed position of pixels given in input.csv, by using a time step of 2.0 time units and the transformation change.v2df, and writes the updated positions to updated.csv.

mia-2dtrackpixelmovement -i input.csv -o output.cvs --time-step 2.0 --transformation change.v2df

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,19 +7,19 @@ │ │ │ │ │ Description: │ │ │ │ │ Track the position of a pixel by means of a transformation obtained by using │ │ │ │ │ image registration. The pixel data is given in CSV format │ │ │ │ │ id;time;x;y;z;reserved The fields 'time', 'x', 'y', and 'z' are updated, and │ │ │ │ │ the fields 'id' and 'reserved' are preserved, empty lines are ignored. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input point set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output point set │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation describing the monitored change. For supported file types │ │ │ │ │ see Plugin_type:_2dtransform/io │ │ │ │ │ Parameters │ │ │ │ │ -T, --time-step=1; float │ │ │ │ │ time step to use for the position update │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dtransform.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dtransform

mia-2dtransform

Sysnopis:

mia-2dtransform {-i io} {-o io} {-t io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to deform a 2D image using a given transformation.

Options:

-i, --in-file=(input, required); io

input image. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(output, required); io

output image. For supported file types see Plugin type: 2dimage/io

-t, --transformation=(input, required); io

transformation file name. For supported file types see Plugin type: 2dtransform/io

-p, --interpolator=STRING

override the interpolator provided by the transformation

-b, --boundary=mirror; stringSTRING

override the boundary conditions provided by the transformation. This is only used if the interpolator is overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.png by the transfromation stored in trans.v by using linear interpolation and zero boundary conditions and store the result in output.png

mia-2dtransform -i input.png -t trans.v  -o output.png  -p bspline:d=1 -b zero

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to deform a 2D image using a given transformation.

Options:

-i, --in-file=(required, input); io

input image. For supported file types see Plugin type: 2dimage/io

-o, --out-file=(required, output); io

output image. For supported file types see Plugin type: 2dimage/io

-t, --transformation=(required, input); io

transformation file name. For supported file types see Plugin type: 2dtransform/io

-p, --interpolator=STRING

override the interpolator provided by the transformation

-b, --boundary=mirror; stringSTRING

override the boundary conditions provided by the transformation. This is only used if the interpolator is overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.png by the transfromation stored in trans.v by using linear interpolation and zero boundary conditions and store the result in output.png

mia-2dtransform -i input.png -t trans.v  -o output.png  -p bspline:d=1 -b zero

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,19 +3,19 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-2dtransform │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dtransform {-i io} {-o io} {-t io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to deform a 2D image using a given transformation. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation file name. For supported file types see Plugin_type: │ │ │ │ │ 2dtransform/io │ │ │ │ │ -p, --interpolator=STRING │ │ │ │ │ override the interpolator provided by the transformation │ │ │ │ │ -b, --boundary=mirror; stringSTRING │ │ │ │ │ override the boundary conditions provided by the transformation. This is │ │ │ │ │ only used if the interpolator is overridden. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia2dtransformationtostrain.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-2dtransformation-to-strain

mia-2dtransformation-to-strain

Sysnopis:

mia-2dtransformation-to-strain {-i io} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Evaluate the Green strain tensor corresponding to a given 2D transformation for each grid point.

Options:

-i, --in-file=(input, required); io

input transformation. For supported file types see Plugin type: 2dtransform/io

-o, --out-file=(output, required); string

output Green's strain tensor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Green strain tensor from the transformation stored in trans.v and save it to output.v

mia-2dtransformation-to-strain -i  trans.v  -o output.mt

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Evaluate the Green strain tensor corresponding to a given 2D transformation for each grid point.

Options:

-i, --in-file=(required, input); io

input transformation. For supported file types see Plugin type: 2dtransform/io

-o, --out-file=(required, output); string

output Green's strain tensor

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the Green strain tensor from the transformation stored in trans.v and save it to output.v

mia-2dtransformation-to-strain -i  trans.v  -o output.mt

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,18 +4,18 @@ │ │ │ │ │ mia-2dtransformation-to-strain │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-2dtransformation-to-strain {-i io} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Evaluate the Green strain tensor corresponding to a given 2D transformation for │ │ │ │ │ each grid point. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input transformation. For supported file types see Plugin_type: │ │ │ │ │ 2dtransform/io │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output Green's strain tensor │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dbinarycombine.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dbinarycombine

mia-3dbinarycombine

Sysnopis:

mia-3dbinarycombine {-1 io} {-2 io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(input, required); io

input mask image 1. For supported file types see Plugin type: 3dimage/io

-2, --file2=(input, required); io

input mask image 2. For supported file types see Plugin type: 3dimage/io

-p, --operation=nor; dict

Operation to be applied

or:logocal or
nor:logocal nor
and:logocal and
nand:logocal nand
xor:logocal xor
nxor:logocal nxor
-o, --out-file=(output, required); io

output mask image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-3dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to combine two binary images by some kind of operation.

Options:

-1, --file1=(required, input); io

input mask image 1. For supported file types see Plugin type: 3dimage/io

-2, --file2=(required, input); io

input mask image 2. For supported file types see Plugin type: 3dimage/io

-p, --operation=nor; dict

Operation to be applied

or:logocal or
nor:logocal nor
and:logocal and
nand:logocal nand
xor:logocal xor
nxor:logocal nxor
-o, --out-file=(required, output); io

output mask image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Combine the binary images b1.png and b2.png by using the 'nor' operation and store the result in b1nor2.png.

mia-3dbinarycombine -1 b1.png -2 b2.png -p nor -o b1nor2.png

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,27 +3,27 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dbinarycombine │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dbinarycombine {-1 io} {-2 io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to combine two binary images by some kind of operation. │ │ │ │ │ Options: │ │ │ │ │ - -1, --file1=(input, required); io │ │ │ │ │ + -1, --file1=(required, input); io │ │ │ │ │ input mask image 1. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -2, --file2=(input, required); io │ │ │ │ │ + -2, --file2=(required, input); io │ │ │ │ │ input mask image 2. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ -p, --operation=nor; dict │ │ │ │ │ Operation to be applied │ │ │ │ │ or: logocal or │ │ │ │ │ nor: logocal nor │ │ │ │ │ and: logocal and │ │ │ │ │ nand: logocal nand │ │ │ │ │ xor: logocal xor │ │ │ │ │ nxor: logocal nxor │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output mask image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dbrainextractT1.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dbrainextractT1

mia-3dbrainextractT1

Sysnopis:

mia-3dbrainextractT1 {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to extract the brain from T1 MR images. It first runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image. Then various fiters are run to obtain a white matter segmentation as initial mask that is then used to run a region growing to obtain a mask of the whole brain. Finally, this mask is used to extact the brain from the B0 field corrected images.

Options:

-i, --in-file=(input, required); io

input image(s) to be segmented. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

brain mask. For supported file types see Plugin type: 3dimage/io

-n, --no-of-classes=3; int

number of classes

-w, --wm-class=2; int

index of white matter

-p, --wm-prob=0.7; float

white matter class probability for initial mask creation

-t, --grow-threshold=20; int

intensity threshold for region growing

--grow-shape=18n; stringSTRING

neighbourhood mask region growing

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a mask from the input image by running a 5-class segmentation over inpt image input.v and use class 4 as white matter class and store the masked image in masked.v and the B0-field corrected image in b0.v

mia-3dbrainextractT1 -i input.v -n 5 -w 4 -o masked.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to extract the brain from T1 MR images. It first runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image. Then various fiters are run to obtain a white matter segmentation as initial mask that is then used to run a region growing to obtain a mask of the whole brain. Finally, this mask is used to extact the brain from the B0 field corrected images.

Options:

-i, --in-file=(required, input); io

input image(s) to be segmented. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

brain mask. For supported file types see Plugin type: 3dimage/io

-n, --no-of-classes=3; int

number of classes

-w, --wm-class=2; int

index of white matter

-p, --wm-prob=0.7; float

white matter class probability for initial mask creation

-t, --grow-threshold=20; int

intensity threshold for region growing

--grow-shape=18n; stringSTRING

neighbourhood mask region growing

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a mask from the input image by running a 5-class segmentation over inpt image input.v and use class 4 as white matter class and store the masked image in masked.v and the B0-field corrected image in b0.v

mia-3dbrainextractT1 -i input.v -n 5 -w 4 -o masked.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -8,18 +8,18 @@ │ │ │ │ │ This program is used to extract the brain from T1 MR images. It first runs a │ │ │ │ │ combined fuzzy c-means clustering and B-field correction to facilitate a 3D │ │ │ │ │ segmentation of 3D image. Then various fiters are run to obtain a white matter │ │ │ │ │ segmentation as initial mask that is then used to run a region growing to │ │ │ │ │ obtain a mask of the whole brain. Finally, this mask is used to extact the │ │ │ │ │ brain from the B0 field corrected images. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be segmented. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ brain mask. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ -n, --no-of-classes=3; int │ │ │ │ │ number of classes │ │ │ │ │ -w, --wm-class=2; int │ │ │ │ │ index of white matter │ │ │ │ │ -p, --wm-prob=0.7; float │ │ │ │ │ white matter class probability for initial mask creation │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcombineimageseries.html │ │ │ │ @@ -1,8 +1,8 @@ │ │ │ │ mia-3dcombine-imageseries

mia-3dcombine-imageseries

Sysnopis:

mia-3dcombine-imageseries {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/io │ │ │ │ │ │ │ │ - ...]

Description:

This programs takes various input images of the same dimensions and creates a combined output images that uses the define operation for the combination.

Options:

-o, --out-file=(output, required); io

output file that contains the combined image.. For supported file types see Plugin type: 3dimage/io

-p, --operation=mean; dict

Operation to be applied when combining the images

mean:mean image intensities
max:select max per pixel intensity
add:add pixel intensities
-r, --repn=none; dict

Output pixel representation (if not given, then the representation of the first input image will be used

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

This programs takes various input images of the same dimensions and creates a combined output images that uses the define operation for the combination.

Options:

-o, --out-file=(required, output); io

output file that contains the combined image.. For supported file types see Plugin type: 3dimage/io

-p, --operation=mean; dict

Operation to be applied when combining the images

mean:mean image intensities
max:select max per pixel intensity
add:add pixel intensities
-r, --repn=none; dict

Output pixel representation (if not given, then the representation of the first input image will be used

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-3dcombine-imageseries 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-3dcombine-imageseries │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dcombine-imageseries {-o io} [ options ...] [ Plugin_type:_3dimage/io ...] │ │ │ │ │ Description: │ │ │ │ │ This programs takes various input images of the same dimensions and creates a │ │ │ │ │ combined output images that uses the define operation for the combination. │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file that contains the combined image.. For supported file types │ │ │ │ │ see Plugin_type:_3dimage/io │ │ │ │ │ -p, --operation=mean; dict │ │ │ │ │ Operation to be applied when combining the images │ │ │ │ │ mean: mean image intensities │ │ │ │ │ max: select max per pixel intensity │ │ │ │ │ add: add pixel intensities │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcombinemrsegmentations.html │ │ │ │ @@ -1,8 +1,8 @@ │ │ │ │ mia-3dcombine-mr-segmentations

mia-3dcombine-mr-segmentations

Sysnopis:

mia-3dcombine-mr-segmentations {-i io} {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/io │ │ │ │ │ │ │ │ - ...]

Description:

This programs takes various segmentation masks of the same data and a tissue probability image set and combines them into one labeled image. The masks are translated to labels according to the position on the command line. If a voxel is set as belonging to more then one mask, the probabilities are consulted.

Options:

-i, --in-file=(input, required); io

input probability images. The number of mask images must correspond to the number of probability images given here.. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output image that contains the labeling.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

This programs takes various segmentation masks of the same data and a tissue probability image set and combines them into one labeled image. The masks are translated to labels according to the position on the command line. If a voxel is set as belonging to more then one mask, the probabilities are consulted.

Options:

-i, --in-file=(required, input); io

input probability images. The number of mask images must correspond to the number of probability images given here.. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image that contains the labeling.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-3dcombine-mr-segmentations 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,19 +7,19 @@ │ │ │ │ │ 3dimage/io ...] │ │ │ │ │ Description: │ │ │ │ │ This programs takes various segmentation masks of the same data and a tissue │ │ │ │ │ probability image set and combines them into one labeled image. The masks are │ │ │ │ │ translated to labels according to the position on the command line. If a voxel │ │ │ │ │ is set as belonging to more then one mask, the probabilities are consulted. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input probability images. The number of mask images must correspond to │ │ │ │ │ the number of probability images given here.. For supported file types │ │ │ │ │ see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image that contains the labeling.. For supported file types see │ │ │ │ │ Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcosttranslatedgrad.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dcost-translatedgrad

mia-3dcost-translatedgrad

Sysnopis:

mia-3dcost-translatedgrad {-i io} {-r io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Evaluate the cost gradient between two images and evaluate the transformation related gradient for it based on the given transformation model.

Options:

-i, --in-file=(input, required); io

input image . For supported file types see Plugin type: 3dimage/io

-r, --ref-file=(input, required); io

reference image . For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output vector field . For supported file types see Plugin type: 3dtransform/io

-g, --gradimg-file=(output); io

norm image of the spline transformed gradient. For supported file types see Plugin type: 3dimage/io

-C, --cost-gradimg-file=(output); io

norm image of the cost gradient. For supported file types see Plugin type: 3dimage/io

-f, --transForm=spline:rate=5; factory

Transformation the gradient relates to. For supported plug-ins see Plugin type: 3dimage/transform

-c, --cost=ssd; factory

cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the SSD cost between src.v and ref.v and store the gradient gradient corresponding to a spline transformation in grad.v3dt.

mia-3dcost-translatedgrad -i src.v -o grad.v3dt -f spline:rate=8 -c ssd

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Evaluate the cost gradient between two images and evaluate the transformation related gradient for it based on the given transformation model.

Options:

-i, --in-file=(required, input); io

input image . For supported file types see Plugin type: 3dimage/io

-r, --ref-file=(required, input); io

reference image . For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output vector field . For supported file types see Plugin type: 3dtransform/io

-g, --gradimg-file=(output); io

norm image of the spline transformed gradient. For supported file types see Plugin type: 3dimage/io

-C, --cost-gradimg-file=(output); io

norm image of the cost gradient. For supported file types see Plugin type: 3dimage/io

-f, --transForm=spline:rate=5; factory

Transformation the gradient relates to. For supported plug-ins see Plugin type: 3dimage/transform

-c, --cost=ssd; factory

cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the SSD cost between src.v and ref.v and store the gradient gradient corresponding to a spline transformation in grad.v3dt.

mia-3dcost-translatedgrad -i src.v -o grad.v3dt -f spline:rate=8 -c ssd

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,19 +4,19 @@ │ │ │ │ │ mia-3dcost-translatedgrad │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dcost-translatedgrad {-i io} {-r io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Evaluate the cost gradient between two images and evaluate the transformation │ │ │ │ │ related gradient for it based on the given transformation model. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image . For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -r, --ref-file=(input, required); io │ │ │ │ │ + -r, --ref-file=(required, input); io │ │ │ │ │ reference image . For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output vector field . For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ -g, --gradimg-file=(output); io │ │ │ │ │ norm image of the spline transformed gradient. For supported file types │ │ │ │ │ see Plugin_type:_3dimage/io │ │ │ │ │ -C, --cost-gradimg-file=(output); io │ │ │ │ │ norm image of the cost gradient. For supported file types see Plugin │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dcrispsegment.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dcrispsegment

mia-3dcrispsegment

Sysnopis:

mia-3dcrispsegment {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the higest probability plus a given offset

Options:

-i, --in-file=(input, required); io

input class file, should contain multiple images with tissue class probabilities. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output class label image. For supported file types see Plugin type: 3dimage/io

-l, --label-offset=1; uint

label offset

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Set the labels based on the input class probability file cls.v adding the offset 2 to each label and save the result to labeled.v.

mia-3dcrispsegment -i cls.v -o labeled.v -l 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the higest probability plus a given offset

Options:

-i, --in-file=(required, input); io

input class file, should contain multiple images with tissue class probabilities. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output class label image. For supported file types see Plugin type: 3dimage/io

-l, --label-offset=1; uint

label offset

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Set the labels based on the input class probability file cls.v adding the offset 2 to each label and save the result to labeled.v.

mia-3dcrispsegment -i cls.v -o labeled.v -l 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,18 +4,18 @@ │ │ │ │ │ mia-3dcrispsegment │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dcrispsegment {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program creates a label image from a fuzzy segmentation. or each pixel the │ │ │ │ │ label is set to the class with the higest probability plus a given offset │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input class file, should contain multiple images with tissue class │ │ │ │ │ probabilities. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output class label image. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -l, --label-offset=1; uint │ │ │ │ │ label offset │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3ddeform.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3ddeform

mia-3ddeform

Sysnopis:

mia-3ddeform {-i io} {-o io} {-t io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Transform a 3D image by applying a given 3D transformation that is defined by a 3D vector field v according to x:=x-v(x)

Options:

-i, --in-image=(input, required); io

input image. For supported file types see Plugin type: 3dimage/io

-o, --out-image=(output, required); io

transformed image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(input, required); io

transformation vector field. For supported file types see Plugin type: 3dvf/io

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transformation defined by the vector field field.v by using bspline interpolation of degree 4 and store the result in output.v

mia-3ddeform -i input.v -t field.v  -o output.v  -p bspline:d=4

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Transform a 3D image by applying a given 3D transformation that is defined by a 3D vector field v according to x:=x-v(x)

Options:

-i, --in-image=(required, input); io

input image. For supported file types see Plugin type: 3dimage/io

-o, --out-image=(required, output); io

transformed image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(required, input); io

transformation vector field. For supported file types see Plugin type: 3dvf/io

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transformation defined by the vector field field.v by using bspline interpolation of degree 4 and store the result in output.v

mia-3ddeform -i input.v -t field.v  -o output.v  -p bspline:d=4

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,19 +4,19 @@ │ │ │ │ │ mia-3ddeform │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3ddeform {-i io} {-o io} {-t io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Transform a 3D image by applying a given 3D transformation that is defined by a │ │ │ │ │ 3D vector field v according to x:=x-v(x) │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-image=(output, required); io │ │ │ │ │ + -o, --out-image=(required, output); io │ │ │ │ │ transformed image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation vector field. For supported file types see Plugin_type: │ │ │ │ │ 3dvf/io │ │ │ │ │ -p, --interpolator=bspline:d=3; factory │ │ │ │ │ image interpolator kernel. For supported plug-ins see Plugin_type:_1d/ │ │ │ │ │ splinekernel │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3ddistance.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3ddistance

mia-3ddistance

Sysnopis:

mia-3ddistance {-i string} {-r string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program takes two binary masks as input and evaluates the distance of one mask with respect to the other in voxel space. The output is given as text file with the coordinates of the source voxels and their distance to the reference mask. Correction for voxel size must be done after processing.

Options:

File IO

-i, --in-file=(input, required); string

input image(s) that contain the source pixel mask

-r, --ref-file=(input, required); string

reference mask to evaluate the distance from

-o, --out-file=(output, required); string

output file name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--self-test

run a self test

Example:

Evaluate the distance of the mask given in the images srcXXXX.png to the mask given in refXXXX.png and save the result to distances.txt

mia-3ddistance -i srcXXXX.png -r refXXXX.png -o distances.txt

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program takes two binary masks as input and evaluates the distance of one mask with respect to the other in voxel space. The output is given as text file with the coordinates of the source voxels and their distance to the reference mask. Correction for voxel size must be done after processing.

Options:

File IO

-i, --in-file=(required, input); string

input image(s) that contain the source pixel mask

-r, --ref-file=(required, input); string

reference mask to evaluate the distance from

-o, --out-file=(required, output); string

output file name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--self-test

run a self test

Example:

Evaluate the distance of the mask given in the images srcXXXX.png to the mask given in refXXXX.png and save the result to distances.txt

mia-3ddistance -i srcXXXX.png -r refXXXX.png -o distances.txt

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,19 +7,19 @@ │ │ │ │ │ Description: │ │ │ │ │ This program takes two binary masks as input and evaluates the distance of one │ │ │ │ │ mask with respect to the other in voxel space. The output is given as text file │ │ │ │ │ with the coordinates of the source voxels and their distance to the reference │ │ │ │ │ mask. Correction for voxel size must be done after processing. │ │ │ │ │ Options: │ │ │ │ │ File IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input image(s) that contain the source pixel mask │ │ │ │ │ - -r, --ref-file=(input, required); string │ │ │ │ │ + -r, --ref-file=(required, input); string │ │ │ │ │ reference mask to evaluate the distance from │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output file name │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3ddistancestats.html │ │ │ │ @@ -14,8 +14,8 @@ │ │ │ │ end_range <- 2 + as.numeric(line[2]) │ │ │ │ s <- as.numeric(line[3:end_range]) │ │ │ │ result <- sprintf("%d %8.4f %8.4f %8.4f %8.4f\n" │ │ │ │ label, mean(s), sqrt(var(s)), median(s), max(s)) │ │ │ │ cat(result) │ │ │ │ } │ │ │ │ │ │ │ │ -

Options:

File-IO

-i, --in-labels=(input, required); io

input label image. For supported file types see Plugin type: 3dimage/io

-r, --ref-labels=(input, required); io

reference label image. For supported file types see Plugin type: 3dimage/io

-l, --label-map=(input); string

optional mapping of label numbers

-o, --out-file=(output, required); string

output file name to write the distances to. The output file is a csv file, containing distances listed for each label.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distances for each label available in image.v to the corresponding labels in the image reference.v ans store the result a coma separated list of values, i.e. distances.csv.

mia-3ddistance-stats -i image.v -r reference.v -o distances.csv

Author(s):

Gert Wollny

│ │ │ │ +

Options:

File-IO

-i, --in-labels=(required, input); io

input label image. For supported file types see Plugin type: 3dimage/io

-r, --ref-labels=(required, input); io

reference label image. For supported file types see Plugin type: 3dimage/io

-l, --label-map=(input); string

optional mapping of label numbers

-o, --out-file=(required, output); string

output file name to write the distances to. The output file is a csv file, containing distances listed for each label.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distances for each label available in image.v to the corresponding labels in the image reference.v ans store the result a coma separated list of values, i.e. distances.csv.

mia-3ddistance-stats -i image.v -r reference.v -o distances.csv

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -12,22 +12,22 @@ │ │ │ │ │ statistics from this data would look like args <- commandArgs(TRUE) data <- │ │ │ │ │ read.csv(args[1], header=FALSE) for ( i in 1:dim(data)[1] ) { line <- data[i,] │ │ │ │ │ label <- as.integer(line[1]) end_range <- 2 + as.numeric(line[2]) s <- │ │ │ │ │ as.numeric(line[3:end_range]) result <- sprintf("%d %8.4f %8.4f %8.4f %8.4f\n" │ │ │ │ │ label, mean(s), sqrt(var(s)), median(s), max(s)) cat(result) } │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-labels=(input, required); io │ │ │ │ │ + -i, --in-labels=(required, input); io │ │ │ │ │ input label image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -r, --ref-labels=(input, required); io │ │ │ │ │ + -r, --ref-labels=(required, input); io │ │ │ │ │ reference label image. For supported file types see Plugin_type:_3dimage/ │ │ │ │ │ io │ │ │ │ │ -l, --label-map=(input); string │ │ │ │ │ optional mapping of label numbers │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output file name to write the distances to. The output file is a csv │ │ │ │ │ file, containing distances listed for each label. │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3devaltransformquantity.html │ │ │ │ @@ -14,9 +14,9 @@ │ │ │ │ style=sparse #storage style (sparse|grid) │ │ │ │ repn=float32 #representation of values │ │ │ │ size=1000 1000 200 #grid size of the transformation │ │ │ │ endian=low #endianess of binary data (low|big) │ │ │ │ } │ │ │ │ │ │ │ │ This example header has to be interpreted like follows: three-dimensional data, each entry consists of 13 values the values etry consists of a 3D vector, a scalar, and a 3x3 matrix (saved in row-major format).The data records represent strain tensors, and only a sparse set of points is given. The values are given as single floating point (32 bit). The original transformation field corresponds to images of 1000x1000x200 voxels and the binary data is stored in low endian format.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input); string

input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.

