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  0 root         (0) root         (0)      850 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-plugin-help.1.gz\n--rw-r--r--   0 root         (0) root         (0)     1741 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-raw2image.1.gz\n--rw-r--r--   0 root         (0) root         (0)     1806 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-raw2volume.1.gz\n+-rw-r--r--   0 root         (0) root         (0)     1737 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-raw2image.1.gz\n+-rw-r--r--   0 root         (0) root         (0)     1801 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-raw2volume.1.gz\n -rw-r--r--   0 root         (0) root         (0)     1086 2021-01-11 21:49:29.000000 ./usr/share/man/man1/mia-wavelettrans.1.gz\n"}, {"source1": "./usr/share/man/man1/mia-2davgmasked.1.gz", "source2": "./usr/share/man/man1/mia-2davgmasked.1.gz", "unified_diff": null, "details": [{"source1": "mia-2davgmasked.1", "source2": "mia-2davgmasked.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-2davgmasked \\-i <in\\-files> \\-m <mask\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2davgmasked\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-files=(input, required); io\"\n+.IP \"\\-i \\-\\-in-files=(required, input); io\"\n input image(s)\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-m \\-\\-mask-file=(input, required); io\"\n+.IP \"\\-m \\-\\-mask-file=(required, input); io\"\n mask image, must be of type byte\n  For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dbinarycombine.1.gz", "source2": "./usr/share/man/man1/mia-2dbinarycombine.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dbinarycombine.1", "source2": "mia-2dbinarycombine.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B  mia\\-2dbinarycombine \\-1 <file1> \\-2 <file2> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dbinarycombine\n This program is used to combine two binary images by some kind of operation.\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-file1=(input, required); io\"\n+.IP \"\\-1 \\-\\-file1=(required, input); io\"\n input mask image 1\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-2 \\-\\-file2=(input, required); io\"\n+.IP \"\\-2 \\-\\-file2=(required, input); io\"\n input mask image 2\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output mask image\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-p \\-\\-operation=nor\"\n Operation to be applied\n \n .RS 10\n .I\n"}]}, {"source1": "./usr/share/man/man1/mia-2ddistance.1.gz", "source2": "./usr/share/man/man1/mia-2ddistance.1.gz", "unified_diff": null, "details": [{"source1": "mia-2ddistance.1", "source2": "mia-2ddistance.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B  mia\\-2ddistance \\-i <in\\-file> \\-d <distance\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2ddistance\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-d \\-\\-distance-file=(required, input); io\"\n+.IP \"\\-d \\-\\-distance-file=(input, required); io\"\n distance field image (floating point)\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output file, '\\-': write to stdout\n \n .IP \"\\-s \\-\\-scale=1\"\n distance scaling factor\n \n .IP \"\\-m \\-\\-method=avg\"\n distance measuring method\n"}]}, {"source1": "./usr/share/man/man1/mia-2deval-transformquantity.1.gz", "source2": "./usr/share/man/man1/mia-2deval-transformquantity.1.gz", "unified_diff": null, "details": [{"source1": "mia-2deval-transformquantity.1", "source2": "mia-2deval-transformquantity.1", "unified_diff": "@@ -24,21 +24,21 @@\n }\n \n 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.\n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n 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.\n \n .IP \"\\-o \\-\\-out-file=(required, output); string\"\n output strains file, for a format description see above.\n \n-.IP \"\\-t \\-\\-transformation=(input, required); io\"\n+.IP \"\\-t \\-\\-transformation=(required, input); io\"\n transformation of which the quantity will be evaluated.\n  For supported file types see PLUGINS:2dtransform/io\n .RE\n .SS \n Parameters\n .RS\n .IP \"\\-q \\-\\-quantity=strain\"\n"}]}, {"source1": "./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz", "source2": "./usr/share/man/man1/mia-2dfluid-syn-registration.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dfluid-syn-registration.1", "source2": "mia-2dfluid-syn-registration.1", "unified_diff": "@@ -64,18 +64,18 @@\n \n .IP \"   \\-\\-version\"\n print the version number and exit\n \n .RE\n .SS IO\n .RS\n-.IP \"\\-i \\-\\-in-image=(input, required); io\"\n+.IP \"\\-i \\-\\-in-image=(required, input); io\"\n test image\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-r \\-\\-ref-image=(input, required); io\"\n+.IP \"\\-r \\-\\-ref-image=(required, input); io\"\n reference image\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-transform=(required, output); io\"\n output transformation\n  For supported file types see PLUGINS:2dtransform/io\n .IP \"\\-O \\-\\-inverse-transform=(required, output); io\"\n inverse output transformation\n"}]}, {"source1": "./usr/share/man/man1/mia-2dforce.1.gz", "source2": "./usr/share/man/man1/mia-2dforce.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dforce.1", "source2": "mia-2dforce.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B  mia\\-2dforce \\-i <src\\-file> \\-r <ref\\-file> \\-o <out\\-file> \\-c <cost> [options]\n .SH DESCRIPTION\n .B mia\\-2dforce\n This image evaluate the force field between two images based on a given cost function.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-src-file=(required, input); io\"\n+.IP \"\\-i \\-\\-src-file=(input, required); io\"\n input image\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-r \\-\\-ref-file=(required, input); io\"\n+.IP \"\\-r \\-\\-ref-file=(input, required); io\"\n reference image\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output force norm image\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-c \\-\\-cost=(required); string\"\n cost function to use\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dfuzzysegment.1.gz", "source2": "./usr/share/man/man1/mia-2dfuzzysegment.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dfuzzysegment.1", "source2": "mia-2dfuzzysegment.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B  mia\\-2dfuzzysegment \\-i <in\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dfuzzysegment\n 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\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be segmenetd\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-c \\-\\-cls-file=(output); io\"\n output class probability images (floating point values and multi\\-image)\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-b0-file=(output); io\"\n image corrected for intensity non\\-uniformity\n"}]}, {"source1": "./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz", "source2": "./usr/share/man/man1/mia-2dgrayimage-combine-to-rgb.