-o, --out-file=(output, required); string

output strains file, for a format description see above.

-t, --transformation=(input, required); io

transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 3dtransform/io

│ │ │ │ +File-IO

-i, --in-file=(input); string

input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.

-o, --out-file=(required, output); string

output strains file, for a format description see above.

-t, --transformation=(required, input); io

transformation of which the quantity will be evaluated.. For supported file types see Plugin type: 3dtransform/io

│ │ │ │ Parameters

-q, --quantity=strain; dict

Specify the quantity to be evaluated at the given points

derivative:Evaluate the transformation derivative at the given points
strain:Evaluate the strain tensor at the given points

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Derivative of the transformation change.v3df for each point given in input.csv are evaluated and written to output.s.

mia-3deval-transformquantity -i input.csv -o output.s --transformation change.v3df

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -24,17 +24,17 @@ │ │ │ │ │ the binary data is stored in low endian format. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ -i, --in-file=(input); string │ │ │ │ │ input point set, if this parameter is given a sparse evaluation of the │ │ │ │ │ quantity will be done, otherwise the quantity is evaluated for each grid │ │ │ │ │ point of the transformation range. │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output strains file, for a format description see above. │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation of which the quantity will be evaluated.. For supported │ │ │ │ │ file types see Plugin_type:_3dtransform/io │ │ │ │ │ Parameters │ │ │ │ │ -q, --quantity=strain; dict │ │ │ │ │ Specify the quantity to be evaluated at the given points │ │ │ │ │ derivative: Evaluate the transformation derivative at the given points │ │ │ │ │ strain: Evaluate the strain tensor at the given points │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfield2norm.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dfield2norm

mia-3dfield2norm

Sysnopis:

mia-3dfield2norm {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program converts a 3d vector field to an image of its voxel-wise norm.

Options:

-i, --in-vectorfield=(input, required); io

input vector field. For supported file types see Plugin type: 3dvf/io

-o, --out-image=(output, required); io

output image comprising the per voxel norm of each image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the norm image norm.v from a vector field field.v.

mia-3dfield2norm -i field.v -o norm.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program converts a 3d vector field to an image of its voxel-wise norm.

Options:

-i, --in-vectorfield=(required, input); io

input vector field. For supported file types see Plugin type: 3dvf/io

-o, --out-image=(required, output); io

output image comprising the per voxel norm of each image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the norm image norm.v from a vector field field.v.

mia-3dfield2norm -i field.v -o norm.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,17 +3,17 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dfield2norm │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dfield2norm {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program converts a 3d vector field to an image of its voxel-wise norm. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-vectorfield=(input, required); io │ │ │ │ │ + -i, --in-vectorfield=(required, input); io │ │ │ │ │ input vector field. For supported file types see Plugin_type:_3dvf/io │ │ │ │ │ - -o, --out-image=(output, required); io │ │ │ │ │ + -o, --out-image=(required, output); io │ │ │ │ │ output image comprising the per voxel norm of each image. For supported │ │ │ │ │ file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfluid.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dfluid

mia-3dfluid

Sysnopis:

mia-3dfluid {-i io} {-r io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used for non-rigid registration based on fluid dynamics as described in:

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(input, required); io

input image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(input, required); io

reference image . For supported file types see Plugin type: 3dimage/io

-o, --out-transformation=(output, required); io

output transformation comprising the registering transformation field. For supported file types see Plugin type: 3dtransform/io

-d, --out-image=(output); io

save deformed image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

--disable-multigrid

disable multi-grid processing

--disable-fullres

disable processing on the full resolution image

--lambda=1; float

elasticy constant

--mu=1; float

elasticy constant

-s, --start-size=16; int

initial multigrided size

-m, --method=sora; dict

method for solving PDE

sor:successive overrelaxation
sora:Gauss Southwell relexation
--step=0.8; float

Initial stepsize

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

--relax=1; float

overrelaxation factor vor method sor

--maxiter=10; int

maximum iterations

--epsilon=0.01; float

truncation condition

--matter=4; float

intensity above which real matter is assumed (experimental)

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used for non-rigid registration based on fluid dynamics as described in:

Wollny, G. and Kruggel, F., 'Computational cost of non-rigid registration algorithms based on fluid dynamics', IEEE Transactions on Medical Imaging, 11(8), pp. 946-952, 2002.

It uses SSD as the sole registration criterion.

Options:

File-IO

-i, --in-image=(required, input); io

input image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(required, input); io

reference image . For supported file types see Plugin type: 3dimage/io

-o, --out-transformation=(required, output); io

output transformation comprising the registering transformation field. For supported file types see Plugin type: 3dtransform/io

-d, --out-image=(output); io

save deformed image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration parameters

--disable-multigrid

disable multi-grid processing

--disable-fullres

disable processing on the full resolution image

--lambda=1; float

elasticy constant

--mu=1; float

elasticy constant

-s, --start-size=16; int

initial multigrided size

-m, --method=sora; dict

method for solving PDE

sor:successive overrelaxation
sora:Gauss Southwell relexation
--step=0.8; float

Initial stepsize

-p, --interpolator=bspline:d=3; factory

image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

--relax=1; float

overrelaxation factor vor method sor

--maxiter=10; int

maximum iterations

--epsilon=0.01; float

truncation condition

--matter=4; float

intensity above which real matter is assumed (experimental)

Example:

Register image test.v to image ref.v and write the deformation vector field regfield.v. Start registration at the smallest size above 16 pixel.

mia-3dfluid -i test.v -r ref.v -o regfield.v -s 16

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -9,19 +9,19 @@ │ │ │ │ │ described in: │ │ │ │ │ Wollny,_G._and_Kruggel,_F.,_'Computational_cost_of_non-rigid_registration │ │ │ │ │ algorithms_based_on_fluid_dynamics',_IEEE_Transactions_on_Medical_Imaging,_11 │ │ │ │ │ (8),_pp._946-952,_2002. │ │ │ │ │ It uses SSD as the sole registration criterion. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -r, --ref-image=(input, required); io │ │ │ │ │ + -r, --ref-image=(required, input); io │ │ │ │ │ reference image . For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-transformation=(output, required); io │ │ │ │ │ + -o, --out-transformation=(required, output); io │ │ │ │ │ output transformation comprising the registering transformation field. │ │ │ │ │ For supported file types see Plugin_type:_3dtransform/io │ │ │ │ │ -d, --out-image=(output); io │ │ │ │ │ save deformed image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfluidsynregistration.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dfluid-syn-registration

mia-3dfluid-syn-registration

Sysnopis:

mia-3dfluid-syn-registration {-i io} {-r io} {-o io} {-O io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements the registration of two gray scale 3D images. The transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently, this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have the same voxel spacing, and any intensity range normalization or equalization should also be done before calling this program.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(input, required); io

test image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(input, required); io

reference image. For supported file types see Plugin type: 3dimage/io

-o, --transform=(output, required); io

output transformation. For supported file types see Plugin type: 3dtransform/io

-O, --inverse-transform=(output, required); io

inverse output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint

Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.

-S, --step=0.25; float in (0, 0.5]

Initial step size for all levels

-c, --cost=ssd; factory

Image similarity function to be minimized. For supported plug-ins see Plugin type: 3dimage/cost

-R, --regularizer=sor:kernel=fluid,maxiter=50; factory

Regularization for the force to transformation update. For supported plug-ins see Plugin type: 3dvf/regularizer

-T, --conv-test-interval= in [4, 40]

Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-D, --stop-decline-rate= in [0, inf)

Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-C, --stop-cost=

Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-I, --iter= in [4, inf)

Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-3dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements the registration of two gray scale 3D images. The transformation applied is a symmeric diffeomorpic fluid dynamic registration. To work most efficiently, this program makes a few assumptions about the imput data, i.e. the image must be of the same size, have the same voxel spacing, and any intensity range normalization or equalization should also be done before calling this program.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(required, input); io

test image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(required, input); io

reference image. For supported file types see Plugin type: 3dimage/io

-o, --transform=(required, output); io

output transformation. For supported file types see Plugin type: 3dtransform/io

-O, --inverse-transform=(required, output); io

inverse output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --mg-levels=3; uint

Number of multi-resolution levels to run the registration on. Not that some registration parameters can be given as a coma seperated list to indicate per level values. In these cases if the number of given values is smaller than the number of multi-resolution levels (this parameter), the the last given value is used for all subsequest multi-resolution levels.

-S, --step=0.25; float in (0, 0.5]

Initial step size for all levels

-c, --cost=ssd; factory

Image similarity function to be minimized. For supported plug-ins see Plugin type: 3dimage/cost

-R, --regularizer=sor:kernel=fluid,maxiter=50; factory

Regularization for the force to transformation update. For supported plug-ins see Plugin type: 3dvf/regularizer

-T, --conv-test-interval= in [4, 40]

Convergence test interations intervall: In order to measure convergence the cost function value is averaged over this amount of iterations, and the decline rate is evaluated based on the linare regression of the cost function values in this intervall. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-D, --stop-decline-rate= in [0, inf)

Stopping criterium for registration based on the cost decline rate. If the rate below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-C, --stop-cost=

Stopping criterium for registration based on the cost value. If the cost drops below this value, the iteration is stopped. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

-I, --iter= in [4, inf)

Naximum number if iterations done on each multi-resolution level. This parameter can be given as a coma-seperated list with values corresponding to the multi-resolution levels, see option --mg-levels for more information.

Example:

Register image test.v to image ref.v saving the transformation to transform.v and the inverse transform to inverse-transform.v. Use three multiresolution levels, ssd as image cost function.

mia-3dfluid-syn-registration -i test.v -r ref.v -t transform.v -T inverse-transform.v  -l 3 ssd

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -29,22 +29,22 @@ │ │ │ │ │ -h, --help=(); bool │ │ │ │ │ print this help │ │ │ │ │ -?, --usage=(); bool │ │ │ │ │ print a short help │ │ │ │ │ --version=(); bool │ │ │ │ │ print the version number and exit │ │ │ │ │ IO │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ test image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -r, --ref-image=(input, required); io │ │ │ │ │ + -r, --ref-image=(required, input); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --transform=(output, required); io │ │ │ │ │ + -o, --transform=(required, output); io │ │ │ │ │ output transformation. For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ - -O, --inverse-transform=(output, required); io │ │ │ │ │ + -O, --inverse-transform=(required, output); io │ │ │ │ │ inverse output transformation. For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ Processing │ │ │ │ │ --threads=-1; int │ │ │ │ │ Maxiumum number of threads to use for processing,This number should be │ │ │ │ │ lower or equal to the number of logical processor cores in the machine. │ │ │ │ │ (-1: automatic estimation). │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dforce.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dforce

mia-3dforce

Sysnopis:

mia-3dforce {-i io} {-r io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to create an image comprising the pixel-wise norm of the ggradient of a given cost function.

Options:

-i, --src-file=(input, required); io

input image. For supported file types see Plugin type: 3dimage/io

-r, --ref-file=(input, required); io

output force norm image. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

reference image. For supported file types see Plugin type: 3dimage/io

-c, --cost=ssd; factory

cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the weigtes sum of SSD between src.v and ref.v and store the result in forcenorm.v.

mia-3dforce -i src.v -r ref.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to create an image comprising the pixel-wise norm of the ggradient of a given cost function.

Options:

-i, --src-file=(required, input); io

input image. For supported file types see Plugin type: 3dimage/io

-r, --ref-file=(required, input); io

output force norm image. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

reference image. For supported file types see Plugin type: 3dimage/io

-c, --cost=ssd; factory

cost function to use. For supported plug-ins see Plugin type: 3dimage/cost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the weigtes sum of SSD between src.v and ref.v and store the result in forcenorm.v.

mia-3dforce -i src.v -r ref.v -c ssd -o forcenorm.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,20 +4,20 @@ │ │ │ │ │ mia-3dforce │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dforce {-i io} {-r io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to create an image comprising the pixel-wise norm of the │ │ │ │ │ ggradient of a given cost function. │ │ │ │ │ Options: │ │ │ │ │ - -i, --src-file=(input, required); io │ │ │ │ │ + -i, --src-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -r, --ref-file=(input, required); io │ │ │ │ │ + -r, --ref-file=(required, input); io │ │ │ │ │ output force norm image. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ -c, --cost=ssd; factory │ │ │ │ │ cost function to use. For supported plug-ins see Plugin_type:_3dimage/ │ │ │ │ │ cost │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dfuzzysegment.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dfuzzysegment

mia-3dfuzzysegment

Sysnopis:

mia-3dfuzzysegment {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image

Options:

-i, --in-file=(input, required); io

input image(s) to be segmenetd. For supported file types see Plugin type: 3dimage/io

-c, --cls-file=(output); io

output class probability images. Note, the used file format must support multible images (best is to use vista). For supported file types see Plugin type: 3dimage/io

-o, --b0-file=(output); io

image corrected for intensity non-uniformity. For supported file types see Plugin type: 3dimage/io

-n, --no-of-classes=3; int

number of classes

-r, --residuum=0.1; float

relative residuum

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-3dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image

Options:

-i, --in-file=(required, input); io

input image(s) to be segmenetd. For supported file types see Plugin type: 3dimage/io

-c, --cls-file=(output); io

output class probability images. Note, the used file format must support multible images (best is to use vista). For supported file types see Plugin type: 3dimage/io

-o, --b0-file=(output); io

image corrected for intensity non-uniformity. For supported file types see Plugin type: 3dimage/io

-n, --no-of-classes=3; int

number of classes

-r, --residuum=0.1; float

relative residuum

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over inpt image input.v and store the class probability images in cls.v and the B0-field corrected image in b0.v.

mia-3dfuzzysegment -i input.v -c 5 -o b0.v -c cls.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-3dfuzzysegment │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dfuzzysegment {-i io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs a combined fuzzy c-means clustering and B-field correction to │ │ │ │ │ facilitate a 3D segmentation of 3D image │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be segmenetd. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -c, --cls-file=(output); io │ │ │ │ │ output class probability images. Note, the used file format must support │ │ │ │ │ multible images (best is to use vista). For supported file types see │ │ │ │ │ Plugin_type:_3dimage/io │ │ │ │ │ -o, --b0-file=(output); io │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dgetsize.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dgetsize

mia-3dgetsize

Sysnopis:

mia-3dgetsize {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Write the dimensions of the input 3D image to stdout.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Print out the size of image.v.

mia-3dgetsize -i image.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Write the dimensions of the input 3D image to stdout.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Print out the size of image.v.

mia-3dgetsize -i image.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,15 +3,15 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dgetsize │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dgetsize {-i io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Write the dimensions of the input 3D image to stdout. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dgetslice.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dgetslice

mia-3dgetslice

Sysnopis:

mia-3dgetslice {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to extract 2D slices from a 3D data set and store them in separate files. Output files will be numbered according to their slice index.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output image(s). If number != 1 than this is used as a base name and should be given without extension since this will be based on the '--type' option. If number=1 then this exact file name will be used.. For supported file types see Plugin type: 2dimage/io

-t, --type=png; set

output file type for number != 1 Supported values are:(bmp, datapool, dicom, exr, jpg, png, raw, tif, vista, )

-s, --start=0; uint

start slice number

-n, --number=1; uint

number of slices (all=0)

--ndigits=4; int

minimum number of digits of the file name numbers (if n != 1)

-d, --dir=xy; dict

slice direction (xy=axial, xz=coronal, yz=saggital)

xy:get xy (axial) slice
xz:get xz (coronal) slice
yz:get yz (saggital) slice

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store 5 coronal slices starting at slice 120 coronalXXXX.png from image.v.

mia-3dgetslice -i image.v -o coronal -t png -n 5 -s 120

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to extract 2D slices from a 3D data set and store them in separate files. Output files will be numbered according to their slice index.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image(s). If number != 1 than this is used as a base name and should be given without extension since this will be based on the '--type' option. If number=1 then this exact file name will be used.. For supported file types see Plugin type: 2dimage/io

-t, --type=png; set

output file type for number != 1 Supported values are:(bmp, datapool, dicom, exr, jpg, png, raw, tif, vista, )

-s, --start=0; uint

start slice number

-n, --number=1; uint

number of slices (all=0)

--ndigits=4; int

minimum number of digits of the file name numbers (if n != 1)

-d, --dir=xy; dict

slice direction (xy=axial, xz=coronal, yz=saggital)

xy:get xy (axial) slice
xz:get xz (coronal) slice
yz:get yz (saggital) slice

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store 5 coronal slices starting at slice 120 coronalXXXX.png from image.v.

mia-3dgetslice -i image.v -o coronal -t png -n 5 -s 120

Author(s):

Gert Wollny

│ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimageaddattributes.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dimageaddattributes

mia-3dimageaddattributes

Sysnopis:

mia-3dimageaddattributes {-i io} {-o io} {-a io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program appends all the meta-data attributes found in a 2D input image to a 3D image (if the output format supports such attributes). Attributes that are already present in the 3D image are not overwritten.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output image(s) with the added attributes. For supported file types see Plugin type: 3dimage/io

-a, --attr=(input, required); io

2D image providing the attributes. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Append the attributes found in 2d.v to 3d.v and store the result in attr3d.v

mia-3dimageaddattributes  -i 3d.v -o attr3d.v -a 2d.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program appends all the meta-data attributes found in a 2D input image to a 3D image (if the output format supports such attributes). Attributes that are already present in the 3D image are not overwritten.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image(s) with the added attributes. For supported file types see Plugin type: 3dimage/io

-a, --attr=(required, input); io

2D image providing the attributes. For supported file types see Plugin type: 2dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Append the attributes found in 2d.v to 3d.v and store the result in attr3d.v

mia-3dimageaddattributes  -i 3d.v -o attr3d.v -a 2d.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dimageaddattributes {-i io} {-o io} {-a io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program appends all the meta-data attributes found in a 2D input image to │ │ │ │ │ a 3D image (if the output format supports such attributes). Attributes that are │ │ │ │ │ already present in the 3D image are not overwritten. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image(s) with the added attributes. For supported file types see │ │ │ │ │ Plugin_type:_3dimage/io │ │ │ │ │ - -a, --attr=(input, required); io │ │ │ │ │ + -a, --attr=(required, input); io │ │ │ │ │ 2D image providing the attributes. For supported file types see Plugin │ │ │ │ │ type:_2dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagecombine.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dimagecombine

mia-3dimagecombine

Sysnopis:

mia-3dimagecombine {-1 io} {-2 io} {-c factory} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to combine two images using a given image combiner.

Options:

-1, --image1=(input, required); io

input image 1 to be combined. For supported file types see Plugin type: 3dimage/io

-2, --image2=(input, required); io

input image 2 to be combined. For supported file types see Plugin type: 3dimage/io

-c, --combiner=(required); factory

combiner operation. For supported plug-ins see Plugin type: 3dimage/combiner

-o, --out-file=(output, required); io

output image file. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Take two images l1.v and l2.v and evaluate the per-voxel sum.

mia-3dimagecombine -1 l1.v -2 l2.v -c sum.v -c add

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to combine two images using a given image combiner.

Options:

-1, --image1=(required, input); io

input image 1 to be combined. For supported file types see Plugin type: 3dimage/io

-2, --image2=(required, input); io

input image 2 to be combined. For supported file types see Plugin type: 3dimage/io

-c, --combiner=(required); factory

combiner operation. For supported plug-ins see Plugin type: 3dimage/combiner

-o, --out-file=(required, output); io

output image file. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Take two images l1.v and l2.v and evaluate the per-voxel sum.

mia-3dimagecombine -1 l1.v -2 l2.v -c sum.v -c add

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,24 +3,24 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dimagecombine │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dimagecombine {-1 io} {-2 io} {-c factory} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to combine two images using a given image combiner. │ │ │ │ │ Options: │ │ │ │ │ - -1, --image1=(input, required); io │ │ │ │ │ + -1, --image1=(required, input); io │ │ │ │ │ input image 1 to be combined. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -2, --image2=(input, required); io │ │ │ │ │ + -2, --image2=(required, input); io │ │ │ │ │ input image 2 to be combined. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -c, --combiner=(required); factory │ │ │ │ │ combiner operation. For supported plug-ins see Plugin_type:_3dimage/ │ │ │ │ │ combiner │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image file. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagecreator.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dimagecreator

mia-3dimagecreator

Sysnopis:

mia-3dimagecreator {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program creates a 3D image that contains an object created by one of the object creator plug-ins (creator/3dimage)

Options:

-o, --out-file=(output, required); io

output file for create object. For supported file types see Plugin type: 3dimage/io

-s, --size=[128,128,128]; 3dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-j, --object=sphere; factory

object to be created. For supported plug-ins see Plugin type: 3dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create an image output.v of size <64,128,256> that contains a lattic with frequencys 8, 16, and 4 in x, y and, z-direction respectively.

mia-3dimagecreator -o lattic.v -j lattic:fx=8,fy=16,fz=4 -s "<64,128,256>"

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program creates a 3D image that contains an object created by one of the object creator plug-ins (creator/3dimage)

Options:

-o, --out-file=(required, output); io

output file for create object. For supported file types see Plugin type: 3dimage/io

-s, --size=[128,128,128]; 3dbounds

size of the object

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-j, --object=sphere; factory

object to be created. For supported plug-ins see Plugin type: 3dimage/creator

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create an image output.v of size <64,128,256> that contains a lattic with frequencys 8, 16, and 4 in x, y and, z-direction respectively.

mia-3dimagecreator -o lattic.v -j lattic:fx=8,fy=16,fz=4 -s "<64,128,256>"

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-3dimagecreator │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dimagecreator {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program creates a 3D image that contains an object created by one of the │ │ │ │ │ object creator plug-ins (creator/3dimage) │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file for create object. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -s, --size=[128,128,128]; 3dbounds │ │ │ │ │ size of the object │ │ │ │ │ -r, --repn=ubyte; dict │ │ │ │ │ input pixel type │ │ │ │ │ bit: binary data │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagefilter.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-3dimagefilter

mia-3dimagefilter

Sysnopis:

mia-3dimagefilter {-i io} {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/filter │ │ │ │ │ │ │ │ - ...]

Description:

This program is used to filter and convert gray scale 3D images.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on input.v, then run a 5-class k-means classification and binarize by selecting the 4th class.

mia-3dimagefilter -i image.v -o filtered.v mlv:w=2 kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to filter and convert gray scale 3D images.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on input.v, then run a 5-class k-means classification and binarize by selecting the 4th class.

mia-3dimagefilter -i image.v -o filtered.v mlv:w=2 kmeans:c=5 binarize:min=4,max=4

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,18 +4,18 @@ │ │ │ │ │ mia-3dimagefilter │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dimagefilter {-i io} {-o io} [ options ...] [ Plugin_type:_3dimage/filter │ │ │ │ │ ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to filter and convert gray scale 3D images. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image(s) that have been filtered. For supported file types see │ │ │ │ │ Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagefilterstack.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-3dimagefilterstack

mia-3dimagefilterstack

Sysnopis:

mia-3dimagefilterstack {-i io} {-o io} {-t set} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/filter │ │ │ │ │ │ │ │ - ...]

Description:

This program is used to filter and convert a consecutive numbered series gray of scale images. File names must follow the pattern 'dataXXXX.v' (X being digits), i.e. the numbering comes right before the dot.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output file name base, numbers are added accorfing to the input file pattern, and the file extension is added according to the 'type' option.. For supported file types see Plugin type: 3dimage/io

-t, --type=(required); set

output file type Supported values are:(analyze, datapool, dicom, hdf5, inria, mhd, nifti, vff, vista, vti, vtk, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.hdr and store the output in images filteredXXXX.hdr

mia-3dimagefilterstack -i image0000.hdr -o filtered -t hdr mlv:w=2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to filter and convert a consecutive numbered series gray of scale images. File names must follow the pattern 'dataXXXX.v' (X being digits), i.e. the numbering comes right before the dot.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output file name base, numbers are added accorfing to the input file pattern, and the file extension is added according to the 'type' option.. For supported file types see Plugin type: 3dimage/io

-t, --type=(required); set

output file type Supported values are:(analyze, datapool, dicom, hdf5, inria, mhd, nifti, vff, vista, vti, vtk, )

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a mean-least-varaiance filter on a series of images that follow the numbering pattern imageXXXX.hdr and store the output in images filteredXXXX.hdr

mia-3dimagefilterstack -i image0000.hdr -o filtered -t hdr mlv:w=2

Author(s):

Gert Wollny

│ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimageselect.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dimageselect

mia-3dimageselect

Sysnopis:

mia-3dimageselect {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to select one 3D images from a multi-image file.

Options:

-i, --in-file=(input, required); io

input images. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output image. For supported file types see Plugin type: 3dimage/io

-n, --number=0; uint

image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-3dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to select one 3D images from a multi-image file.

Options:

-i, --in-file=(required, input); io

input images. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image. For supported file types see Plugin type: 3dimage/io

-n, --number=0; uint

image number to be selected

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Store the third image in multiimage.v to image.v (note: counting starts with zero).

mia-3dimageselect -i multiimage.v -o image.v -n 2

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,17 +3,17 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dimageselect │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dimageselect {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to select one 3D images from a multi-image file. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input images. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ -n, --number=0; uint │ │ │ │ │ image number to be selected │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagestatisticsinmask.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dimagestatistics-in-mask

mia-3dimagestatistics-in-mask

Sysnopis:

mia-3dimagestatistics-in-mask {-i io} {-m io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values.

Options:

File-IO

-i, --image=(input, required); io

input image to be analyzed. For supported file types see Plugin type: 3dimage/io

-m, --mask=(input, required); io

mask image to use to restrict the analysis. For supported file types see Plugin type: 3dimage/io

-s, --summary=(output); string

File to write the summary statistics to as plain text.

-H, --histogram=(output); string

File to write the histogram to

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

--struct-name=undefined; stringSTRING

Name of the structure the statistics are evaluated for

-l, --limit=20; uint in [20, inf)

Number of pixels the mask should at least contain.

-b, --bins=8; uint in [4, inf)

number of histogram bins to be used

--hmin=0; float

lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.

--hmax=0; float

hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

evaluate the summary statistics on the input and a histogram with 10 bins and automtically evaluated boundaries. Save summary in summary.txt and the histogram in hist.txt

mia-3dimagestatistics-in-mask --image image.v.gz --mask mask.v.gz --summary summary.txt --histogram hist.txt

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values.

Options:

File-IO

-i, --image=(required, input); io

input image to be analyzed. For supported file types see Plugin type: 3dimage/io

-m, --mask=(required, input); io

mask image to use to restrict the analysis. For supported file types see Plugin type: 3dimage/io

-s, --summary=(output); string

File to write the summary statistics to as plain text.

-H, --histogram=(output); string

File to write the histogram to

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

--struct-name=undefined; stringSTRING

Name of the structure the statistics are evaluated for

-l, --limit=20; uint in [20, inf)

Number of pixels the mask should at least contain.

-b, --bins=8; uint in [4, inf)

number of histogram bins to be used

--hmin=0; float

lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.

--hmax=0; float

hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

evaluate the summary statistics on the input and a histogram with 10 bins and automtically evaluated boundaries. Save summary in summary.txt and the histogram in hist.txt

mia-3dimagestatistics-in-mask --image image.v.gz --mask mask.v.gz --summary summary.txt --histogram hist.txt

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dimagestatistics-in-mask {-i io} {-m io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program evaluates the statistics of an image within a masked region of the │ │ │ │ │ image. Possible outputs are a summary statistics and a histogram of the values. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --image=(input, required); io │ │ │ │ │ + -i, --image=(required, input); io │ │ │ │ │ input image to be analyzed. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -m, --mask=(input, required); io │ │ │ │ │ + -m, --mask=(required, input); io │ │ │ │ │ mask image to use to restrict the analysis. For supported file types see │ │ │ │ │ Plugin_type:_3dimage/io │ │ │ │ │ -s, --summary=(output); string │ │ │ │ │ File to write the summary statistics to as plain text. │ │ │ │ │ -H, --histogram=(output); string │ │ │ │ │ File to write the histogram to │ │ │ │ │ Help & Info │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dimagestats.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dimagestats

mia-3dimagestats

Sysnopis:

mia-3dimagestats {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to evaluate certain image statistics and print them out on the console.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-t, --thresh=10; float

intensity thresh to ignore

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.v and ignore all voxels with an intensity below 5.

mia-3dimagestats -i input.v -t 5

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to evaluate certain image statistics and print them out on the console.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-t, --thresh=10; float

intensity thresh to ignore

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the statistics of image input.v and ignore all voxels with an intensity below 5.

mia-3dimagestats -i input.v -t 5

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-3dimagestats │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dimagestats {-i io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to evaluate certain image statistics and print them out on │ │ │ │ │ the console. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -t, --thresh=10; float │ │ │ │ │ intensity thresh to ignore │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3disosurfacefromstack.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3disosurface-from-stack

mia-3disosurface-from-stack

Sysnopis:

mia-3disosurface-from-stack {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to extract an iso-surface from the input gray scale image given as slices.

Options:

File-IO

-i, --in-image=(input, required); string

input image filename pattern

-o, --out-mesh=(output, required); string

output mesh

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float

iso-value of iso surface to be extracted

Mesh options

-f, --max-faces=-1; int

maximum number of Faces,

-e, --max-edges=-1; int

maximum number of Edges

-c, --max-cost=0.1; float

maximum cost for edge collaps

-r, --ratio=4; float

ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized

-w, --reverse-winding

reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface from an image set with numbers imageXXXX.png that corresponds to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-stack -i image0000.png -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to extract an iso-surface from the input gray scale image given as slices.

Options:

File-IO

-i, --in-image=(required, input); string

input image filename pattern

-o, --out-mesh=(required, output); string

output mesh

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float

iso-value of iso surface to be extracted

Mesh options

-f, --max-faces=-1; int

maximum number of Faces,

-e, --max-edges=-1; int

maximum number of Edges

-c, --max-cost=0.1; float

maximum cost for edge collaps

-r, --ratio=4; float

ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized

-w, --reverse-winding

reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface from an image set with numbers imageXXXX.png that corresponds to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-stack -i image0000.png -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,17 +5,17 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3disosurface-from-stack {-i string} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to extract an iso-surface from the input gray scale image │ │ │ │ │ given as slices. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-image=(input, required); string │ │ │ │ │ + -i, --in-image=(required, input); string │ │ │ │ │ input image filename pattern │ │ │ │ │ - -o, --out-mesh=(output, required); string │ │ │ │ │ + -o, --out-mesh=(required, output); string │ │ │ │ │ output mesh │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3disosurfacefromvolume.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3disosurface-from-volume

mia-3disosurface-from-volume

Sysnopis:

mia-3disosurface-from-volume {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra.

Options:

File-IO

-i, --in-file=(input, required); io

input image. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float

iso-value of iso surface to be extracted

-b, --bordered

put an empty border around the image to ensure a closed surface

Mesh options

-f, --max-faces=-1; int

maximum number of Faces,

-e, --max-edges=-1; int

maximum number of Edges

-c, --max-cost=0.1; float

maximum cost for edge collaps

-r, --ratio=4; float

ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized

-w, --reverse-winding

reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface corresponding to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-volume -i image.v -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra.

Options:

File-IO

-i, --in-file=(required, input); io

input image. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Image options

-s, --iso-value=128; float

iso-value of iso surface to be extracted

-b, --bordered

put an empty border around the image to ensure a closed surface

Mesh options

-f, --max-faces=-1; int

maximum number of Faces,

-e, --max-edges=-1; int

maximum number of Edges

-c, --max-cost=0.1; float

maximum cost for edge collaps

-r, --ratio=4; float

ratio of faces(edges) to target number, at which the optimization changes from edge-length to volume-optimized

-w, --reverse-winding

reverse the winding of the triangles in order to make normals point away from the high intensity area

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Extract the surface corresponding to the value 30 and stop optimizing when the mesh consists of less than 100000 triangles.

mia-3disosurface-from-volume -i image.v -o mesh.vmesh -s 30 -f 100000

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,17 +5,17 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3disosurface-from-volume {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to extract an iso-surface from the input gray scale image │ │ │ │ │ by using marching thetrahedra. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output mesh. For supported file types see Plugin_type:_mesh/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dlandmarksdistances.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dlandmarks-distances

mia-3dlandmarks-distances

Sysnopis:

mia-3dlandmarks-distances {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. The programs prints out only values for landmarks that are available and have location values in both sets

Options:

-i, --in-file-1=(input, required); io

input landmark set 1. For supported file types see Plugin type: 3dlandmarklist/io

-o, --in-file-2=(input, required); io

input landmark set 2. For supported file types see Plugin type: 3dlandmarklist/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance between the landmarks in set input1.lmx and input2.lmx and write the result to stdout

mia-3dlandmarks-distances -1 input1.lmx -2 input2.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Evaluate Euclidian distances between the corresponding landmarks in two landmark sets. The programs prints out only values for landmarks that are available and have location values in both sets

Options:

-i, --in-file-1=(required, input); io

input landmark set 1. For supported file types see Plugin type: 3dlandmarklist/io

-o, --in-file-2=(required, input); io

input landmark set 2. For supported file types see Plugin type: 3dlandmarklist/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance between the landmarks in set input1.lmx and input2.lmx and write the result to stdout

mia-3dlandmarks-distances -1 input1.lmx -2 input2.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dlandmarks-distances {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Evaluate Euclidian distances between the corresponding landmarks in two │ │ │ │ │ landmark sets. The programs prints out only values for landmarks that are │ │ │ │ │ available and have location values in both sets │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file-1=(input, required); io │ │ │ │ │ + -i, --in-file-1=(required, input); io │ │ │ │ │ input landmark set 1. For supported file types see Plugin_type: │ │ │ │ │ 3dlandmarklist/io │ │ │ │ │ - -o, --in-file-2=(input, required); io │ │ │ │ │ + -o, --in-file-2=(required, input); io │ │ │ │ │ input landmark set 2. For supported file types see Plugin_type: │ │ │ │ │ 3dlandmarklist/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dlandmarkstransform.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dlandmarks-transform

mia-3dlandmarks-transform

Sysnopis:

mia-3dlandmarks-transform {-i io} {-o io} {-t io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Transform the locations of the landmarks by means of a given 3D transformation. Note, landmark transformations do the inverse of an image transformation (in a manner of speaking), i.e. given a transformation V(x) in an image transformation the pixel intensity at x is set to the original intensity at V(x), while a landmark at x is moved to V(x).

Options:

-i, --in-file=(input, required); io

input landmark set. For supported file types see Plugin type: 3dlandmarklist/io

-o, --out-file=(output, required); io

output landmark set. For supported file types see Plugin type: 3dlandmarklist/io

-t, --transformation=(input, required); io

transformation file. For supported file types see Plugin type: 3dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the landmarks given in input.lmx by applyning the transfromation stored in trans.v and store the result in output.lmx

mia-3dlandmarks-transform -i input.lmx -t trans.v  -o output.lmx

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Transform the locations of the landmarks by means of a given 3D transformation. Note, landmark transformations do the inverse of an image transformation (in a manner of speaking), i.e. given a transformation V(x) in an image transformation the pixel intensity at x is set to the original intensity at V(x), while a landmark at x is moved to V(x).

Options:

-i, --in-file=(required, input); io

input landmark set. For supported file types see Plugin type: 3dlandmarklist/io

-o, --out-file=(required, output); io

output landmark set. For supported file types see Plugin type: 3dlandmarklist/io

-t, --transformation=(required, input); io

transformation file. For supported file types see Plugin type: 3dtransform/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the landmarks given in input.lmx by applyning the transfromation stored in trans.v and store the result in output.lmx

mia-3dlandmarks-transform -i input.lmx -t trans.v  -o output.lmx

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,21 +7,21 @@ │ │ │ │ │ Description: │ │ │ │ │ Transform the locations of the landmarks by means of a given 3D transformation. │ │ │ │ │ Note, landmark transformations do the inverse of an image transformation (in a │ │ │ │ │ manner of speaking), i.e. given a transformation V(x) in an image │ │ │ │ │ transformation the pixel intensity at x is set to the original intensity at V │ │ │ │ │ (x), while a landmark at x is moved to V(x). │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input landmark set. For supported file types see Plugin_type: │ │ │ │ │ 3dlandmarklist/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output landmark set. For supported file types see Plugin_type: │ │ │ │ │ 3dlandmarklist/io │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation file. For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dlerp.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-3dlerp

mia-3dlerp

Sysnopis:

mia-3dlerp {-1 io} {-2 io} {-o io} {-p vfloat} [ │ │ │ │ options │ │ │ │ - ...]

Description:

merge two images by linear combination.

Options:

-1, --first=(input, required); io

first input image . For supported file types see Plugin type: 3dimage/io

-2, --second=(input, required); io

second input image . For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

linearly interpolated image. For supported file types see Plugin type: 3dimage/io

-p, --positions=(required); vfloat

image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(

run a self test of the program

Example:

Combine image inputA.v and inputB.v by using position coordinates 4, 7, and 9. This means the output pixel values will be evaluated according to │ │ │ │ + ...]

Description:

merge two images by linear combination.

Options:

-1, --first=(required, input); io

first input image . For supported file types see Plugin type: 3dimage/io

-2, --second=(required, input); io

second input image . For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

linearly interpolated image. For supported file types see Plugin type: 3dimage/io

-p, --positions=(required); vfloat

image series positions (first, target, second)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Test

--selftest=(

run a self test of the program

Example:

Combine image inputA.v and inputB.v by using position coordinates 4, 7, and 9. This means the output pixel values will be evaluated according to │ │ │ │ │ │ │ │ (9-7)/(9-4) * A + (7-4)/(9-4) * B │ │ │ │ │ │ │ │ The result image will be written to output.v

mia-3dlerp -1 inputA.v -2 inputB.v -p 4,7,9 -o output.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,19 +3,19 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dlerp │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dlerp {-1 io} {-2 io} {-o io} {-p vfloat} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ merge two images by linear combination. │ │ │ │ │ Options: │ │ │ │ │ - -1, --first=(input, required); io │ │ │ │ │ + -1, --first=(required, input); io │ │ │ │ │ first input image . For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -2, --second=(input, required); io │ │ │ │ │ + -2, --second=(required, input); io │ │ │ │ │ second input image . For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ linearly interpolated image. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -p, --positions=(required); vfloat │ │ │ │ │ image series positions (first, target, second) │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dmany2onenonrigid.html │ │ │ │ @@ -1,9 +1,9 @@ │ │ │ │ mia-3dmany2one-nonrigid

mia-3dmany2one-nonrigid

Sysnopis:

mia-3dmany2one-nonrigid {-i io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ │ │ ...]

Description:

This program runs the non-rigid registration of an image series by registereing all images to a user-selected reference.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); io

input perfusion data set. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output); io

file name for registered files. For supported file types see Plugin type: 3dimage/io

│ │ │ │ +File-IO

-i, --in-file=(required, input); io

input perfusion data set. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output); io

file name for registered files. For supported file types see Plugin type: 3dimage/io

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING

Optimizer used for minimization

-l, --mg-levels=3; uint

multi-resolution levels

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

-r, --ref=-1; int

reference frame (-1 == use image in the middle)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the images given as numbered files imagesXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel using a weighted combination of normalized gradient fields and SSD as cost measure, and penalize the transformation by using divcurl with aweight of 2.0. Store the resultsing images in registeredXXXX.v.

mia-3dmany2one-nonrigid -i images0000.v -o  registered%04d.v -F spline:rate=16 image:cost=[ngf:eval=ds],weight=2.0 image:cost=ssd,weight=0.1 divcurl:weight=2.0

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ mia-3dmany2one-nonrigid {-i io} [ options ...] [ Plugin_type:_3dimage/fullcost │ │ │ │ │ ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs the non-rigid registration of an image series by registereing │ │ │ │ │ all images to a user-selected reference. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input perfusion data set. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -o, --out-file=(output); io │ │ │ │ │ file name for registered files. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ Registration │ │ │ │ │ -O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dmaskseeded.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dmaskseeded

mia-3dmaskseeded

Sysnopis:

mia-3dmaskseeded {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

3D image segmentation based on region growing from a seed point. Neighboring points are added, either when their intensity is equal or higher than that of the seed point, or of the intensity is lower or equal then that of the neighoring point. After region growing is finished, this mask is used to zero out the region in the original image yielding the resulting image.

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io

-s, --seed=[0,0,0]; 3dbounds

seed point

-n, --neighborhood=6n; factory

neighborhood shape. For supported plug-ins see Plugin type: 3dimage/shape

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a region growing on input.v starting at point <10,23,21> and use the 18n neighbourhood.

mia-3dmaskseeded -i image.v -o masked.v -s '<10,23,21>' -n 18n

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

3D image segmentation based on region growing from a seed point. Neighboring points are added, either when their intensity is equal or higher than that of the seed point, or of the intensity is lower or equal then that of the neighoring point. After region growing is finished, this mask is used to zero out the region in the original image yielding the resulting image.

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image(s) that have been filtered. For supported file types see Plugin type: 3dimage/io

-s, --seed=[0,0,0]; 3dbounds

seed point

-n, --neighborhood=6n; factory

neighborhood shape. For supported plug-ins see Plugin type: 3dimage/shape

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a region growing on input.v starting at point <10,23,21> and use the 18n neighbourhood.

mia-3dmaskseeded -i image.v -o masked.v -s '<10,23,21>' -n 18n

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,18 +7,18 @@ │ │ │ │ │ Description: │ │ │ │ │ 3D image segmentation based on region growing from a seed point. Neighboring │ │ │ │ │ points are added, either when their intensity is equal or higher than that of │ │ │ │ │ the seed point, or of the intensity is lower or equal then that of the │ │ │ │ │ neighoring point. After region growing is finished, this mask is used to zero │ │ │ │ │ out the region in the original image yielding the resulting image. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image(s) that have been filtered. For supported file types see │ │ │ │ │ Plugin_type:_3dimage/io │ │ │ │ │ -s, --seed=[0,0,0]; 3dbounds │ │ │ │ │ seed point │ │ │ │ │ -n, --neighborhood=6n; factory │ │ │ │ │ neighborhood shape. For supported plug-ins see Plugin_type:_3dimage/shape │ │ │ │ │ Help & Info │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dmotioncompicanonrigid.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dmotioncompica-nonrigid

mia-3dmotioncompica-nonrigid

Sysnopis:

mia-3dmotioncompica-nonrigid {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements a 3D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012

.

Options:

File-IO

-i, --in-file=(input, required); io

input images of consecutively numbered filed (nameXXXX.ext). For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

output image name (as C format string including a %04d in order to define the file numbering). For supported file types see Plugin type: 3dimage/io

--save-refs=STRING

save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'

--save-regs=STRING

save intermediate registered images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'

--save-coeffs=STRING

save mixing matrix to a text file

--save-features=STRING

save feature images as PNG

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--no-normalize

don't normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING

Optimizer used for minimization

-a, --start-c-rate=32; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4; double

cofficient rate divider for each pass

-d, --start-divcurl=20; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4; double

divcurl weight scaling with each new pass

-w, --imagecost=image:weight=1,cost=ssd,; stringSTRING

image cost

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=3; uint

registration passes

Example:

Register the perfusion series given in images imagesXXXX.v by using 4-class ICA estimation. Skip two images at the beginning, use at most 4 registration threads, a nlopt based optimizer and otherwiese use the default parameters. Store the result in registeredXXXX.v

mia-3dmotioncompica-nonrigid -i images0000.v -o  registered%04d.v  -k 2 -C 4 -t 4 -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements a 3D version of the motion compensation algorithm described in

Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012

.

Options:

File-IO

-i, --in-file=(required, input); io

input images of consecutively numbered filed (nameXXXX.ext). For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

output image name (as C format string including a %04d in order to define the file numbering). For supported file types see Plugin type: 3dimage/io

--save-refs=STRING

save reference images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'

--save-regs=STRING

save intermediate registered images, the given string is used as file name base, the number pattern follows the input images, and the output format is always 'vista'

--save-coeffs=STRING

save mixing matrix to a text file

--save-features=STRING

save feature images as PNG

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

ICA

--fastica=internal; factory

FastICA implementationto be used. For supported plug-ins see Plugin type: fastica/implementation

-C, --components=0; uint

ICA components 0 = automatic estimation

--no-normalize

don't normalized ICs

--no-meanstrip

don't strip the mean from the mixing curves

-k, --skip=0; uint

skip images at the beginning of the series e.g. because as they are of other modalities

-m, --max-ica-iter=400; uint

maximum number of iterations in ICA

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-O, --optimizer=gsl:opt=gd,step=0.1; stringSTRING

Optimizer used for minimization

-a, --start-c-rate=32; double

start coefficinet rate in spines, gets divided by --c-rate-divider with every pass

--c-rate-divider=4; double

cofficient rate divider for each pass

-d, --start-divcurl=20; double

start divcurl weight, gets divided by --divcurl-divider with every pass

--divcurl-divider=4; double

divcurl weight scaling with each new pass

-w, --imagecost=image:weight=1,cost=ssd,; stringSTRING

image cost

-l, --mg-levels=3; uint

multi-resolution levels

-P, --passes=3; uint

registration passes

Example:

Register the perfusion series given in images imagesXXXX.v by using 4-class ICA estimation. Skip two images at the beginning, use at most 4 registration threads, a nlopt based optimizer and otherwiese use the default parameters. Store the result in registeredXXXX.v

mia-3dmotioncompica-nonrigid -i images0000.v -o  registered%04d.v  -k 2 -C 4 -t 4 -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -9,18 +9,18 @@ │ │ │ │ │ described in │ │ │ │ │ Wollny_G,_Kellman_P,_Santos_A,_Ledesma-Carbayo_M-J,_"Automatic_Motion │ │ │ │ │ Compensation_of_Free_Breathing_acquired_Myocardial_Perfusion_Data_by_using │ │ │ │ │ Independent_Component_Analysis"_Medical_Image_Analysis,_2012 │ │ │ │ │ . │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input images of consecutively numbered filed (nameXXXX.ext). For │ │ │ │ │ supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image name (as C format string including a %04d in order to define │ │ │ │ │ the file numbering). For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ --save-refs=STRING │ │ │ │ │ save reference images, the given string is used as file name base, the │ │ │ │ │ number pattern follows the input images, and the output format is always │ │ │ │ │ 'vista' │ │ │ │ │ --save-regs=STRING │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dnonrigidreg.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-3dnonrigidreg

mia-3dnonrigidreg

Sysnopis:

mia-3dnonrigidreg {-i io} {-r io} {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ │ │ - ...]

Description:

This program implements the registration of two gray scale 3D images.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(input, required); io

test image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(input, required); io

reference image. For supported file types see Plugin type: 3dimage/io

-o, --out-image=(output, required); io

registered output image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(output); io

output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline:rate=10; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Example:

Register image test.v to image ref.v by using a spline transformation with a coefficient rate of 5 and write the registered image to reg.v. Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 as transformation smoothness penalty.

mia-3dnonrigidreg -i test.v -r ref.v -o reg.v -l 2 -f spline:rate=3  image:cost=ssd divcurl:weight=10

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements the registration of two gray scale 3D images.

Options:

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

IO

-i, --in-image=(required, input); io

test image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(required, input); io

reference image. For supported file types see Plugin type: 3dimage/io

-o, --out-image=(required, output); io

registered output image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(output); io

output transformation. For supported file types see Plugin type: 3dtransform/io

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Registration

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline:rate=10; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Example:

Register image test.v to image ref.v by using a spline transformation with a coefficient rate of 5 and write the registered image to reg.v. Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 as transformation smoothness penalty.

mia-3dnonrigidreg -i test.v -r ref.v -o reg.v -l 2 -f spline:rate=3  image:cost=ssd divcurl:weight=10

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -25,19 +25,19 @@ │ │ │ │ │ -h, --help=(); bool │ │ │ │ │ print this help │ │ │ │ │ -?, --usage=(); bool │ │ │ │ │ print a short help │ │ │ │ │ --version=(); bool │ │ │ │ │ print the version number and exit │ │ │ │ │ IO │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ test image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -r, --ref-image=(input, required); io │ │ │ │ │ + -r, --ref-image=(required, input); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-image=(output, required); io │ │ │ │ │ + -o, --out-image=(required, output); io │ │ │ │ │ registered output image. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -t, --transformation=(output); io │ │ │ │ │ output transformation. For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ Processing │ │ │ │ │ --threads=-1; int │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dnonrigidregalt.html │ │ │ │ @@ -1,7 +1,7 @@ │ │ │ │ mia-3dnonrigidreg-alt

mia-3dnonrigidreg-alt

Sysnopis:

mia-3dnonrigidreg-alt {-o io} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ │ │ - ...]

Description:

This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-3dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels)

Options:

-o, --out-transform=(output, required); io

output transformation. For supported file types see Plugin type: 3dtransform/io

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline:rate=10; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v by using a spline transformation with a coefficient rate of 5 and write the registered image to reg.v. Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 as transformation smoothness penalty. The resulting transformation is saved in reg.vf.

mia-3dnonrigidreg-alt -o reg.vf -l 2 -f spline:rate=3 image:cost=ssd,src=test.v,ref=ref.v divcurl:weight=10

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-3dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels)

Options:

-o, --out-transform=(required, output); io

output transformation. For supported file types see Plugin type: 3dtransform/io

-l, --levels=3; uint

multi-resolution levels

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=spline:rate=10; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v by using a spline transformation with a coefficient rate of 5 and write the registered image to reg.v. Use two multiresolution levels, ssd as image cost function and divcurl weighted by 10.0 as transformation smoothness penalty. The resulting transformation is saved in reg.vf.

mia-3dnonrigidreg-alt -o reg.vf -l 2 -f spline:rate=3 image:cost=ssd,src=test.v,ref=ref.v divcurl:weight=10

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ │ a given transformation model. Other than mia-3dnonrigidreg it doesn't support │ │ │ │ │ specific command line parameters to provide the images. Instead the images are │ │ │ │ │ specified dirctly when defining the cost function. Hence, image registrations │ │ │ │ │ can be executed that optimize the aligmnet of more than one image pair at the │ │ │ │ │ same time. Note, however, that all input images must be of the same dimension │ │ │ │ │ (in pixels) │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-transform=(output, required); io │ │ │ │ │ + -o, --out-transform=(required, output); io │ │ │ │ │ output transformation. For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ -l, --levels=3; uint │ │ │ │ │ multi-resolution levels │ │ │ │ │ -O, --optimizer=gsl:opt=gd,step=0.1; factory │ │ │ │ │ Optimizer used for minimization. For supported plug-ins see Plugin_type: │ │ │ │ │ minimizer/singlecost │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dprealignnonrigid.html │ │ │ │ @@ -1,6 +1,6 @@ │ │ │ │ mia-3dprealign-nonrigid

mia-3dprealign-nonrigid

Sysnopis:

mia-3dprealign-nonrigid {-i io} {-o io} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program runs the non-rigid registration of an image series by first registering an already aligned subset of the images to one reference, and then by registering the remaining images by using synthetic references. This is a 3D version of

G. Wollny, M-J Ledesma-Cabryo, P.Kellman, and A.Santos, "Exploiting Quasiperiodicity in Motion Correction of Free-Breathing," IEEE Transactions on Medical Imaging, 29(8), 2010.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); io

input images following the naming pattern nameXXXX.ext. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

file name base for registered files given as C-format string. For supported file types see Plugin type: 3dimage/io

--save-references

Save synthetic references to files refXXXX.v

│ │ │ │ +File-IO

-i, --in-file=(required, input); io

input images following the naming pattern nameXXXX.ext. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

file name base for registered files given as C-format string. For supported file types see Plugin type: 3dimage/io

--save-references

Save synthetic references to files refXXXX.v

│ │ │ │ Preconditions & Preprocessing

-k, --skip=0; uint

Skip images at the begin of the series

--preskip=20; uint

Skip images at the beginning+skip of the series when searching for high contrats image

--postskip=2; uint

Skip images at the end of the series when searching for high contrats image

--max-candidates=20; uint

maximum number of candidates for global reference image

-S, --cost-series=image:cost=[ngf:eval=ds]; factory

Const function to use for the analysis of the series. For supported plug-ins see Plugin type: 3dimage/fullcost

--ref-idx=STRING

save reference index number to this file

-R, --global-reference=-1; int

save reference index number to this file

-D, --max-subset-delta=0; uint

Maximum delta between two elements of the prealigned subset

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.01; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-l, --mr-levels=3; uint

multi-resolution levels

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

-1, --cost-subset=image:cost=[ngf:eval=ds]; factory

Cost function for registration during the subset registration. For supported plug-ins see Plugin type: 3dimage/fullcost

-2, --cost-final=image:cost=ssd; factory

Cost function for registration during the final registration. For supported plug-ins see Plugin type: 3dimage/fullcost

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register the image series given by images imageXXXX.v by optimizing a spline based transformation with a coefficient rate of 16 pixel, skipping two images at the beginning and using normalized gradient fields as initial cost measure and SSD as final measure. Penalize the transformation by using divcurl with aweight of 2.0. As optimizer an nlopt based newton method is used.

mia-3dprealign-nonrigid mia-3dprealign-nonrigid  -i imageXXXX.v -o registered -t vista -k 2-F spline:rate=16,penalty=[divcurl:weight=2] -1 image:cost=[ngf:eval=ds] -2 image:cost=ssd -O nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -10,18 +10,18 @@ │ │ │ │ │ by registering the remaining images by using synthetic references. This is a 3D │ │ │ │ │ version of │ │ │ │ │ G._Wollny,_M-J_Ledesma-Cabryo,_P.Kellman,_and_A.Santos,_"Exploiting │ │ │ │ │ Quasiperiodicity_in_Motion_Correction_of_Free-Breathing,"_IEEE_Transactions_on │ │ │ │ │ Medical_Imaging,_29(8),_2010. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input images following the naming pattern nameXXXX.ext. For supported │ │ │ │ │ file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ file name base for registered files given as C-format string. For │ │ │ │ │ supported file types see Plugin_type:_3dimage/io │ │ │ │ │ --save-references │ │ │ │ │ Save synthetic references to files refXXXX.v │ │ │ │ │ Preconditions & Preprocessing │ │ │ │ │ -k, --skip=0; uint │ │ │ │ │ Skip images at the begin of the series │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dproposeboundingbox.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dpropose-boundingbox

mia-3dpropose-boundingbox

Sysnopis:

mia-3dpropose-boundingbox {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program evaluates a box that contains all the pixels of a given mask image. If the input image is not a binary image, a pre-filter must be applied that converts the imput image into a mask.

Options:

File-IO

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-f, --filter=

Filter to be applied to the image before the bounding box is evaluated. Must return a bit-valued image.. For supported plug-ins see Plugin type: 3dimage/filter

-p, --padding=0; uint in [0, inf)

Padding of boundaries.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate a bounding box with boundary padding of 5 of a mask resulting from a binarization with a minimum value 10.10 and a boundary padding of 5 from image image.v .

mia-3dpropose-boundingbox -i image.v -f binarize:min=10 -p 5

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program evaluates a box that contains all the pixels of a given mask image. If the input image is not a binary image, a pre-filter must be applied that converts the imput image into a mask.

Options:

File-IO

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-f, --filter=

Filter to be applied to the image before the bounding box is evaluated. Must return a bit-valued image.. For supported plug-ins see Plugin type: 3dimage/filter

-p, --padding=0; uint in [0, inf)

Padding of boundaries.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate a bounding box with boundary padding of 5 of a mask resulting from a binarization with a minimum value 10.10 and a boundary padding of 5 from image image.v .

mia-3dpropose-boundingbox -i image.v -f binarize:min=10 -p 5

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ mia-3dpropose-boundingbox {-i io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program evaluates a box that contains all the pixels of a given mask │ │ │ │ │ image. If the input image is not a binary image, a pre-filter must be applied │ │ │ │ │ that converts the imput image into a mask. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3drigidreg.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3drigidreg

mia-3drigidreg

Sysnopis:

mia-3drigidreg {-i io} {-r io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements the registration of two gray scale 3D images. The transformation is not penalized, therefore, one should only use translation, rigid, or affine transformations as target and run mia-3dnonrigidreg of nonrigid registration is to be achieved.

Options:

File I/O

-i, --in-image=(input, required); io

test image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(input, required); io

reference image. For supported file types see Plugin type: 3dimage/io

-o, --out-image=(output, required); io

registered output image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(output); io

transformation output file name. For supported file types see Plugin type: 3dtransform/io

-c, --cost=ssd; factory

cost function. For supported plug-ins see Plugin type: 3dimage/cost

-l, --levels=3; uint

multigrid levels

-O, --optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=rigid; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v affine and write the registered image to reg.v. Use two multiresolution levels and ssd as cost function.

mia-3drigidreg -i test.v -r ref.v -o reg.v -l 2 -f affine -c ssd

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements the registration of two gray scale 3D images. The transformation is not penalized, therefore, one should only use translation, rigid, or affine transformations as target and run mia-3dnonrigidreg of nonrigid registration is to be achieved.

Options:

File I/O

-i, --in-image=(required, input); io

test image. For supported file types see Plugin type: 3dimage/io

-r, --ref-image=(required, input); io

reference image. For supported file types see Plugin type: 3dimage/io

-o, --out-image=(required, output); io

registered output image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(output); io

transformation output file name. For supported file types see Plugin type: 3dtransform/io

-c, --cost=ssd; factory

cost function. For supported plug-ins see Plugin type: 3dimage/cost

-l, --levels=3; uint

multigrid levels

-O, --optimizer=gsl:opt=simplex,step=1.0; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-f, --transForm=rigid; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Register image test.v to image ref.v affine and write the registered image to reg.v. Use two multiresolution levels and ssd as cost function.

mia-3drigidreg -i test.v -r ref.v -o reg.v -l 2 -f affine -c ssd

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,19 +7,19 @@ │ │ │ │ │ Description: │ │ │ │ │ This program implements the registration of two gray scale 3D images. The │ │ │ │ │ transformation is not penalized, therefore, one should only use translation, │ │ │ │ │ rigid, or affine transformations as target and run mia-3dnonrigidreg of │ │ │ │ │ nonrigid registration is to be achieved. │ │ │ │ │ Options: │ │ │ │ │ File I/O │ │ │ │ │ - -i, --in-image=(input, required); io │ │ │ │ │ + -i, --in-image=(required, input); io │ │ │ │ │ test image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -r, --ref-image=(input, required); io │ │ │ │ │ + -r, --ref-image=(required, input); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-image=(output, required); io │ │ │ │ │ + -o, --out-image=(required, output); io │ │ │ │ │ registered output image. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ -t, --transformation=(output); io │ │ │ │ │ transformation output file name. For supported file types see Plugin │ │ │ │ │ type:_3dtransform/io │ │ │ │ │ -c, --cost=ssd; factory │ │ │ │ │ cost function. For supported plug-ins see Plugin_type:_3dimage/cost │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dsegmentahmed.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dsegment-ahmed

mia-3dsegment-ahmed

Sysnopis:

mia-3dsegment-ahmed {-i io} {-c io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

File-IO

-i, --in-file=(input, required); io

image to be segmented. For supported file types see Plugin type: 3dimage/io

-c, --class-file=(output, required); io

class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 3dimage/io

-b, --out-file=(output); io

Bias corrected image will be of the same type like the input image. If this parameter is not given, then the bias correction will not be applied.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int

number of classes

-C, --class-centres=

initial class centers, this parameter overrides 'no-of-clases'.

-s, --spread=64; float

spread parameter describing the strength of mattar distinction

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-3dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program implements a variation of the paper:

Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002,

changes are: p=2, and exp

Options:

File-IO

-i, --in-file=(required, input); io

image to be segmented. For supported file types see Plugin type: 3dimage/io

-c, --class-file=(required, output); io

class probability images, the image type must support multiple images and floating point values. For supported file types see Plugin type: 3dimage/io

-b, --out-file=(output); io

Bias corrected image will be of the same type like the input image. If this parameter is not given, then the bias correction will not be applied.. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-n, --no-of-classes=3; int

number of classes

-C, --class-centres=

initial class centers, this parameter overrides 'no-of-clases'.

-s, --spread=64; float

spread parameter describing the strength of mattar distinction

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a 5-class segmentation over input image input.v and store the class probability images in cls.v.

mia-3dsegment-ahmed -i input.v -a 5 -o cls.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -8,18 +8,18 @@ │ │ │ │ │ This program implements a variation of the paper: │ │ │ │ │ Mohamed_N._Ahmed_et._al,_"A_Modified_Fuzzy_C-Means_Algorithm_for_Bias_Field │ │ │ │ │ estimation_and_Segmentation_of_MRI_Data",_IEEE_Trans._on_Medical_Imaging,_Vol. │ │ │ │ │ 21,_No._3,_March_2002, │ │ │ │ │ changes are: p=2, and exp │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ image to be segmented. For supported file types see Plugin_type:_3dimage/ │ │ │ │ │ io │ │ │ │ │ - -c, --class-file=(output, required); io │ │ │ │ │ + -c, --class-file=(required, output); io │ │ │ │ │ class probability images, the image type must support multiple images and │ │ │ │ │ floating point values. For supported file types see Plugin_type:_3dimage/ │ │ │ │ │ io │ │ │ │ │ -b, --out-file=(output); io │ │ │ │ │ Bias corrected image will be of the same type like the input image. If │ │ │ │ │ this parameter is not given, then the bias correction will not be │ │ │ │ │ applied.. For supported file types see Plugin_type:_3dimage/io │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dsegmentlocalcmeans.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dsegment-local-cmeans

mia-3dsegment-local-cmeans

Sysnopis:

mia-3dsegment-local-cmeans {-i io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs the segmentation of a 3D image by applying a localized c-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global c-means clustering, and then separates the image into overlapping regions where more c-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. This program implements algorithm described in:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(input, required); io

image to be segmented. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output); io

class label image based on merging local labels. For supported file types see Plugin type: 3dimage/io

-G, --out-global-crisp=(output); io

class label image based on global segmentation. For supported file types see Plugin type: 3dimage/io

-C, --class-prob=(output); io

class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf)

Spacing of the grid used to modulate the intensity inhomogeneities

-c, --cmeans=kmeans:nc=3; factory

c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans

-e, --c-means-epsilon=0.0001; float in (0, inf)

c-means breaking condition for update tolerance

-t, --relative-cluster-threshold=0.02; double in [0, 1)

threshhold to ignore classes when initializing the local cmeans from the global one.

-B, --ignore-background

Don't take background probablities into account when desiding whether classes are to be ignored

-L, --label-threshold=0; float in [0, 1]

for values <= 0.5: create segmentation based on highest class probability, labels start at 0. For values >0.5: create labels only for voxels with a class probability higher than the given value, labels start at 1 and voxels without an according class probability are set to 0; this output is suitable for the seeded watershed filter.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-3dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs the segmentation of a 3D image by applying a localized c-means approach that helps to overcome intensity inhomogeneities in the image. The approach evaluates a global c-means clustering, and then separates the image into overlapping regions where more c-means iterations are run only including the locally present classes, i.e. the classes that relatively contain more pixels than a given threshold. This program implements algorithm described in:

Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.

Options:

File-IO

-i, --in-file=(required, input); io

image to be segmented. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output); io

class label image based on merging local labels. For supported file types see Plugin type: 3dimage/io

-G, --out-global-crisp=(output); io

class label image based on global segmentation. For supported file types see Plugin type: 3dimage/io

-C, --class-prob=(output); io

class probability image file, filetype must support floating point multi-frame images. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Parameters

-g, --grid-spacing=15; int in [3, inf)

Spacing of the grid used to modulate the intensity inhomogeneities

-c, --cmeans=kmeans:nc=3; factory

c-means initializer. For supported plug-ins see Plugin type: 1d/cmeans

-e, --c-means-epsilon=0.0001; float in (0, inf)

c-means breaking condition for update tolerance

-t, --relative-cluster-threshold=0.02; double in [0, 1)

threshhold to ignore classes when initializing the local cmeans from the global one.

-B, --ignore-background

Don't take background probablities into account when desiding whether classes are to be ignored

-L, --label-threshold=0; float in [0, 1]

for values <= 0.5: create segmentation based on highest class probability, labels start at 0. For values >0.5: create labels only for voxels with a class probability higher than the given value, labels start at 1 and voxels without an according class probability are set to 0; this output is suitable for the seeded watershed filter.

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run the segmentation on image test.png using three classes, local regions of 40 pixels (grid width 20 pixels), and a class ignore threshold of 0.01.

mia-3dsegment-local-cmeans -i test.png -o label.png -n 3 -g 20 -t 0.01

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -12,15 +12,15 @@ │ │ │ │ │ including the locally present classes, i.e. the classes that relatively contain │ │ │ │ │ more pixels than a given threshold. This program implements algorithm described │ │ │ │ │ in: │ │ │ │ │ Dunmore_CJ,_Wollny_G,_Skinner_MM._(2018)_MIA-Clustering:_a_novel_method_for │ │ │ │ │ segmentation_of_paleontological_material._PeerJ_6:e4374. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ image to be segmented. For supported file types see Plugin_type:_3dimage/ │ │ │ │ │ io │ │ │ │ │ -o, --out-file=(output); io │ │ │ │ │ class label image based on merging local labels. For supported file types │ │ │ │ │ see Plugin_type:_3dimage/io │ │ │ │ │ -G, --out-global-crisp=(output); io │ │ │ │ │ class label image based on global segmentation. For supported file types │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dserialnonrigid.html │ │ │ │ @@ -1,9 +1,9 @@ │ │ │ │ mia-3dserial-nonrigid

mia-3dserial-nonrigid

Sysnopis:

mia-3dserial-nonrigid {-i string} [ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: 3dimage/fullcost │ │ │ │ │ │ │ │ ...]

Description:

This program runs the image registration of a consecutively numbered image series. The registration is run in a serial manner, this is, only images in temporal succession (i.e. consecutive numbers) are registered, and the obtained transformations are applied accumulated to reach full registration.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input perfusion data set

-o, --out-file=(output); string

file name for registered fiels

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input perfusion data set

-o, --out-file=(output); string

file name for registered fiels

│ │ │ │ Registration

-O, --optimizer=gsl:opt=gd,step=0.1; factory

Optimizer used for minimization. For supported plug-ins see Plugin type: minimizer/singlecost

-l, --mg-levels=3; uint

multi-resolution levels

-f, --transForm=spline; factory

transformation type. For supported plug-ins see Plugin type: 3dimage/transform

-r, --ref=-1; int

reference frame (-1 == use image in the middle)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run a serial registration of images inputXXXX.v (X digit) to reference image 20 and store the result in regXXXX.v. Optimize the sum of squared differences and spline transformations with coefficient rate 10.

mia-3dserial-nonrigid -i input0000.v -o 'reg%04d.v' -f spline:rate=10 -r 20 ssd

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ Description: │ │ │ │ │ This program runs the image registration of a consecutively numbered image │ │ │ │ │ series. The registration is run in a serial manner, this is, only images in │ │ │ │ │ temporal succession (i.e. consecutive numbers) are registered, and the obtained │ │ │ │ │ transformations are applied accumulated to reach full registration. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input perfusion data set │ │ │ │ │ -o, --out-file=(output); string │ │ │ │ │ file name for registered fiels │ │ │ │ │ Registration │ │ │ │ │ -O, --optimizer=gsl:opt=gd,step=0.1; factory │ │ │ │ │ Optimizer used for minimization. For supported plug-ins see Plugin_type: │ │ │ │ │ minimizer/singlecost │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dseriestrackintensity.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-3dseries-track-intensity

mia-3dseries-track-intensity

Sysnopis:

mia-3dseries-track-intensity {-i io} {-o string} [ │ │ │ │ options │ │ │ │ ...]

Description:

This program tracks the intensity of a pixel at the given coordinates.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); io

input perfusion data set. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); string

file name for output intensity slopes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the intensity-time curves at points <12,13,14> and <222,113,214>

mia-3dseries-track-intensity -i images0000.v -o curves.txt '<12,13,14>' '<222,113,214>'

Author(s):

Gert Wollny

│ │ │ │ +File-IO
-i, --in-file=(required, input); io

input perfusion data set. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); string

file name for output intensity slopes

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the intensity-time curves at points <12,13,14> and <222,113,214>

mia-3dseries-track-intensity -i images0000.v -o curves.txt '<12,13,14>' '<222,113,214>'

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,18 +4,18 @@ │ │ │ │ │ mia-3dseries-track-intensity │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dseries-track-intensity {-i io} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program tracks the intensity of a pixel at the given coordinates. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input perfusion data set. For supported file types see Plugin_type: │ │ │ │ │ 3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ file name for output intensity slopes │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dtrackpixelmovement.html │ │ │ │ @@ -1,8 +1,8 @@ │ │ │ │ mia-3dtrackpixelmovement

mia-3dtrackpixelmovement

Sysnopis:

mia-3dtrackpixelmovement {-i string} {-o string} {-t io} [ │ │ │ │ options │ │ │ │ ...]

Description:

Track the position of a pixel by means of a transformation obtained by using image registration. The pixel data is given in CSV format │ │ │ │ id;time;x;y;z;reserved │ │ │ │ │ │ │ │ The fields 'time', 'x', 'y', and 'z' are updated, and the fields 'id' and 'reserved' are preserved, empty lines are ignored.

Options:

│ │ │ │ -File-IO

-i, --in-file=(input, required); string

input point set

-o, --out-file=(output, required); string

output point set

-t, --transformation=(input, required); io

transformation describing the monitored change. For supported file types see Plugin type: 3dtransform/io

│ │ │ │ +File-IO

-i, --in-file=(required, input); string

input point set

-o, --out-file=(required, output); string

output point set

-t, --transformation=(required, input); io

transformation describing the monitored change. For supported file types see Plugin type: 3dtransform/io

│ │ │ │ Parameters

-T, --time-step=1; float

time step to use for the position update

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

This program evaluated the changed position of pixels given in input.csv, by using a time step of 2.0 time units and the transformation change.v3df, and writes the updated positions to updated.csv.

mia-3dtrackpixelmovement -i input.csv -o output.cvs --time-step 2.0 --transformation change.v3df

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -7,19 +7,19 @@ │ │ │ │ │ Description: │ │ │ │ │ Track the position of a pixel by means of a transformation obtained by using │ │ │ │ │ image registration. The pixel data is given in CSV format │ │ │ │ │ id;time;x;y;z;reserved The fields 'time', 'x', 'y', and 'z' are updated, and │ │ │ │ │ the fields 'id' and 'reserved' are preserved, empty lines are ignored. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input point set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output point set │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation describing the monitored change. For supported file types │ │ │ │ │ see Plugin_type:_3dtransform/io │ │ │ │ │ Parameters │ │ │ │ │ -T, --time-step=1; float │ │ │ │ │ time step to use for the position update │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dtransform.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dtransform

mia-3dtransform

Sysnopis:

mia-3dtransform {-i io} {-o io} {-t io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Transform a 3D image by applying a given 3D transformation.

Options:

-i, --in-file=(input, required); io

input image. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(output, required); io

transformed image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(input, required); io

transformation file. For supported file types see Plugin type: 3dtransform/io

-p, --interpolator=STRING

override the interpolator provided by the transformation

-b, --boundary=mirror; stringSTRING

override the boundary conditions provided by the transformation. This is only used if the interpolator is also overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transfromation stored in trans.v by using nearest neighbour interpolation ans store the result in output.v

mia-3dtransform -i input.v -t trans.v  -o output.v  -p bspline:d=0

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Transform a 3D image by applying a given 3D transformation.

Options:

-i, --in-file=(required, input); io

input image. For supported file types see Plugin type: 3dimage/io

-o, --out-file=(required, output); io

transformed image. For supported file types see Plugin type: 3dimage/io

-t, --transformation=(required, input); io

transformation file. For supported file types see Plugin type: 3dtransform/io

-p, --interpolator=STRING

override the interpolator provided by the transformation

-b, --boundary=mirror; stringSTRING

override the boundary conditions provided by the transformation. This is only used if the interpolator is also overridden.

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform an image input.v by the transfromation stored in trans.v by using nearest neighbour interpolation ans store the result in output.v

mia-3dtransform -i input.v -t trans.v  -o output.v  -p bspline:d=0

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,19 +3,19 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dtransform │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dtransform {-i io} {-o io} {-t io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Transform a 3D image by applying a given 3D transformation. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ transformed image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ - -t, --transformation=(input, required); io │ │ │ │ │ + -t, --transformation=(required, input); io │ │ │ │ │ transformation file. For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ -p, --interpolator=STRING │ │ │ │ │ override the interpolator provided by the transformation │ │ │ │ │ -b, --boundary=mirror; stringSTRING │ │ │ │ │ override the boundary conditions provided by the transformation. This is │ │ │ │ │ only used if the interpolator is also overridden. │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dtransform2vf.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dtransform2vf

mia-3dtransform2vf

Sysnopis:

mia-3dtransform2vf {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Create a 3D vector field from a given transformation. The output vector field will have the dimesions as given in the transformation description.

Options:

-i, --in-file=(input, required); io

input transformation . For supported file types see Plugin type: 3dtransform/io

-o, --out-file=(output, required); io

output vector field . For supported file types see Plugin type: 3dvf/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input transformation trans.v3df to a vector field field.vtk.

mia-3dtransform2vf -i trans.v3df   -o field.vtk

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Create a 3D vector field from a given transformation. The output vector field will have the dimesions as given in the transformation description.

Options:

-i, --in-file=(required, input); io

input transformation . For supported file types see Plugin type: 3dtransform/io

-o, --out-file=(required, output); io

output vector field . For supported file types see Plugin type: 3dvf/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input transformation trans.v3df to a vector field field.vtk.

mia-3dtransform2vf -i trans.v3df   -o field.vtk

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,18 +4,18 @@ │ │ │ │ │ mia-3dtransform2vf │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dtransform2vf {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Create a 3D vector field from a given transformation. The output vector field │ │ │ │ │ will have the dimesions as given in the transformation description. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input transformation . For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output vector field . For supported file types see Plugin_type:_3dvf/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dvectorfieldcreate.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dvectorfieldcreate

mia-3dvectorfieldcreate

Sysnopis:

mia-3dvectorfieldcreate {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to create a file containing a 3D vector field.

Options:

-o, --out-file=(output, required); io

output file for the vector field. For supported file types see Plugin type: 3dvf/io

-s, --size=[64,64,64]; 3dbounds

size of the vector field

-y, --ftype=0; short

vector field type

-f, --fun=1; float

just some parameter to vary the field ;-)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a field of type 2 with fun 3.0 and size 128x128x128.

mia-3dvectorfieldcreate -o field.v -s '<128,128,128>' -t 2 -f 3.0

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to create a file containing a 3D vector field.

Options:

-o, --out-file=(required, output); io

output file for the vector field. For supported file types see Plugin type: 3dvf/io

-s, --size=[64,64,64]; 3dbounds

size of the vector field

-y, --ftype=0; short

vector field type

-f, --fun=1; float

just some parameter to vary the field ;-)

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Create a field of type 2 with fun 3.0 and size 128x128x128.

mia-3dvectorfieldcreate -o field.v -s '<128,128,128>' -t 2 -f 3.0

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,15 +3,15 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-3dvectorfieldcreate │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dvectorfieldcreate {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to create a file containing a 3D vector field. │ │ │ │ │ Options: │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file for the vector field. For supported file types see Plugin │ │ │ │ │ type:_3dvf/io │ │ │ │ │ -s, --size=[64,64,64]; 3dbounds │ │ │ │ │ size of the vector field │ │ │ │ │ -y, --ftype=0; short │ │ │ │ │ vector field type │ │ │ │ │ -f, --fun=1; float │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dvf2transform.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dvf2transform

mia-3dvf2transform

Sysnopis:

mia-3dvf2transform {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Creates a 3D transformation from a vector field. The input vector field is simply encapsulated into the transformation file format. The boundary conditions and the image interpolator kernel can be set at the command line.

Options:

-i, --in-file=(input, required); io

input transformation . For supported file types see Plugin type: 3dvf/io

-o, --out-file=(output, required); io

output vector field . For supported file types see Plugin type: 3dtransform/io

-k, --imgkernel=bspline:d=3; factory

image interpolator kernel which is used when the transformation is applied to an image. For supported plug-ins see Plugin type: 1d/splinekernel

-b, --imgboundary=mirror; factory

Boundary condition applied when the transformation is used to transform an image. For supported plug-ins see Plugin type: 1d/splinebc

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input vector field field.vtk to the transformation trans.v3df and specify zero boundary conditions and b-splines of degree 2 for image interpolation.

mia-3dvf2transform -i field.vtk -o trans.v3df --imgkernel bspline:d=2 --imgboundary zero

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Creates a 3D transformation from a vector field. The input vector field is simply encapsulated into the transformation file format. The boundary conditions and the image interpolator kernel can be set at the command line.

Options:

-i, --in-file=(required, input); io

input transformation . For supported file types see Plugin type: 3dvf/io

-o, --out-file=(required, output); io

output vector field . For supported file types see Plugin type: 3dtransform/io

-k, --imgkernel=bspline:d=3; factory

image interpolator kernel which is used when the transformation is applied to an image. For supported plug-ins see Plugin type: 1d/splinekernel

-b, --imgboundary=mirror; factory

Boundary condition applied when the transformation is used to transform an image. For supported plug-ins see Plugin type: 1d/splinebc

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Transform the input vector field field.vtk to the transformation trans.v3df and specify zero boundary conditions and b-splines of degree 2 for image interpolation.

mia-3dvf2transform -i field.vtk -o trans.v3df --imgkernel bspline:d=2 --imgboundary zero

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,17 +5,17 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dvf2transform {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Creates a 3D transformation from a vector field. The input vector field is │ │ │ │ │ simply encapsulated into the transformation file format. The boundary │ │ │ │ │ conditions and the image interpolator kernel can be set at the command line. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input transformation . For supported file types see Plugin_type:_3dvf/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output vector field . For supported file types see Plugin_type: │ │ │ │ │ 3dtransform/io │ │ │ │ │ -k, --imgkernel=bspline:d=3; factory │ │ │ │ │ image interpolator kernel which is used when the transformation is │ │ │ │ │ applied to an image. For supported plug-ins see Plugin_type:_1d/ │ │ │ │ │ splinekernel │ │ │ │ │ -b, --imgboundary=mirror; factory │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmia3dvfcompare.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-3dvfcompare

mia-3dvfcompare

Sysnopis:

mia-3dvfcompare {-1 io} {-2 io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

Compare two vector fields and print the out the difference norm per pixel to cout it it is larger than delta.

Options:

-1, --in-file-1=(input, required); io

input vector field 1. For supported file types see Plugin type: 3dvf/io

-2, --in-file-2=(input, required); io

input vector field 2. For supported file types see Plugin type: 3dvf/io

-d, --delta=0; float

Maximum difference between vector to be ignored

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Compare vector fields vf1.v and vf2.v and print out all differences above 0.01.

mia-3dvfcompare -1 vf1.v -2 vf2.v -d 0.01

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

Compare two vector fields and print the out the difference norm per pixel to cout it it is larger than delta.

Options:

-1, --in-file-1=(required, input); io

input vector field 1. For supported file types see Plugin type: 3dvf/io

-2, --in-file-2=(required, input); io

input vector field 2. For supported file types see Plugin type: 3dvf/io

-d, --delta=0; float

Maximum difference between vector to be ignored

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Compare vector fields vf1.v and vf2.v and print out all differences above 0.01.

mia-3dvfcompare -1 vf1.v -2 vf2.v -d 0.01

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-3dvfcompare │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-3dvfcompare {-1 io} {-2 io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ Compare two vector fields and print the out the difference norm per pixel to │ │ │ │ │ cout it it is larger than delta. │ │ │ │ │ Options: │ │ │ │ │ - -1, --in-file-1=(input, required); io │ │ │ │ │ + -1, --in-file-1=(required, input); io │ │ │ │ │ input vector field 1. For supported file types see Plugin_type:_3dvf/io │ │ │ │ │ - -2, --in-file-2=(input, required); io │ │ │ │ │ + -2, --in-file-2=(required, input); io │ │ │ │ │ input vector field 2. For supported file types see Plugin_type:_3dvf/io │ │ │ │ │ -d, --delta=0; float │ │ │ │ │ Maximum difference between vector to be ignored │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiacmeans.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-cmeans

mia-cmeans

Sysnopis:

mia-cmeans {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This Program reads a histogram from stdin and evaluates a cmeans classification of the intensity values into the given number of classes.

Options:

-i, --in-file=(input, required); string

input file name containing the histogram

-o, --out-file=(output, required); string

output file name to store probabilities

-n, --nclasses=3; int

number of classes to partition into

-m, --max-iter=100; int

maximum number of iterations

-e, --even-start

start with centers evenly distributed over the histogram

-c, --class-centers=

initial class centers

-a, --auto

atomatic adaption of variance (experimental)

-t, --cut-histo

cut empty histogram at the end

-k, --variance=1; double

variance parameter

--self-test

run self test

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

This Program reads a histogram from stdin and evaluates a cmeans classification of the intensity values into the given number of classes.

Options:

-i, --in-file=(required, input); string

input file name containing the histogram

-o, --out-file=(required, output); string

output file name to store probabilities

-n, --nclasses=3; int

number of classes to partition into

-m, --max-iter=100; int

maximum number of iterations

-e, --even-start

start with centers evenly distributed over the histogram

-c, --class-centers=

initial class centers

-a, --auto

atomatic adaption of variance (experimental)

-t, --cut-histo

cut empty histogram at the end

-k, --variance=1; double

variance parameter

--self-test

run self test

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-cmeans 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-cmeans │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-cmeans {-i string} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This Program reads a histogram from stdin and evaluates a cmeans classification │ │ │ │ │ of the intensity values into the given number of classes. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input file name containing the histogram │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output file name to store probabilities │ │ │ │ │ -n, --nclasses=3; int │ │ │ │ │ number of classes to partition into │ │ │ │ │ -m, --max-iter=100; int │ │ │ │ │ maximum number of iterations │ │ │ │ │ -e, --even-start │ │ │ │ │ start with centers evenly distributed over the histogram │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiafilenumberpattern.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-filenumberpattern

mia-filenumberpattern

Sysnopis:

mia-filenumberpattern {-i string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to extract a extract the number pattern for file012312.ext type file names.

Options:

-i, --in-file=(input, required); string

input image example name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

This program is used to extract a extract the number pattern for file012312.ext type file names.

Options:

-i, --in-file=(required, input); string

input image example name

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-filenumberpattern 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,15 +4,15 @@ │ │ │ │ │ mia-filenumberpattern │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-filenumberpattern {-i string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to extract a extract the number pattern for file012312.ext │ │ │ │ │ type file names. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input image example name │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmialabelsort.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-labelsort

mia-labelsort

Sysnopis:

mia-labelsort {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used create a mapping based on a histogram that puts the intensities with high values at the beginning of the histogram. The main use case will be to sort labels of connected components in out-of-core image processing.

Options:

-i, --in-file=(input, required); string

input file name containing the histogram

-o, --out-file=(output, required); string

output file name to store probabilities

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

This program is used create a mapping based on a histogram that puts the intensities with high values at the beginning of the histogram. The main use case will be to sort labels of connected components in out-of-core image processing.

Options:

-i, --in-file=(required, input); string

input file name containing the histogram

-o, --out-file=(required, output); string

output file name to store probabilities

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-labelsort 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,17 +6,17 @@ │ │ │ │ │ mia-labelsort {-i string} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used create a mapping based on a histogram that puts the │ │ │ │ │ intensities with high values at the beginning of the histogram. The main use │ │ │ │ │ case will be to sort labels of connected components in out-of-core image │ │ │ │ │ processing. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input file name containing the histogram │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output file name to store probabilities │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshdeformablemodel.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-mesh-deformable-model

mia-mesh-deformable-model

Sysnopis:

mia-mesh-deformable-model {-i io} {-o io} {-r io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs a deformable model to adapt a mesh to an iso-value within a given image. <FIXME: Reference>

Options:

File I/O

-i, --in-file=(input, required); io

input mesh to be adapted. For supported file types see Plugin type: mesh/io

-o, --out-file=(output, required); io

output mesh that has been deformed. For supported file types see Plugin type: mesh/io

-r, --ref-file=(input, required); io

reference image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Model parameters

--smoothing-weight=0.04; float in [0, inf)

Weight of the inner force used to smooth the mesh

--gradient-weight=0.04; float

Weight of the gradient force drive the mesh deformation. Use a negative value to invert the search direction.

--intensity-weight=0.02; float in [0, inf)

Weight of the force resulting from the intensity difference at the vertex position versus the reference intensity 'iso'.

--intensity-scaling=1; float in (0, inf)

Scaling of the raw intensity difference.

-s, --iso=64; float

Intensity value the mesh verices should adapt to.

Preprocessing

--image-smoothing=gauss:w=2; factory

Prefilter to smooth the reference image.. For supported plug-ins see Plugin type: 3dimage/filter

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

-m, --maxiter=200; uint in (0, inf)

Maximum number of iterations.

-e, --epsilon=0.001; float in (0, inf)

Stop iteration when the maximum shift of the vertices falls below this value

--reorient

Reorientate the mesh triangles

Example:

Run the deforemable model on input.vmesh with 200 iterations adapting to a value of 128 in the image ref.v and save the result to deformed.vmesh

mia-mesh-deformable-model -i input.vmesh -o deformed.vmesh --iso 128 --maxiter 200

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program runs a deformable model to adapt a mesh to an iso-value within a given image. <FIXME: Reference>

Options:

File I/O

-i, --in-file=(required, input); io

input mesh to be adapted. For supported file types see Plugin type: mesh/io

-o, --out-file=(required, output); io

output mesh that has been deformed. For supported file types see Plugin type: mesh/io

-r, --ref-file=(required, input); io

reference image. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Model parameters

--smoothing-weight=0.04; float in [0, inf)

Weight of the inner force used to smooth the mesh

--gradient-weight=0.04; float

Weight of the gradient force drive the mesh deformation. Use a negative value to invert the search direction.

--intensity-weight=0.02; float in [0, inf)

Weight of the force resulting from the intensity difference at the vertex position versus the reference intensity 'iso'.

--intensity-scaling=1; float in (0, inf)

Scaling of the raw intensity difference.

-s, --iso=64; float

Intensity value the mesh verices should adapt to.

Preprocessing

--image-smoothing=gauss:w=2; factory

Prefilter to smooth the reference image.. For supported plug-ins see Plugin type: 3dimage/filter

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

-m, --maxiter=200; uint in (0, inf)

Maximum number of iterations.

-e, --epsilon=0.001; float in (0, inf)

Stop iteration when the maximum shift of the vertices falls below this value

--reorient

Reorientate the mesh triangles

Example:

Run the deforemable model on input.vmesh with 200 iterations adapting to a value of 128 in the image ref.v and save the result to deformed.vmesh

mia-mesh-deformable-model -i input.vmesh -o deformed.vmesh --iso 128 --maxiter 200

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-mesh-deformable-model {-i io} {-o io} {-r io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs a deformable model to adapt a mesh to an iso-value within a │ │ │ │ │ given image. │ │ │ │ │ Options: │ │ │ │ │ File I/O │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input mesh to be adapted. For supported file types see Plugin_type:_mesh/ │ │ │ │ │ io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output mesh that has been deformed. For supported file types see Plugin │ │ │ │ │ type:_mesh/io │ │ │ │ │ - -r, --ref-file=(input, required); io │ │ │ │ │ + -r, --ref-file=(required, input); io │ │ │ │ │ reference image. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshdistancetostackmask.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-meshdistance-to-stackmask

mia-meshdistance-to-stackmask

Sysnopis:

mia-meshdistance-to-stackmask {-i io} {-r io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program takes a binary masks and a triangular mesh as input and evaluates the distance of the mesh vertices to the binary maskand stores the result in a new mesh.

Options:

-i, --in-mesh=(input, required); io

input mesh. For supported file types see Plugin type: mesh/io

-r, --ref-mask=(input, required); io

reference binary mask. For supported file types see Plugin type: 2dimage/io

-o, --out-mesh=(output, required); io

output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance of the mask given in the images maskXXXX.png to the mesh given in mesh.v and save the result to mesh-dist.v

mia-meshdistance-to-stackmask -i mesh.v -r maskXXXX.png -o mesh-dist.v

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program takes a binary masks and a triangular mesh as input and evaluates the distance of the mesh vertices to the binary maskand stores the result in a new mesh.

Options:

-i, --in-mesh=(required, input); io

input mesh. For supported file types see Plugin type: mesh/io

-r, --ref-mask=(required, input); io

reference binary mask. For supported file types see Plugin type: 2dimage/io

-o, --out-mesh=(required, output); io

output mesh. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the distance of the mask given in the images maskXXXX.png to the mesh given in mesh.v and save the result to mesh-dist.v

mia-meshdistance-to-stackmask -i mesh.v -r maskXXXX.png -o mesh-dist.v

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,20 +5,20 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-meshdistance-to-stackmask {-i io} {-r io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program takes a binary masks and a triangular mesh as input and evaluates │ │ │ │ │ the distance of the mesh vertices to the binary maskand stores the result in a │ │ │ │ │ new mesh. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-mesh=(input, required); io │ │ │ │ │ + -i, --in-mesh=(required, input); io │ │ │ │ │ input mesh. For supported file types see Plugin_type:_mesh/io │ │ │ │ │ - -r, --ref-mask=(input, required); io │ │ │ │ │ + -r, --ref-mask=(required, input); io │ │ │ │ │ reference binary mask. For supported file types see Plugin_type:_2dimage/ │ │ │ │ │ io │ │ │ │ │ - -o, --out-mesh=(output, required); io │ │ │ │ │ + -o, --out-mesh=(required, output); io │ │ │ │ │ output mesh. For supported file types see Plugin_type:_mesh/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshfilter.html │ │ │ │ @@ -2,8 +2,8 @@ │ │ │ │ options │ │ │ │ ...] [ │ │ │ │ │ │ │ │ Plugin type: mesh/filter │ │ │ │ │ │ │ │ ...]

Description:

This program runs a series filters on a given input mesh. The filters are given as extra parameters on the command line and are run in the order in which they are given. To obtain a list of available filters you may run │ │ │ │ 'mia-plugin-help mesh/filter' │ │ │ │ -from the command line

Options:

-i, --in-file=(input, required); io

input mesh to be filtered. For supported file types see Plugin type: mesh/io

-o, --out-file=(output, required); io

output mesh that have been filtered. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run an isotropic scaling on input.vmesh to fit it into the box defined by the corners <0,0,0> - <128,128,128> and save the result to output.vmesh

mia-meshfilter -i input.vmesh -o output.vmesh scale:strategy=iso-fitbox,box-start=[<0,0,0>],box-end=[<128,128,128>]

Author(s):

Gert Wollny

│ │ │ │ +from the command line

Options:

-i, --in-file=(required, input); io

input mesh to be filtered. For supported file types see Plugin type: mesh/io

-o, --out-file=(required, output); io

output mesh that have been filtered. For supported file types see Plugin type: mesh/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Run an isotropic scaling on input.vmesh to fit it into the box defined by the corners <0,0,0> - <128,128,128> and save the result to output.vmesh

mia-meshfilter -i input.vmesh -o output.vmesh scale:strategy=iso-fitbox,box-start=[<0,0,0>],box-end=[<128,128,128>]

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ mia-meshfilter {-i io} {-o io} [ options ...] [ Plugin_type:_mesh/filter ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs a series filters on a given input mesh. The filters are given │ │ │ │ │ as extra parameters on the command line and are run in the order in which they │ │ │ │ │ are given. To obtain a list of available filters you may run 'mia-plugin-help │ │ │ │ │ mesh/filter' from the command line │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input mesh to be filtered. For supported file types see Plugin_type: │ │ │ │ │ mesh/io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output mesh that have been filtered. For supported file types see Plugin │ │ │ │ │ type:_mesh/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiameshtomaskimage.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-mesh-to-maskimage

mia-mesh-to-maskimage

Sysnopis:

mia-mesh-to-maskimage {-i io} {-o io} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program converts a 3D mesh into a binary mask comprising the mesh surface. The output image size is either given on the command line or deducted from the mesh dimensions.

Options:

File I/O

-i, --in-file=(input, required); io

input mesh to be adapted. For supported file types see Plugin type: mesh/io

-o, --out-file=(output, required); io

output image containing the binary mask. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Properties

--origin=[0,0,0]; 3dfvector

coordinate of pixel at index 0,0,0

--spacing=[1,1,1]; 3dfvector

voxel spacing in the output image, all values must be positive.

--size=[0,0,0]; 3dbounds

size of the output image (0,0,0 = deduct)

Example:

The input mesh input.vmesh is converted into the binary mask mask.v. The image size is set to 50,50,50 and the size is obtained automatically to include the whole mesh

mia-mesh-to-maskimage -i input.vmesh -o mask.v --origin 0,0,0

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program converts a 3D mesh into a binary mask comprising the mesh surface. The output image size is either given on the command line or deducted from the mesh dimensions.

Options:

File I/O

-i, --in-file=(required, input); io

input mesh to be adapted. For supported file types see Plugin type: mesh/io

-o, --out-file=(required, output); io

output image containing the binary mask. For supported file types see Plugin type: 3dimage/io

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Properties

--origin=[0,0,0]; 3dfvector

coordinate of pixel at index 0,0,0

--spacing=[1,1,1]; 3dfvector

voxel spacing in the output image, all values must be positive.

--size=[0,0,0]; 3dbounds

size of the output image (0,0,0 = deduct)

Example:

The input mesh input.vmesh is converted into the binary mask mask.v. The image size is set to 50,50,50 and the size is obtained automatically to include the whole mesh

mia-mesh-to-maskimage -i input.vmesh -o mask.v --origin 0,0,0

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ mia-mesh-to-maskimage {-i io} {-o io} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program converts a 3D mesh into a binary mask comprising the mesh surface. │ │ │ │ │ The output image size is either given on the command line or deducted from the │ │ │ │ │ mesh dimensions. │ │ │ │ │ Options: │ │ │ │ │ File I/O │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input mesh to be adapted. For supported file types see Plugin_type:_mesh/ │ │ │ │ │ io │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output image containing the binary mask. For supported file types see │ │ │ │ │ Plugin_type:_3dimage/io │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiamultihist.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-multihist

mia-multihist

Sysnopis:

mia-multihist {-i io} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program evaluates the histogram over a series of 2D images

Options:

-i, --in-file=(input, required); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-histogram=(output, required); string

output file name

--min=0; float

minimum of histogram range

--max=65535; float

maximum of histogram range

--bins=65536; uint

number of histogram bins, set to zero to create a bin for each intensity value available in the input data. In this case the histogram range is also evaluated automatically

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the histogram over all consecutively numbered images that follow the numbering pattern inputXXXX.exr and store the output histogram in histo.txt. Use the range [0,256] and 64 bins.

mia-multihist -i input0000.exr -o histo.txt --min 0 --max 256 --bins 64

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program evaluates the histogram over a series of 2D images

Options:

-i, --in-file=(required, input); io

input image(s) to be filtered. For supported file types see Plugin type: 2dimage/io

-o, --out-histogram=(required, output); string

output file name

--min=0; float

minimum of histogram range

--max=65535; float

maximum of histogram range

--bins=65536; uint

number of histogram bins, set to zero to create a bin for each intensity value available in the input data. In this case the histogram range is also evaluated automatically

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Evaluate the histogram over all consecutively numbered images that follow the numbering pattern inputXXXX.exr and store the output histogram in histo.txt. Use the range [0,256] and 64 bins.

mia-multihist -i input0000.exr -o histo.txt --min 0 --max 256 --bins 64

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,18 +3,18 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-multihist │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-multihist {-i io} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program evaluates the histogram over a series of 2D images │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); io │ │ │ │ │ + -i, --in-file=(required, input); io │ │ │ │ │ input image(s) to be filtered. For supported file types see Plugin_type: │ │ │ │ │ 2dimage/io │ │ │ │ │ - -o, --out-histogram=(output, required); string │ │ │ │ │ + -o, --out-histogram=(required, output); string │ │ │ │ │ output file name │ │ │ │ │ --min=0; float │ │ │ │ │ minimum of histogram range │ │ │ │ │ --max=65535; float │ │ │ │ │ maximum of histogram range │ │ │ │ │ --bins=65536; uint │ │ │ │ │ number of histogram bins, set to zero to create a bin for each intensity │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiamyowavelettest.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-myowavelettest

mia-myowavelettest

Sysnopis:

mia-myowavelettest {-i string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs the wavelet based slope-statistics on the mixing matrix of a ICA perfusion series.

Options:

File-IO

-i, --in-file=(input, required); string

input data set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │ + ...]

Description:

This program runs the wavelet based slope-statistics on the mixing matrix of a ICA perfusion series.

Options:

File-IO

-i, --in-file=(required, input); string

input data set

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

│ │ │ │

mia-myowavelettest 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-myowavelettest {-i string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs the wavelet based slope-statistics on the mixing matrix of a │ │ │ │ │ ICA perfusion series. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input data set │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. │ │ │ │ │ Supported priorities starting at lowest level are: │ │ │ │ │ trace: Function call trace │ │ │ │ │ debug: Debug output │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiaraw2image.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-raw2image

mia-raw2image

Sysnopis:

mia-raw2image {-i string} {-o io} {-s 2dbounds} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to convert raw data to a 2D file format.

Options:

-i, --in-file=(input, required); string

input file name

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 2dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-b, --big-endian

input data is big endian

-f, --scale=[1,1]; 2dfvector

scale of input pixels <FX,FY>

-s, --size=(required); 2dbounds

size of input <NX,NY>

-k, --skip=0; uint

skip number of bytes from beginning of file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a data set data.raw of size <10,20> of short integer data with a pixel size of <1.2, 2.3> to a PNG file image.png

mia-raw2image -i data.raw -o image.png -s '<10,20>' -k '<1.2,2.3>' -r ushort

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to convert raw data to a 2D file format.

Options:

-i, --in-file=(required, input); string

input file name

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 2dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-b, --big-endian

input data is big endian

-f, --scale=[1,1]; 2dfvector

scale of input pixels <FX,FY>

-s, --size=(required); 2dbounds

size of input <NX,NY>

-k, --skip=0; uint

skip number of bytes from beginning of file

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

Convert a data set data.raw of size <10,20> of short integer data with a pixel size of <1.2, 2.3> to a PNG file image.png

mia-raw2image -i data.raw -o image.png -s '<10,20>' -k '<1.2,2.3>' -r ushort

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -3,17 +3,17 @@ │ │ │ │ │ =============================================================================== │ │ │ │ │ mia-raw2image │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-raw2image {-i string} {-o io} {-s 2dbounds} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to convert raw data to a 2D file format. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input file name │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file name. For supported file types see Plugin_type:_2dimage/io │ │ │ │ │ -r, --repn=ubyte; dict │ │ │ │ │ input pixel type │ │ │ │ │ bit: binary data │ │ │ │ │ sbyte: signed 8 bit │ │ │ │ │ ubyte: unsigned 8 bit │ │ │ │ │ sshort: signed 16 bit │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiaraw2volume.html │ │ │ │ @@ -1,3 +1,3 @@ │ │ │ │ mia-raw2volume

mia-raw2volume

Sysnopis:

mia-raw2volume {-i string} {-o io} {-s 3dbounds} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program is used to convert raw data into 3D images with apropriate metadata.

Options:

-i, --in-file=(input, required); string

input file name

-o, --out-file=(output, required); io

output file name. For supported file types see Plugin type: 3dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-b, --big-endian

input data is big endian

-f, --scale=[1,1,1]; 3dfvector

scale of input voxels <FX,FY,FZ>

-k, --skip=0; uint

skip number of bytes from beginning of file

-s, --size=(required); 3dbounds

size of input <NX,NY,NZ>

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr

mia-raw2volume -i data.raw -o image.hdr -s "<10,20,30>" -k "<1.2,2.3,3.4>" -r ushort

Author(s):

Gert Wollny

│ │ │ │ + ...]

Description:

This program is used to convert raw data into 3D images with apropriate metadata.

Options:

-i, --in-file=(required, input); string

input file name

-o, --out-file=(required, output); io

output file name. For supported file types see Plugin type: 3dimage/io

-r, --repn=ubyte; dict

input pixel type

bit:binary data
sbyte:signed 8 bit
ubyte:unsigned 8 bit
sshort:signed 16 bit
ushort:unsigned 16 bit
sint:signed 32 bit
uint:unsigned 32 bit
slong:signed 64 bit
ulong:unsigned 64 bit
float:floating point 32 bit
double:floating point 64 bit
none:no pixel type defined
-b, --big-endian

input data is big endian

-f, --scale=[1,1,1]; 3dfvector

scale of input voxels <FX,FY,FZ>

-k, --skip=0; uint

skip number of bytes from beginning of file

-s, --size=(required); 3dbounds

size of input <NX,NY,NZ>

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Example:

pixel size of <1.2, 2.3, 3.4> to an Analyze file image.hdr

mia-raw2volume -i data.raw -o image.hdr -s "<10,20,30>" -k "<1.2,2.3,3.4>" -r ushort

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -4,17 +4,17 @@ │ │ │ │ │ mia-raw2volume │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-raw2volume {-i string} {-o io} {-s 3dbounds} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program is used to convert raw data into 3D images with apropriate │ │ │ │ │ metadata. │ │ │ │ │ Options: │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input file name │ │ │ │ │ - -o, --out-file=(output, required); io │ │ │ │ │ + -o, --out-file=(required, output); io │ │ │ │ │ output file name. For supported file types see Plugin_type:_3dimage/io │ │ │ │ │ -r, --repn=ubyte; dict │ │ │ │ │ input pixel type │ │ │ │ │ bit: binary data │ │ │ │ │ sbyte: signed 8 bit │ │ │ │ │ ubyte: unsigned 8 bit │ │ │ │ │ sshort: signed 16 bit │ │ │ ├── ./usr/share/doc/mia-2.4/userref/Secmiawavelettrans.html │ │ │ │ @@ -1,4 +1,4 @@ │ │ │ │ mia-wavelettrans

mia-wavelettrans

Sysnopis:

mia-wavelettrans {-i string} {-o string} [ │ │ │ │ options │ │ │ │ - ...]

Description:

This program runs the a column-wise discret wavelet forward transform on the data given by an input text file.

Options:

File-IO

-i, --in-file=(input, required); string

input data set

-o, --out-file=(output, required); string

output data set

-s, --save-wave=(output); string

base name of the output files that will store the wavelet coefficients as matrix

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Wavelet

-w, --wavelet=c-daubechies; dict

wavelet to be used

haar:HAAR wavelet
c-haar:HAAR wavelet (centered)
daubechies:Daubechies wavelet
c-daubechies:Daubechies wavelet (centered)
bspline:B-Spline wavelet
c-bspline:B-Spline wavelet (centered)
-m, --member=10; int

wavelet member ID

Example:

│ │ │ │ + ...]

Description:

This program runs the a column-wise discret wavelet forward transform on the data given by an input text file.

Options:

File-IO

-i, --in-file=(required, input); string

input data set

-o, --out-file=(required, output); string

output data set

-s, --save-wave=(output); string

base name of the output files that will store the wavelet coefficients as matrix

Help & Info

-V, --verbose=warning; dict

verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

trace:Function call trace
debug:Debug output
info:Low level messages
message:Normal messages
warning:Warnings
fail:Report test failures
error:Report errors
fatal:Report only fatal errors
--copyright=(); bool

print copyright information

-h, --help=(); bool

print this help

-?, --usage=(); bool

print a short help

--version=(); bool

print the version number and exit

Processing

--threads=-1; int

Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).

Wavelet

-w, --wavelet=c-daubechies; dict

wavelet to be used

haar:HAAR wavelet
c-haar:HAAR wavelet (centered)
daubechies:Daubechies wavelet
c-daubechies:Daubechies wavelet (centered)
bspline:B-Spline wavelet
c-bspline:B-Spline wavelet (centered)
-m, --member=10; int

wavelet member ID

Example:

│ │ │ │

mia-wavelettrans 

Author(s):

Gert Wollny

│ │ │ │ ├── html2text {} │ │ │ │ │ @@ -5,17 +5,17 @@ │ │ │ │ │ Sysnopis: │ │ │ │ │ mia-wavelettrans {-i string} {-o string} [ options ...] │ │ │ │ │ Description: │ │ │ │ │ This program runs the a column-wise discret wavelet forward transform on the │ │ │ │ │ data given by an input text file. │ │ │ │ │ Options: │ │ │ │ │ File-IO │ │ │ │ │ - -i, --in-file=(input, required); string │ │ │ │ │ + -i, --in-file=(required, input); string │ │ │ │ │ input data set │ │ │ │ │ - -o, --out-file=(output, required); string │ │ │ │ │ + -o, --out-file=(required, output); string │ │ │ │ │ output data set │ │ │ │ │ -s, --save-wave=(output); string │ │ │ │ │ base name of the output files that will store the wavelet coefficients as │ │ │ │ │ matrix │ │ │ │ │ Help & Info │ │ │ │ │ -V, --verbose=warning; dict │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. ├── mia-tools_2.4.7-11_armhf.deb │ ├── file list │ │ @@ -1,3 +1,3 @@ │ │ -rw-r--r-- 0 0 0 4 2022-08-17 13:27:13.000000 debian-binary │ │ --rw-r--r-- 0 0 0 7580 2022-08-17 13:27:13.000000 control.tar.xz │ │ --rw-r--r-- 0 0 0 1688984 2022-08-17 13:27:13.000000 data.tar.xz │ │ +-rw-r--r-- 0 0 0 7556 2022-08-17 13:27:13.000000 control.tar.xz │ │ +-rw-r--r-- 0 0 0 1688760 2022-08-17 13:27:13.000000 data.tar.xz │ ├── control.tar.xz │ │ ├── control.tar │ │ │ ├── ./md5sums │ │ │ │ ├── ./md5sums │ │ │ │ │┄ Files differ │ ├── data.tar.xz │ │ ├── data.tar │ │ │ ├── file list │ │ │ │ @@ -146,139 +146,139 @@ │ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2022-08-17 13:27:13.000000 ./usr/share/lintian/overrides/ │ │ │ │ -rw-r--r-- 0 root (0) root (0) 425 2022-08-17 13:08:50.000000 ./usr/share/lintian/overrides/mia-tools │ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2022-08-17 13:27:13.000000 ./usr/share/man/ │ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2022-08-17 13:27:13.000000 ./usr/share/man/man1/ │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1472 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2davgmasked.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1565 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dbinarycombine.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2633 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dcost.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1746 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1751 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1691 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2ddistance.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1867 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2deval-transformquantity.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 3498 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1915 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1547 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1805 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dfuzzysegment.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1592 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 3499 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1913 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1543 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1810 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dfuzzysegment.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1590 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 3457 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dgroundtruthreg.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1470 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1469 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1620 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagecombiner.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1774 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagecreator.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 6177 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagefilter.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6373 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6370 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1442 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagefullstats.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 5276 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1490 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimageselect.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5279 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1491 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimageselect.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1428 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1952 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1956 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1622 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dimagestats.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1669 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dlerp.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 3672 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1674 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dlerp.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 3675 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2777 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmulti-force.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 5396 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5397 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1857 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmultiimageto3d.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1542 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmultiimagevar.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2193 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyocard-ica.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1817 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1733 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyocard-segment.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6387 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoica-full.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 5449 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 5392 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6381 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoica-full.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5456 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5394 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 3715 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 6765 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoicapgt.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 4504 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyomilles.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 4509 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyomilles.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 5657 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 3372 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 5532 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1005 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 3368 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5537 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1006 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1006 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoseries-dice.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 3685 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 981 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegcompare.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 988 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseghausdorff.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1793 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1798 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 6323 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2310 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1902 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegment-local-kmeans.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1843 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1253 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegmentcropbox.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1648 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegseriesstats.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1692 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegshift.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1133 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1257 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegmentcropbox.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1651 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegseriesstats.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1697 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegshift.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1132 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1578 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseries-mincorr.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1511 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseries-sectionmask.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 977 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseries-segdistance.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6403 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6400 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1725 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseries2sets.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1712 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriescorr.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6305 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1724 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriesgradvariation.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6300 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1723 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriesgradvariation.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 993 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dserieshausdorff.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6342 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6340 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1570 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dseriestovolume.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2132 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dstack-cmeans-presegment.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6951 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dstackfilter.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1876 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6949 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dstackfilter.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1882 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1888 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dto3dimageb.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1365 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1676 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1369 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1672 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1117 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1635 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dbinarycombine.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1879 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dbrainextractT1.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1740 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcombine-imageseries.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1651 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1655 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 3430 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6732 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1647 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1864 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6734 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1651 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1866 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2014 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3ddistance-stats.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1143 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3ddistance.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1878 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1875 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1673 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dfield2norm.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 3570 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 3571 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2319 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dfluid.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 2365 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1706 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dfuzzysegment.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1469 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 2201 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1968 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimageaddattributes.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 2368 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1708 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dfuzzysegment.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1468 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 2199 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1970 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimageaddattributes.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1658 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagecombine.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1906 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1907 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 5698 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagefilter.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 5895 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1548 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5897 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagefilterstack.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1544 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1929 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1544 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dimagestats.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1263 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3disosurface-from-stack.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 2267 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 2262 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1140 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dlandmarks-distances.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1302 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1299 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1722 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dlerp.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 7896 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1877 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 7897 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1874 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 2559 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dmotioncompica-nonrigid.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 9543 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 9406 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 9404 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 10018 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 5803 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 5107 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3drigidreg.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1936 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 2570 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 5112 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3drigidreg.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1931 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 2575 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 9437 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dserial-nonrigid.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1590 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1373 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1713 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1585 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1369 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1714 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1314 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dtransform2vf.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1267 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dvectorfieldcreate.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1661 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1660 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1267 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-3dvfcompare.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1120 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 882 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 987 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 6464 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 2140 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1955 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 2437 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1126 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 883 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-filenumberpattern.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 986 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 6460 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 2143 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1954 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 2433 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1660 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-multihist.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 901 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-myowavelettest.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 850 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-plugin-help.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1736 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1737 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ │ -rw-r--r-- 0 root (0) root (0) 1801 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-raw2volume.1.gz │ │ │ │ --rw-r--r-- 0 root (0) root (0) 1090 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 1086 2022-08-17 13:27:13.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ │ ├── ./usr/share/man/man1/mia-2ddeform.1.gz │ │ │ │ ├── mia-2ddeform.1 │ │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2ddeform \-i \-o \-t [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2ddeform │ │ │ │ │ This program is used to deform a 2D image using a deformation vector field. Input image and deformation field must be of the same size. The transformation formula is 'x -> x - v(x)' │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ transformed image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ │ transformation vector field │ │ │ │ │ For supported file types see PLUGINS:2dvf/io │ │ │ │ │ .IP "\-p \-\-interpolator=bspline:d=3" │ │ │ │ │ image interpolator kernel │ │ │ │ │ For supported plugins see PLUGINS:1d/splinekernel │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-2deval-transformquantity.1.gz │ │ │ │ ├── mia-2deval-transformquantity.1 │ │ │ │ │ @@ -24,21 +24,21 @@ │ │ │ │ │ } │ │ │ │ │ │ │ │ │ │ This example header has to be interpreted like follows: two-dimensional data, each entry consists of 7 values the values etry consists of a 2D vector, a scalar, and a 2x2 matrix (saved in row-major format).The data records represent strain tensors, and only a sparse set of points is given. The values are given as single floating point (32 bit). The original transformation field corresponds to images of 1000x1000 pixels and the binary data is stored in low endian format. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range. │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output strains file, for a format description see above. │ │ │ │ │ │ │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ │ transformation of which the quantity will be evaluated. │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS │ │ │ │ │ Parameters │ │ │ │ │ .RS │ │ │ │ │ .IP "\-q \-\-quantity=strain" │ │ │ ├── ./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz │ │ │ │ ├── mia-2dfluid-syn-registration.1 │ │ │ │ │ @@ -64,24 +64,24 @@ │ │ │ │ │ │ │ │ │ │ .IP " \-\-version" │ │ │ │ │ print the version number and exit │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ │ test image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-transform=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-transform=(required, output); io" │ │ │ │ │ output transformation │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ -.IP "\-O \-\-inverse-transform=(output, required); io" │ │ │ │ │ +.IP "\-O \-\-inverse-transform=(required, output); io" │ │ │ │ │ inverse output transformation │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS Processing │ │ │ │ │ .RS │ │ │ │ │ .IP " \-\-threads=\-1" │ │ │ │ │ Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (\-1: automatic estimation). │ │ │ ├── ./usr/share/man/man1/mia-2dfluid.1.gz │ │ │ │ ├── mia-2dfluid.1 │ │ │ │ │ @@ -14,18 +14,18 @@ │ │ │ │ │ .UE │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ It uses SSD as the sole registration criterion. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ │ input (test) image to be registered │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-out-transformation=(output); io" │ │ │ │ │ output transformation comprising the registration │ │ │ │ │ For supported file types see PLUGINS:2dvf/io │ │ │ │ │ .IP "\-d \-\-out-image=(output); io" │ │ │ │ │ output image deformed according to the transformation │ │ │ ├── ./usr/share/man/man1/mia-2dforce.1.gz │ │ │ │ ├── mia-2dforce.1 │ │ │ │ │ @@ -11,15 +11,15 @@ │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-src-file=(required, input); io" │ │ │ │ │ input image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output force norm image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-c \-\-cost=(required); string" │ │ │ │ │ cost function to use │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-2dfuzzysegment.1.gz │ │ │ │ ├── mia-2dfuzzysegment.1 │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ .B mia\-2dfuzzysegment \-i [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dfuzzysegment │ │ │ │ │ This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a fuzzy segmentation of 2D image. cf D.L. Pham and J.L.Prince, "An adaptive fuzzy C-means algorithm for image segmentation in the presence of intensity inhomogeneities", Pat. Rec. Let., 20:57-68,1999 │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image(s) to be segmenetd │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-c \-\-cls-file=(output); io" │ │ │ │ │ output class probability images (floating point values and multi\-image) │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-b0-file=(output); io" │ │ │ │ │ image corrected for intensity non\-uniformity │ │ │ ├── ./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz │ │ │ │ ├── mia-2dgrayimage-combine-to-rgb.1 │ │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-g \-\-green=(input); io" │ │ │ │ │ input image for green channel │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-r \-\-red=(input); io" │ │ │ │ │ input image for red channel │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ combined output image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-2dgroundtruthreg.1.gz │ │ │ │ ├── mia-2dgroundtruthreg.1 │ │ │ │ │ @@ -15,18 +15,18 @@ │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ Note that for this nonlinear motion correction a preceding linear registration step is usually required. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ │ file name base for registered files │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS │ │ │ ├── ./usr/share/man/man1/mia-2dimagecombine-dice.1.gz │ │ │ │ ├── mia-2dimagecombine-dice.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dimagecombine\-dice \-1 \-2 [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dimagecombine\-dice │ │ │ │ │ This program evaluate the dice index of two binary masks given as binary images. The result is written to stdout. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-1 \-\-in-file-1=(required, input); io" │ │ │ │ │ +.IP "\-1 \-\-in-file-1=(input, required); io" │ │ │ │ │ input image 1 │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-2 \-\-in-file-2=(required, input); io" │ │ │ │ │ +.IP "\-2 \-\-in-file-2=(input, required); io" │ │ │ │ │ input image 2 │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-2dimagecombiner.1.gz │ │ │ │ ├── mia-2dimagecombiner.1 │ │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dimagecombiner \-1 \-2 \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dimagecombiner │ │ │ │ │ Combine two image by a given operation. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-1 \-\-in-file-1=(input, required); io" │ │ │ │ │ +.IP "\-1 \-\-in-file-1=(required, input); io" │ │ │ │ │ first input image to be combined │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-2 \-\-in-file-2=(input, required); io" │ │ │ │ │ +.IP "\-2 \-\-in-file-2=(required, input); io" │ │ │ │ │ second input image to be combined │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output image(s) that have been filtered │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-p \-\-operation=absdiff" │ │ │ │ │ operation to be applied │ │ │ │ │ For supported plugins see PLUGINS:2dimage/combiner │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-2dimagefilterstack.1.gz │ │ │ │ ├── mia-2dimagefilterstack.1 │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ .B mia\-2dimagefilterstack \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dimagefilterstack │ │ │ │ │ This program runs a series filters on a series of consecutive numbered input image. The filters are given as extra parameters on the command line and are run in the order in which they are given. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output file name base, the file type is set accurding to the 'type' option │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-t \-\-type=" │ │ │ │ │ output file type, if not given the input type is used │ │ │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ │ .I │ │ │ │ │ @@ -388,15 +388,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -732,15 +732,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -758,15 +758,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -797,15 +797,15 @@ │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -820,25 +820,25 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B maxflow │ │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ sink-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ source-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -866,15 +866,15 @@ │ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ varfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -902,15 +902,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B medianmad │ │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ madfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -1027,15 +1027,15 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ seed image (bit valued). │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1208,28 +1208,28 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1293,15 +1293,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ ├── ./usr/share/man/man1/mia-2dimageregistration.1.gz │ │ │ │ ├── mia-2dimageregistration.1 │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ .B mia\-2dimageregistration \-i \-r \-t [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dimageregistration │ │ │ │ │ This program runs registration of two images optimizing a transformation of the given transformation model by optimizing certain cost measures that are given as free parameters. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ │ test image to be registered │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ │ +.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ │ reference image to be registered to │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-out-image=(output); io" │ │ │ │ │ registered output image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-t \-\-transformation=(required, output); io" │ │ │ │ │ output transformation comprising the registration │ │ │ ├── ./usr/share/man/man1/mia-2dimageselect.1.gz │ │ │ │ ├── mia-2dimageselect.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dimageselect \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dimageselect │ │ │ │ │ This program is used to select one 2D images from a multi-image file. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input images │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-n \-\-number=0" │ │ │ │ │ image number to be selected │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz │ │ │ │ ├── mia-2dimagestack-cmeans.1 │ │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ │ This program first evaluates a sparse histogram of an input image series, then runs a c-means classification over the histogram and then writes the probability mapping for thr original intensity values │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-probmap=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-probmap=(output, required); string" │ │ │ │ │ Save probability map to this file │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-2dlerp.1.gz │ │ │ │ ├── mia-2dlerp.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dlerp \-1 \-2 \-o \-p [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dlerp │ │ │ │ │ Merge two images by pixel-wise linearly combining their intensities. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-1 \-\-first=(required, input); io" │ │ │ │ │ +.IP "\-1 \-\-first=(input, required); io" │ │ │ │ │ first input image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-2 \-\-second=(required, input); io" │ │ │ │ │ +.IP "\-2 \-\-second=(input, required); io" │ │ │ │ │ second input image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output vector field │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-p \-\-positions=(required); vfloat" │ │ │ │ │ image series positions (first, target, second) │ │ │ ├── ./usr/share/man/man1/mia-2dmany2one-nonrigid.1.gz │ │ │ │ ├── mia-2dmany2one-nonrigid.1 │ │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ file name for registered images, numbering and pattern are deducted from the input data │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS │ │ │ │ │ Registration │ │ │ │ │ .RS │ │ │ │ │ .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" │ │ │ ├── ./usr/share/man/man1/mia-2dmultiimageregistration.1.gz │ │ │ │ ├── mia-2dmultiimageregistration.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dmultiimageregistration \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dmultiimageregistration │ │ │ │ │ This program runs a non-rigid registration based on the given cost criteria and a given transformation model. Other than mia-2dnonrigidreg it doesn't support specific command line parameters to provide the images. Instead the images are specified dirctly when defining the cost function. Hence, image registrations can be executed that optimize the aligmnet of more than one image pair at the same time. Note, however, that all input images must be of the same dimension (in pixels) │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-o \-\-out-transform=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-transform=(required, output); io" │ │ │ │ │ output transformation │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ .IP "\-l \-\-levels=3" │ │ │ │ │ multi\-resolution levels │ │ │ │ │ │ │ │ │ │ .IP "\-O \-\-optimizer=gsl:opt=gd,step=0.1" │ │ │ │ │ Optimizer used for minimization │ │ │ ├── ./usr/share/man/man1/mia-2dmyocard-ica.1.gz │ │ │ │ ├── mia-2dmyocard-ica.1 │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ .B mia\-2dmyocard\-ica \-i [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dmyocard\-ica │ │ │ │ │ This program is used to run a ICA on a series of myocardial perfusion images to create sythetic references that can be used for motion correction by image registration. If the aim is to run a full motion compensation then it is better to create a segmentation set and use mia-2dmyoica-nonrigid. If the input data is given by means of a segmentation set, then on can also use mia-2dmyocard-icaseries. │ │ │ │ │ This program is essentially used to test different options on how to run the ICA forreference image creation. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-base=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-base=(input, required); io" │ │ │ │ │ input file name ofolloing pattern nameXXXX.ext X=numbers │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP " \-\-coefs=" │ │ │ │ │ output mixing coefficients to this file │ │ │ │ │ │ │ │ │ │ .IP "\-o \-\-out-base=(output); string" │ │ │ │ │ output file name base │ │ │ ├── ./usr/share/man/man1/mia-2dmyoica-full.1.gz │ │ │ │ ├── mia-2dmyoica-full.1 │ │ │ │ │ @@ -17,15 +17,15 @@ │ │ │ │ │ The software may first run a linear registration and then a non-linear registration or just one of the two.This version of the program can run all registrations in parallel. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=" │ │ │ │ │ File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set. │ │ │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=(output); string" │ │ │ │ │ save cropped set to this file, the image files will use the stem of the name as file name base │ │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz │ │ │ │ ├── mia-2dmyoica-nonrigid-parallel.1 │ │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ │ .UE │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ This version of the program runs all registrations in parallel. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ │ File name base for the registered images. Image type and numbering scheme are taken from the input images as given in the input data set. │ │ │ ├── ./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz │ │ │ │ ├── mia-2dmyoica-nonrigid.1 │ │ │ │ │ @@ -13,18 +13,18 @@ │ │ │ │ │ Wollny G, Kellman P, Santos A, Ledesma-Carbayo M-J, "Automatic Motion Compensation of Free Breathing acquired Myocardial Perfusion Data by using Independent Component Analysis" Medical Image Analysis, 2012. │ │ │ │ │ .UE │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ │ file name base for registered fiels │ │ │ │ │ │ │ │ │ │ .IP " \-\-save-cropped=" │ │ │ │ │ save cropped set to this file │ │ │ ├── ./usr/share/man/man1/mia-2dmyomilles.1.gz │ │ │ │ ├── mia-2dmyomilles.1 │ │ │ │ │ @@ -15,15 +15,15 @@ │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ Changes include the extraction of the quasi-periodic movement in free breathingly acquired data sets and the option to run affine or rigid registration instead of the optimization of translations only. │ │ │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=" │ │ │ │ │ file name base for registered files │ │ │ ├── ./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz │ │ │ │ ├── mia-2dmyopgt-nonrigid.1 │ │ │ │ │ @@ -15,15 +15,15 @@ │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ . Note that for this nonlinear motion correction a preceding linear registration step is usually required. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-registered=reg" │ │ │ │ │ file name base for registered files, the image file type is the same as given in the input data set │ │ │ ├── ./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz │ │ │ │ ├── mia-2dmyoserial-nonrigid.1 │ │ │ │ │ @@ -17,15 +17,15 @@ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input perfusion data set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output perfusion data set │ │ │ │ │ │ │ │ │ │ .IP "\-R \-\-registered=reg" │ │ │ │ │ file name base for registered fiels │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS │ │ │ ├── ./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz │ │ │ │ ├── mia-2dmyoseries-compdice.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dmyoseries\-compdice \-1 \-2 [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dmyoseries\-compdice │ │ │ │ │ This program is used to evaluate the per-frame dice index of segmented regions of two image series │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-1 \-\-first=(input, required); string" │ │ │ │ │ +.IP "\-1 \-\-first=(required, input); string" │ │ │ │ │ first segmentation set │ │ │ │ │ │ │ │ │ │ -.IP "\-2 \-\-second=(input, required); string" │ │ │ │ │ +.IP "\-2 \-\-second=(required, input); string" │ │ │ │ │ second segmentation set │ │ │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ │ images to skip atthe begin of the series │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-2dseghausdorff.1.gz │ │ │ │ ├── mia-2dseghausdorff.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dseghausdorff \-i \-r [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dseghausdorff │ │ │ │ │ Get the per-slice Hausdorff distance of a segmentation with respect to a given reference frame and print it to stdout. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-ref-frame=(required); uint" │ │ │ │ │ reference frame │ │ │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ │ skip frames at the beginning │ │ │ ├── ./usr/share/man/man1/mia-2dsegment-ahmed.1.gz │ │ │ │ ├── mia-2dsegment-ahmed.1 │ │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ │ Mohamed N. Ahmed et. al, "A Modified Fuzzy C-Means Algorithm for Bias Field estimation and Segmentation of MRI Data", IEEE Trans. on Medical Imaging, Vol. 21, No. 3, March 2002, │ │ │ │ │ .UE │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ changes are: p=2, and exp │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ image to be segmented │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ class probability images, the image type must support multiple images and floating point values │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-a \-\-no-of-classes=3" │ │ │ │ │ number of classes │ │ │ ├── ./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz │ │ │ │ ├── mia-2dsegment-fuzzyw.1 │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ .B mia\-2dsegment\-fuzzyw \-i [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dsegment\-fuzzyw │ │ │ │ │ This program is a implementation of a fuzzy c-means segmentation algorithm │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File I/O │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ image to be segmented │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-c \-\-cls-file=(output); io" │ │ │ │ │ class probability images, the image type must support multiple images and floating point values │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(output); io" │ │ │ │ │ B\-field corrected image │ │ │ │ │ @@ -374,15 +374,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -718,15 +718,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -744,15 +744,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -783,15 +783,15 @@ │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -806,25 +806,25 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B maxflow │ │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ sink-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ source-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1013,15 +1013,15 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ seed image (bit valued). │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1194,15 +1194,15 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ @@ -1279,15 +1279,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ ├── ./usr/share/man/man1/mia-2dsegmentcropbox.1.gz │ │ │ │ ├── mia-2dsegmentcropbox.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dsegmentcropbox \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dsegmentcropbox │ │ │ │ │ This program is used on a segmentation set and evaluates a bounding box that encloses the segmentation in all slices. This bounding box is then used to crop the original images, correct the segmentation and store a new segmentation set with the cropped images. The cropped images will be of the same type as the original images. If no segmentation is given in the set, the result is undefined. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ │ │ .IP "\-p \-\-override-imagepath" │ │ │ │ │ Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory │ │ │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output segmentation set │ │ │ ├── ./usr/share/man/man1/mia-2dsegseriesstats.1.gz │ │ │ │ ├── mia-2dsegseriesstats.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dsegseriesstats \-o \-g [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dsegseriesstats │ │ │ │ │ This program is used evaluate various time-intensity curves over a series of images given by a segmentation set. Specifically, the program is taylored to evaluate average intensities and variations of sections the left ventricle myocardium. The segmentation set must contain the segmentations for all slices that will be accessed during evaluation. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-o \-\-original=(required, input); string" │ │ │ │ │ +.IP "\-o \-\-original=(input, required); string" │ │ │ │ │ original segmentation set │ │ │ │ │ │ │ │ │ │ -.IP "\-g \-\-registered=(required, input); string" │ │ │ │ │ +.IP "\-g \-\-registered=(input, required); string" │ │ │ │ │ registered segmentation set │ │ │ │ │ │ │ │ │ │ .IP "\-k \-\-skip=2" │ │ │ │ │ images to skip at the begin of the series, if (k < 0) use RV peak of the registered set if set │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-reference=\-1" │ │ │ │ │ reference frame for automatic curve extraction. Negative values can be used to indicate specific values (if given in the segmentation set): │ │ │ ├── ./usr/share/man/man1/mia-2dsegshift.1.gz │ │ │ │ ├── mia-2dsegshift.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dsegshift \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dsegshift │ │ │ │ │ This program move the segmentation(s) of an image series by using a shift that is equal for all slices. The program also may remove images from the begin of the series. The program can be used to correct the segmentation of the images if the images where cropped. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input segmentation set │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ input segmentation set │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-g \-\-image-file=crop" │ │ │ │ │ output image filename base │ │ │ ├── ./usr/share/man/man1/mia-2dsegshiftperslice.1.gz │ │ │ │ ├── mia-2dsegshiftperslice.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dsegshiftperslice \-i \-o \-S [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dsegshiftperslice │ │ │ │ │ This program move the segmentation(s) of an image series by using a shift that is given on a per-slice base. The program can be used to correct the segmentation of the images if a linear registration was executed that only applies a translation and does not correct the segmentation automatically. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output segmentation set │ │ │ │ │ │ │ │ │ │ .IP "\-g \-\-image-file=crop" │ │ │ │ │ output image filename base │ │ │ │ │ │ │ │ │ │ .IP "\-S \-\-shift=(required); string" │ │ │ │ │ shift of segmentation \- base name │ │ │ ├── ./usr/share/man/man1/mia-2dseries2dordermedian.1.gz │ │ │ │ ├── mia-2dseries2dordermedian.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-2dseries2dordermedian │ │ │ │ │ This program evaluates the pixel-wise median of the absolute values of the gauss filtered 2nd order temporal derivative of a series of images. In addition, it can be used to output the time-intensity curve of a given pixel.The program supports slice-wise spacial pre-filtering by giving additional filters as free parameters (filter/2dimage). │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output image name │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ │ @@ -842,15 +842,15 @@ │ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ varfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -878,15 +878,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B medianmad │ │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ madfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -1197,15 +1197,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ ├── ./usr/share/man/man1/mia-2dseriesgradMAD.1.gz │ │ │ │ ├── mia-2dseriesgradMAD.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-2dseriesgradMAD │ │ │ │ │ Given a set of images of temporal sucession, evaluates the pixel-wise temporal gradient and then its median average distance (MAD) and stores the result in an image. Spacial pre-filtering may be applied as given additional plugin(s) (filter/2dimage). │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output file name │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ │ @@ -833,15 +833,15 @@ │ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ varfile │ │ │ │ │ -=(required, output, io) │ │ │ │ │ +=(output, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -869,15 +869,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B medianmad │ │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ madfile │ │ │ │ │ -=(required, output, io) │ │ │ │ │ +=(output, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -1188,15 +1188,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(required, output, io) │ │ │ │ │ +=(output, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ ├── ./usr/share/man/man1/mia-2dseriesgradvariation.1.gz │ │ │ │ ├── mia-2dseriesgradvariation.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dseriesgradvariation \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dseriesgradvariation │ │ │ │ │ Given a set of images of temporal sucession, this program evaluates the gradient variation of the pixel-wise time-intensity curves of this series. If the input image set provides a segmentation, then this segmentation can be used to create a bounding box and restrict evaluation to this box. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output file name │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ ├── ./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz │ │ │ │ ├── mia-2dseriessmoothgradMAD.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dseriessmoothgradMAD \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dseriessmoothgradMAD │ │ │ │ │ Given a set of images of temporal sucession, evaluate the temporal pixel-wise gaussian and evaluate pixel-wise its MAD.A spacial pre-filtering may be applied by specifying additional plugins (filter/2dimage) │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input segmentation set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output file name │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-k \-\-skip=0" │ │ │ │ │ Skip files at the beginning │ │ │ │ │ │ │ │ │ │ .IP "\-e \-\-enlarge-boundary=5" │ │ │ │ │ Enlarge cropbox by number of pixels │ │ │ │ │ @@ -358,15 +358,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -702,15 +702,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -728,15 +728,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -767,15 +767,15 @@ │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -790,25 +790,25 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B maxflow │ │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ sink-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ source-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -836,15 +836,15 @@ │ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ varfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -872,15 +872,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B medianmad │ │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ madfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -997,15 +997,15 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ seed image (bit valued). │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1178,28 +1178,28 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1263,15 +1263,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ ├── ./usr/share/man/man1/mia-2dstackfilter.1.gz │ │ │ │ ├── mia-2dstackfilter.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-2dstackfilter \-i \-o \-t [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-2dstackfilter │ │ │ │ │ This program is used to filter and convert a series of 2D gray scale images in a 3D fashion by running filters (filter/2dimage) as given on the command line. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output file name base, the actual names is created by adding the file number based on output order and the extension bysed on the 'type' parameter │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-t \-\-type=(required); set" │ │ │ │ │ output file type │ │ │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ │ .I │ │ │ │ │ @@ -378,15 +378,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -722,15 +722,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -748,15 +748,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -787,15 +787,15 @@ │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -810,25 +810,25 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B maxflow │ │ │ │ │ This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ sink-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the sink. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ source-flow │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Image of float type to define the per\-pixel flow to the source. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -856,15 +856,15 @@ │ │ │ │ │ Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ varfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the variation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -892,15 +892,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B medianmad │ │ │ │ │ Filter that evaluates simultaniously the pixel wise median and the median absolute deviation (MAD) of an image in a given window. Pixel intensities below the given threshold will be ignored and at their loctions the output median and MAD are set to zero. The median intensity image is directly passed to the pipeline, the variation image is saved to a file given with the varfile parameter. Both output images have the same pixel type like the input image., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ madfile │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the median absolute deviation image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -1017,15 +1017,15 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ seed image (bit valued). │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1198,28 +1198,28 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:2dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1283,15 +1283,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1625,15 +1625,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B label │ │ │ │ │ Stack Label filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Mapfile to save label numbers that are joined. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ @@ -1715,15 +1715,15 @@ │ │ │ │ │ low threshold for acceptance probability. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed class map. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ ├── ./usr/share/man/man1/mia-2dto3dimage.1.gz │ │ │ │ ├── mia-2dto3dimage.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-2dto3dimage │ │ │ │ │ This program is used to combine a series of 2D images of equal size and type images following a certain numbering scheme to a 3D image. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image(s) to be combined │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output file name │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-2dtrackpixelmovement.1.gz │ │ │ │ ├── mia-2dtrackpixelmovement.1 │ │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input point set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output point set │ │ │ │ │ │ │ │ │ │ .IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ transformation describing the monitored change │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS │ │ │ ├── ./usr/share/man/man1/mia-2dtransform.1.gz │ │ │ │ ├── mia-2dtransform.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-2dtransform │ │ │ │ │ This program is used to deform a 2D image using a given transformation. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output image │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ transformation file name │ │ │ │ │ For supported file types see PLUGINS:2dtransform/io │ │ │ │ │ .IP "\-p \-\-interpolator=" │ │ │ │ │ override the interpolator provided by the transformation │ │ │ ├── ./usr/share/man/man1/mia-3dbrainextractT1.1.gz │ │ │ │ ├── mia-3dbrainextractT1.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dbrainextractT1 \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dbrainextractT1 │ │ │ │ │ This program is used to extract the brain from T1 MR images. It first runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image. Then various fiters are run to obtain a white matter segmentation as initial mask that is then used to run a region growing to obtain a mask of the whole brain. Finally, this mask is used to extact the brain from the B0 field corrected images. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image(s) to be segmented │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ brain mask │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-n \-\-no-of-classes=3" │ │ │ │ │ number of classes │ │ │ │ │ │ │ │ │ │ .IP "\-w \-\-wm-class=2" │ │ │ │ │ index of white matter │ │ │ ├── ./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz │ │ │ │ ├── mia-3dcombine-mr-segmentations.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-3dcombine\-mr\-segmentations │ │ │ │ │ This programs takes various segmentation masks of the same data and a tissue probability image set and combines them into one labeled image. The masks are translated to labels according to the position on the command line. If a voxel is set as belonging to more then one mask, the probabilities are consulted. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input probability images. The number of mask images must correspond to the number of probability images given here. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output image that contains the labeling. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-3dcost.1.gz │ │ │ │ ├── mia-3dcost.1 │ │ │ │ │ @@ -1254,15 +1254,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(required, output, io) │ │ │ │ │ +=(output, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ ├── ./usr/share/man/man1/mia-3dcrispsegment.1.gz │ │ │ │ ├── mia-3dcrispsegment.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-3dcrispsegment │ │ │ │ │ This program creates a label image from a fuzzy segmentation. or each pixel the label is set to the class with the higest probability plus a given offset │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input class file, should contain multiple images with tissue class probabilities │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output class label image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-l \-\-label-offset=1" │ │ │ │ │ label offset │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-3ddeform.1.gz │ │ │ │ ├── mia-3ddeform.1 │ │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3ddeform \-i \-o \-t [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3ddeform │ │ │ │ │ Transform a 3D image by applying a given 3D transformation that is defined by a 3D vector field v according to x:=x-v(x) │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ │ input image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-image=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-image=(required, output); io" │ │ │ │ │ transformed image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ transformation vector field │ │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ │ .IP "\-p \-\-interpolator=bspline:d=3" │ │ │ │ │ image interpolator kernel │ │ │ │ │ For supported plugins see PLUGINS:1d/splinekernel │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-3deval-transformquantity.1.gz │ │ │ │ ├── mia-3deval-transformquantity.1 │ │ │ │ │ @@ -27,15 +27,15 @@ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(input); string" │ │ │ │ │ input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range. │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output strains file, for a format description see above. │ │ │ │ │ │ │ │ │ │ .IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ transformation of which the quantity will be evaluated. │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS │ │ │ ├── ./usr/share/man/man1/mia-3dfluid-syn-registration.1.gz │ │ │ │ ├── mia-3dfluid-syn-registration.1 │ │ │ │ │ @@ -64,24 +64,24 @@ │ │ │ │ │ │ │ │ │ │ .IP " \-\-version" │ │ │ │ │ print the version number and exit │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ │ test image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-transform=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-transform=(required, output); io" │ │ │ │ │ output transformation │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ -.IP "\-O \-\-inverse-transform=(output, required); io" │ │ │ │ │ +.IP "\-O \-\-inverse-transform=(required, output); io" │ │ │ │ │ inverse output transformation │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS Processing │ │ │ │ │ .RS │ │ │ │ │ .IP " \-\-threads=\-1" │ │ │ │ │ Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (\-1: automatic estimation). │ │ │ ├── ./usr/share/man/man1/mia-3dforce.1.gz │ │ │ │ ├── mia-3dforce.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dforce \-i \-r \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dforce │ │ │ │ │ This program is used to create an image comprising the pixel-wise norm of the ggradient of a given cost function. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-src-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-src-file=(required, input); io" │ │ │ │ │ input image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-r \-\-ref-file=(input, required); io" │ │ │ │ │ +.IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ │ output force norm image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-c \-\-cost=ssd" │ │ │ │ │ cost function to use │ │ │ ├── ./usr/share/man/man1/mia-3dfuzzysegment.1.gz │ │ │ │ ├── mia-3dfuzzysegment.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dfuzzysegment \-i [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dfuzzysegment │ │ │ │ │ This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image(s) to be segmenetd │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-c \-\-cls-file=(output); io" │ │ │ │ │ output class probability images. Note, the used file format must support multible images (best is to use vista) │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-o \-\-b0-file=(output); io" │ │ │ │ │ image corrected for intensity non\-uniformity │ │ │ ├── ./usr/share/man/man1/mia-3dgetsize.1.gz │ │ │ │ ├── mia-3dgetsize.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dgetsize \-i [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dgetsize │ │ │ │ │ Write the dimensions of the input 3D image to stdout. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-3dgetslice.1.gz │ │ │ │ ├── mia-3dgetslice.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dgetslice \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dgetslice │ │ │ │ │ This program is used to extract 2D slices from a 3D data set and store them in separate files. Output files will be numbered according to their slice index. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output image(s). If number != 1 than this is used as a base name and should be given without extension since this will be based on the '\-\-type' option. If number=1 then this exact file name will be used. │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-t \-\-type=png" │ │ │ │ │ output file type for number != 1 │ │ │ ├── ./usr/share/man/man1/mia-3dimageaddattributes.1.gz │ │ │ │ ├── mia-3dimageaddattributes.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-3dimageaddattributes │ │ │ │ │ This program appends all the meta-data attributes found in a 2D input image to a 3D image (if the output format supports such attributes). Attributes that are already present in the 3D image are not overwritten. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output image(s) with the added attributes │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-a \-\-attr=(required, input); io" │ │ │ │ │ 2D image providing the attributes │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-3dimagecombine.1.gz │ │ │ │ ├── mia-3dimagecombine.1 │ │ │ │ │ @@ -5,24 +5,24 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dimagecombine \-1 \-2 \-c \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dimagecombine │ │ │ │ │ This program is used to combine two images using a given image combiner. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-1 \-\-image1=(required, input); io" │ │ │ │ │ +.IP "\-1 \-\-image1=(input, required); io" │ │ │ │ │ input image 1 to be combined │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-2 \-\-image2=(required, input); io" │ │ │ │ │ +.IP "\-2 \-\-image2=(input, required); io" │ │ │ │ │ input image 2 to be combined │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-c \-\-combiner=(required); factory" │ │ │ │ │ combiner operation │ │ │ │ │ For supported plugins see PLUGINS:3dimage/combiner │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output image file │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-3dimagecreator.1.gz │ │ │ │ ├── mia-3dimagecreator.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dimagecreator \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dimagecreator │ │ │ │ │ This program creates a 3D image that contains an object created by one of the object creator plug-ins (creator/3dimage) │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output file for create object │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-s \-\-size=[128,128,128]" │ │ │ │ │ size of the object │ │ │ │ │ │ │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ │ input pixel type │ │ │ ├── ./usr/share/man/man1/mia-3dimagefilterstack.1.gz │ │ │ │ ├── mia-3dimagefilterstack.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dimagefilterstack \-i \-o \-t [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dimagefilterstack │ │ │ │ │ This program is used to filter and convert a consecutive numbered series gray of scale images. File names must follow the pattern 'dataXXXX.v' (X being digits), i.e. the numbering comes right before the dot. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output file name base, numbers are added accorfing to the input file pattern, and the file extension is added according to the 'type' option. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-t \-\-type=(required); set" │ │ │ │ │ output file type │ │ │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ │ .I │ │ │ │ │ @@ -283,15 +283,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(required, input, io) │ │ │ │ │ +=(input, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -597,15 +597,15 @@ │ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ ref │ │ │ │ │ -=(required, input, io) │ │ │ │ │ +=(input, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ reference image for mask region growing. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -678,15 +678,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(required, input, string) │ │ │ │ │ +=(input, required, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -704,15 +704,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(required, input, io) │ │ │ │ │ +=(input, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -731,15 +731,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B mask │ │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(required, input, io) │ │ │ │ │ +=(input, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1121,28 +1121,28 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(required, input, string) │ │ │ │ │ +=(input, required, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(required, output, io) │ │ │ │ │ +=(output, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1155,15 +1155,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(required, input, io) │ │ │ │ │ +=(input, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ ├── ./usr/share/man/man1/mia-3dimageselect.1.gz │ │ │ │ ├── mia-3dimageselect.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-3dimageselect │ │ │ │ │ This program is used to select one 3D images from a multi-image file. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input images │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-n \-\-number=0" │ │ │ │ │ image number to be selected │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-3dimagestatistics-in-mask.1.gz │ │ │ │ ├── mia-3dimagestatistics-in-mask.1 │ │ │ │ │ @@ -6,18 +6,18 @@ │ │ │ │ │ .B mia\-3dimagestatistics\-in\-mask \-i \-m [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dimagestatistics\-in\-mask │ │ │ │ │ This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-image=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-image=(input, required); io" │ │ │ │ │ input image to be analyzed │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-m \-\-mask=(required, input); io" │ │ │ │ │ +.IP "\-m \-\-mask=(input, required); io" │ │ │ │ │ mask image to use to restrict the analysis │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-s \-\-summary=(output); string" │ │ │ │ │ File to write the summary statistics to as plain text. │ │ │ │ │ │ │ │ │ │ .IP "\-H \-\-histogram=(output); string" │ │ │ │ │ File to write the histogram to │ │ │ ├── ./usr/share/man/man1/mia-3disosurface-from-volume.1.gz │ │ │ │ ├── mia-3disosurface-from-volume.1 │ │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ │ This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output mesh │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-3dlandmarks-transform.1.gz │ │ │ │ ├── mia-3dlandmarks-transform.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-3dlandmarks\-transform │ │ │ │ │ Transform the locations of the landmarks by means of a given 3D transformation. Note, landmark transformations do the inverse of an image transformation (in a manner of speaking), i.e. given a transformation V(x) in an image transformation the pixel intensity at x is set to the original intensity at V(x), while a landmark at x is moved to V(x). │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input landmark set │ │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output landmark set │ │ │ │ │ For supported file types see PLUGINS:3dlandmarklist/io │ │ │ │ │ .IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ transformation file │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz │ │ │ │ ├── mia-3dmany2one-nonrigid.1 │ │ │ │ │ @@ -1280,15 +1280,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(output, required, io) │ │ │ │ │ +=(required, output, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ ├── ./usr/share/man/man1/mia-3dmaskseeded.1.gz │ │ │ │ ├── mia-3dmaskseeded.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-3dmaskseeded │ │ │ │ │ 3D image segmentation based on region growing from a seed point. Neighboring points are added, either when their intensity is equal or higher than that of the seed point, or of the intensity is lower or equal then that of the neighoring point. After region growing is finished, this mask is used to zero out the region in the original image yielding the resulting image. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output image(s) that have been filtered │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-s \-\-seed=[0,0,0]" │ │ │ │ │ seed point │ │ │ │ │ │ │ │ │ │ .IP "\-n \-\-neighborhood=6n" │ │ │ │ │ neighborhood shape │ │ │ ├── ./usr/share/man/man1/mia-3dnonrigidreg.1.gz │ │ │ │ ├── mia-3dnonrigidreg.1 │ │ │ │ │ @@ -64,21 +64,21 @@ │ │ │ │ │ │ │ │ │ │ .IP " \-\-version" │ │ │ │ │ print the version number and exit │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-image=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-image=(required, input); io" │ │ │ │ │ test image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-r \-\-ref-image=(input, required); io" │ │ │ │ │ +.IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-image=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-image=(output, required); io" │ │ │ │ │ registered output image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-t \-\-transformation=(output); io" │ │ │ │ │ output transformation │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS Processing │ │ │ │ │ @@ -430,15 +430,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -744,15 +744,15 @@ │ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ ref │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ reference image for mask region growing. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -825,15 +825,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -851,15 +851,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -878,15 +878,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B mask │ │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1268,28 +1268,28 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(required, output, io) │ │ │ │ │ +=(output, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1302,15 +1302,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ ├── ./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz │ │ │ │ ├── mia-3dpropose-boundingbox.1 │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ .B mia\-3dpropose\-boundingbox \-i [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dpropose\-boundingbox │ │ │ │ │ This program evaluates a box that contains all the pixels of a given mask image. If the input image is not a binary image, a pre-filter must be applied that converts the imput image into a mask. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image(s) to be filtered │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ │ │ @@ -271,15 +271,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -585,15 +585,15 @@ │ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ ref │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ reference image for mask region growing. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -666,15 +666,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -692,15 +692,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -719,15 +719,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B mask │ │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1109,15 +1109,15 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ @@ -1143,15 +1143,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ ├── ./usr/share/man/man1/mia-3drigidreg.1.gz │ │ │ │ ├── mia-3drigidreg.1 │ │ │ │ │ @@ -12,15 +12,15 @@ │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-image=(required, input); io" │ │ │ │ │ test image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-r \-\-ref-image=(required, input); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-image=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-image=(output, required); io" │ │ │ │ │ registered output image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-t \-\-transformation=(output); io" │ │ │ │ │ transformation output file name │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .IP "\-c \-\-cost=ssd" │ │ │ │ │ cost function │ │ │ ├── ./usr/share/man/man1/mia-3dsegment-ahmed.1.gz │ │ │ │ ├── mia-3dsegment-ahmed.1 │ │ │ │ │ @@ -14,15 +14,15 @@ │ │ │ │ │ .UE │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ changes are: p=2, and exp │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ image to be segmented │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-c \-\-class-file=(required, output); io" │ │ │ │ │ class probability images, the image type must support multiple images and floating point values │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-b \-\-out-file=(output); io" │ │ │ │ │ Bias corrected image will be of the same type like the input image. If this parameter is not given, then the bias correction will not be applied. │ │ │ ├── ./usr/share/man/man1/mia-3dsegment-local-cmeans.1.gz │ │ │ │ ├── mia-3dsegment-local-cmeans.1 │ │ │ │ │ @@ -13,15 +13,15 @@ │ │ │ │ │ Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374. │ │ │ │ │ .UE │ │ │ │ │ .RE │ │ │ │ │ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ image to be segmented │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-o \-\-out-file=(output); io" │ │ │ │ │ class label image based on merging local labels │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-G \-\-out-global-crisp=(output); io" │ │ │ │ │ class label image based on global segmentation │ │ │ ├── ./usr/share/man/man1/mia-3dseries-track-intensity.1.gz │ │ │ │ ├── mia-3dseries-track-intensity.1 │ │ │ │ │ @@ -10,15 +10,15 @@ │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input perfusion data set │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ file name for output intensity slopes │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-3dtrackpixelmovement.1.gz │ │ │ │ ├── mia-3dtrackpixelmovement.1 │ │ │ │ │ @@ -10,21 +10,21 @@ │ │ │ │ │ id;time;x;y;z;reserved │ │ │ │ │ │ │ │ │ │ The fields 'time', 'x', 'y', and 'z' are updated, and the fields 'id' and 'reserved' are preserved, empty lines are ignored. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS │ │ │ │ │ File-IO │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input point set │ │ │ │ │ │ │ │ │ │ .IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ output point set │ │ │ │ │ │ │ │ │ │ -.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ +.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ │ transformation describing the monitored change │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .RE │ │ │ │ │ .SS │ │ │ │ │ Parameters │ │ │ │ │ .RS │ │ │ │ │ .IP "\-T \-\-time-step=1" │ │ │ ├── ./usr/share/man/man1/mia-3dtransform.1.gz │ │ │ │ ├── mia-3dtransform.1 │ │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dtransform \-i \-o \-t [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dtransform │ │ │ │ │ Transform a 3D image by applying a given 3D transformation. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ transformed image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ -.IP "\-t \-\-transformation=(input, required); io" │ │ │ │ │ +.IP "\-t \-\-transformation=(required, input); io" │ │ │ │ │ transformation file │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .IP "\-p \-\-interpolator=" │ │ │ │ │ override the interpolator provided by the transformation │ │ │ │ │ │ │ │ │ │ .IP "\-b \-\-boundary=mirror" │ │ │ │ │ override the boundary conditions provided by the transformation. This is only used if the interpolator is also overridden. │ │ │ ├── ./usr/share/man/man1/mia-3dvf2transform.1.gz │ │ │ │ ├── mia-3dvf2transform.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-3dvf2transform \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-3dvf2transform │ │ │ │ │ Creates a 3D transformation from a vector field. The input vector field is simply encapsulated into the transformation file format. The boundary conditions and the image interpolator kernel can be set at the command line. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input transformation │ │ │ │ │ For supported file types see PLUGINS:3dvf/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output vector field │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ .IP "\-k \-\-imgkernel=bspline:d=3" │ │ │ │ │ image interpolator kernel which is used when the transformation is applied to an image │ │ │ │ │ For supported plugins see PLUGINS:1d/splinekernel │ │ │ │ │ .IP "\-b \-\-imgboundary=mirror" │ │ │ │ │ Boundary condition applied when the transformation is used to transform an image │ │ │ ├── ./usr/share/man/man1/mia-cmeans.1.gz │ │ │ │ ├── mia-cmeans.1 │ │ │ │ │ @@ -8,15 +8,15 @@ │ │ │ │ │ .B mia\-cmeans │ │ │ │ │ This Program reads a histogram from stdin and evaluates a cmeans classification of the intensity values into the given number of classes. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ input file name containing the histogram │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output file name to store probabilities │ │ │ │ │ │ │ │ │ │ .IP "\-n \-\-nclasses=3" │ │ │ │ │ number of classes to partition into │ │ │ │ │ │ │ │ │ │ .IP "\-m \-\-max-iter=100" │ │ │ │ │ maximum number of iterations │ │ │ ├── ./usr/share/man/man1/mia-filenumberpattern.1.gz │ │ │ │ ├── mia-filenumberpattern.1 │ │ │ │ │ @@ -5,15 +5,15 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-filenumberpattern \-i [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-filenumberpattern │ │ │ │ │ This program is used to extract a extract the number pattern for file012312.ext type file names. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input image example name │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-labelsort.1.gz │ │ │ │ ├── mia-labelsort.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-labelsort \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-labelsort │ │ │ │ │ This program is used create a mapping based on a histogram that puts the intensities with high values at the beginning of the histogram. The main use case will be to sort labels of connected components in out-of-core image processing. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input file name containing the histogram │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output file name to store probabilities │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-mesh-deformable-model.1.gz │ │ │ │ ├── mia-mesh-deformable-model.1 │ │ │ │ │ @@ -6,21 +6,21 @@ │ │ │ │ │ .B mia\-mesh\-deformable\-model \-i \-o \-r [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-mesh\-deformable\-model │ │ │ │ │ This program runs a deformable model to adapt a mesh to an iso-value within a given image. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File I/O │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input mesh to be adapted │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ -.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ output mesh that has been deformed │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ -.IP "\-r \-\-ref-file=(input, required); io" │ │ │ │ │ +.IP "\-r \-\-ref-file=(required, input); io" │ │ │ │ │ reference image │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ │ │ @@ -301,15 +301,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B combiner │ │ │ │ │ Combine two images with the given combiner operator. if 'reverse' is set to false, the first operator is the image passed through the filter pipeline, and the second image is loaded from the file given with the 'image' parameter the moment the filter is run., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ image │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second image that is needed in the combiner. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -615,15 +615,15 @@ │ │ │ │ │ lower threshold for mask growing. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ ref │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ reference image for mask region growing. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ @@ -696,15 +696,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelmap │ │ │ │ │ Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ map │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ Label mapping file. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B labelscale │ │ │ │ │ @@ -722,15 +722,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B load │ │ │ │ │ Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the input file to load from.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -749,15 +749,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B mask │ │ │ │ │ Mask an image, one image is taken from the parameters list and the other from the normal filter input. Both images must be of the same dimensions and one must be binary. The attributes of the image coming through the filter pipeline are preserved. The output pixel type corresponds to the input image that is not binary., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ input │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ second input image file name. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1139,28 +1139,28 @@ │ │ │ │ │ For supported plug-ins see PLUGINS:3dimage/shape │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ seed │ │ │ │ │ -=(input, required, string) │ │ │ │ │ +=(required, input, string) │ │ │ │ │ .RS 2 │ │ │ │ │ seed input image containing the lables for the initial regions. │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ .B tee │ │ │ │ │ Save the input image to a file and also pass it through to the next filter, supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(required, output, io) │ │ │ │ │ +=(output, required, io) │ │ │ │ │ .RS 2 │ │ │ │ │ name of the output file to save the image too.. │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .TP 10 │ │ │ │ │ @@ -1173,15 +1173,15 @@ │ │ │ │ │ .TP 10 │ │ │ │ │ .B transform │ │ │ │ │ Transform the input image with the given transformation., supported parameters are: │ │ │ │ │ .P │ │ │ │ │ .RS 14 │ │ │ │ │ .I │ │ │ │ │ file │ │ │ │ │ -=(input, required, io) │ │ │ │ │ +=(required, input, io) │ │ │ │ │ .RS 2 │ │ │ │ │ Name of the file containing the transformation.. │ │ │ │ │ For supported file types see PLUGINS:3dtransform/io │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .RE │ │ │ │ │ .RS 14 │ │ │ ├── ./usr/share/man/man1/mia-mesh-to-maskimage.1.gz │ │ │ │ ├── mia-mesh-to-maskimage.1 │ │ │ │ │ @@ -6,15 +6,15 @@ │ │ │ │ │ .B mia\-mesh\-to\-maskimage \-i \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-mesh\-to\-maskimage │ │ │ │ │ This program converts a 3D mesh into a binary mask comprising the mesh surface. The output image size is either given on the command line or deducted from the mesh dimensions. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File I/O │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ input mesh to be adapted │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output image containing the binary mask │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz │ │ │ │ ├── mia-meshdistance-to-stackmask.1 │ │ │ │ │ @@ -5,21 +5,21 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-meshdistance\-to\-stackmask \-i \-r \-o [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-meshdistance\-to\-stackmask │ │ │ │ │ This program takes a binary masks and a triangular mesh as input and evaluates the distance of the mesh vertices to the binary maskand stores the result in a new mesh. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-mesh=(required, input); io" │ │ │ │ │ +.IP "\-i \-\-in-mesh=(input, required); io" │ │ │ │ │ input mesh │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ -.IP "\-r \-\-ref-mask=(required, input); io" │ │ │ │ │ +.IP "\-r \-\-ref-mask=(input, required); io" │ │ │ │ │ reference binary mask │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ -.IP "\-o \-\-out-mesh=(required, output); io" │ │ │ │ │ +.IP "\-o \-\-out-mesh=(output, required); io" │ │ │ │ │ output mesh │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ │ │ .RS │ │ │ │ │ .IP "\-V \-\-verbose=warning" │ │ │ │ │ verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are: │ │ │ ├── ./usr/share/man/man1/mia-meshfilter.1.gz │ │ │ │ ├── mia-meshfilter.1 │ │ │ │ │ @@ -7,15 +7,15 @@ │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-meshfilter │ │ │ │ │ This program runs a series filters on a given input mesh. The filters are given as extra parameters on the command line and are run in the order in which they are given. To obtain a list of available filters you may run │ │ │ │ │ 'mia-plugin-help mesh/filter' │ │ │ │ │ from the command line │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); io" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); io" │ │ │ │ │ input mesh to be filtered │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ .IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output mesh that have been filtered │ │ │ │ │ For supported file types see PLUGINS:mesh/io │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info │ │ │ ├── ./usr/share/man/man1/mia-raw2image.1.gz │ │ │ │ ├── mia-raw2image.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-raw2image \-i \-o \-s [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-raw2image │ │ │ │ │ This program is used to convert raw data to a 2D file format. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input file name │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output file name │ │ │ │ │ For supported file types see PLUGINS:2dimage/io │ │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ │ input pixel type │ │ │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ │ .I │ │ │ ├── ./usr/share/man/man1/mia-raw2volume.1.gz │ │ │ │ ├── mia-raw2volume.1 │ │ │ │ │ @@ -5,18 +5,18 @@ │ │ │ │ │ .SH SYNOPSIS │ │ │ │ │ .B mia\-raw2volume \-i \-o \-s [options] │ │ │ │ │ .SH DESCRIPTION │ │ │ │ │ .B mia\-raw2volume │ │ │ │ │ This program is used to convert raw data into 3D images with apropriate metadata. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .RS │ │ │ │ │ -.IP "\-i \-\-in-file=(input, required); string" │ │ │ │ │ +.IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input file name │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); io" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); io" │ │ │ │ │ output file name │ │ │ │ │ For supported file types see PLUGINS:3dimage/io │ │ │ │ │ .IP "\-r \-\-repn=ubyte" │ │ │ │ │ input pixel type │ │ │ │ │ │ │ │ │ │ .RS 10 │ │ │ │ │ .I │ │ │ ├── ./usr/share/man/man1/mia-wavelettrans.1.gz │ │ │ │ ├── mia-wavelettrans.1 │ │ │ │ │ @@ -9,15 +9,15 @@ │ │ │ │ │ This program runs the a column-wise discret wavelet forward transform on the data given by an input text file. │ │ │ │ │ .SH OPTIONS │ │ │ │ │ .SS File-IO │ │ │ │ │ .RS │ │ │ │ │ .IP "\-i \-\-in-file=(required, input); string" │ │ │ │ │ input data set │ │ │ │ │ │ │ │ │ │ -.IP "\-o \-\-out-file=(output, required); string" │ │ │ │ │ +.IP "\-o \-\-out-file=(required, output); string" │ │ │ │ │ output data set │ │ │ │ │ │ │ │ │ │ .IP "\-s \-\-save-wave=(output); string" │ │ │ │ │ base name of the output files that will store the wavelet coefficients as matrix │ │ │ │ │ │ │ │ │ │ .RE │ │ │ │ │ .SS Help & Info