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dgrayimage-combine-to-rgb.1", "source2": "mia-2dgrayimage-combine-to-rgb.1", "unified_diff": "@@ -14,15 +14,15 @@\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-g \\-\\-green=(input); io\"\n input image for green channel\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-r \\-\\-red=(input); io\"\n input image for red channel\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n combined output image\n  For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagecombine-dice.1.gz", "source2": "./usr/share/man/man1/mia-2dimagecombine-dice.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagecombine-dice.1", "source2": "mia-2dimagecombine-dice.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-2dimagecombine\\-dice \\-1 <in\\-file\\-1> \\-2 <in\\-file\\-2> [options]\n .SH DESCRIPTION\n .B mia\\-2dimagecombine\\-dice\n This program evaluate the dice index of two binary masks given as binary images. The result is written to stdout.\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-in-file-1=(input, required); io\"\n+.IP \"\\-1 \\-\\-in-file-1=(required, input); io\"\n input image 1\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-2 \\-\\-in-file-2=(input, required); io\"\n+.IP \"\\-2 \\-\\-in-file-2=(required, input); io\"\n input image 2\n  For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagecombiner.1.gz", "source2": "./usr/share/man/man1/mia-2dimagecombiner.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagecombiner.1", "source2": "mia-2dimagecombiner.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B  mia\\-2dimagecombiner \\-1 <in\\-file\\-1> \\-2 <in\\-file\\-2> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dimagecombiner\n Combine two image by a given operation.\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-in-file-1=(input, required); io\"\n+.IP \"\\-1 \\-\\-in-file-1=(required, input); io\"\n first input image to be combined\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-2 \\-\\-in-file-2=(input, required); io\"\n+.IP \"\\-2 \\-\\-in-file-2=(required, input); io\"\n second input image to be combined\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output image(s) that have been filtered\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-p \\-\\-operation=absdiff\"\n operation to be applied\n  For supported plugins see PLUGINS:2dimage/combiner\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagefilter.1.gz", "source2": "./usr/share/man/man1/mia-2dimagefilter.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagefilter.1", "source2": "mia-2dimagefilter.1", "unified_diff": "@@ -10,15 +10,15 @@\n    'mia-plugin-help filter/2dimage'\n from the command line\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image(s) that have been filtered\n  For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n@@ -826,15 +826,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -862,15 +862,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -1181,15 +1181,15 @@\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagefilterstack.1.gz", "source2": "./usr/share/man/man1/mia-2dimagefilterstack.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagefilterstack.1", "source2": "mia-2dimagefilterstack.1", "unified_diff": "@@ -6,18 +6,18 @@\n .B  mia\\-2dimagefilterstack \\-i <in\\-file> \\-o <out\\-file> [options] <PLUGINS:2dimage/filter>\n .SH DESCRIPTION\n .B mia\\-2dimagefilterstack\n 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.\n .SH OPTIONS\n .SS File IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name base, the file type is set  accurding to the 'type' option\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-t \\-\\-type=\"\n output file type, if not given the input type is used\n \n .RS 10\n .I\n@@ -388,15 +388,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -732,15 +732,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -758,15 +758,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -797,15 +797,15 @@\n .RE\n \n .RE\n .RE\n .RS 14\n .I\n input\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -820,25 +820,25 @@\n .TP 10\n .B maxflow\n This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: \n .P\n .RS 14\n .I\n sink-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the sink.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n .I\n source-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the source.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -866,15 +866,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -902,15 +902,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -1027,15 +1027,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n seed image (bit valued).\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1208,28 +1208,28 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1293,15 +1293,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:2dtransform/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimageselect.1.gz", "source2": "./usr/share/man/man1/mia-2dimageselect.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimageselect.1", "source2": "mia-2dimageselect.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dimageselect \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dimageselect\n This program is used to select one 2D images from a multi-image file.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input images\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-n \\-\\-number=0\"\n image number to be selected\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz", "source2": "./usr/share/man/man1/mia-2dimageseries-maximum-intensity-projection.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimageseries-maximum-intensity-projection.1", "source2": "mia-2dimageseries-maximum-intensity-projection.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dimageseries\\-maximum\\-intensity\\-projection \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dimageseries\\-maximum\\-intensity\\-projection\n This program is used to evaluate the per-pixel maximum intensity of an image series.\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output image\n  For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz", "source2": "./usr/share/man/man1/mia-2dimagestack-cmeans.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dimagestack-cmeans.1", "source2": "mia-2dimagestack-cmeans.1", "unified_diff": "@@ -6,18 +6,18 @@\n .B  mia\\-2dimagestack\\-cmeans \\-i <in\\-file> \\-o <out\\-probmap> [options]\n .SH DESCRIPTION\n .B mia\\-2dimagestack\\-cmeans\n 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\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-probmap=(required, output); string\"\n+.IP \"\\-o \\-\\-out-probmap=(output, required); string\"\n Save probability map to this file\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dlerp.1.gz", "source2": "./usr/share/man/man1/mia-2dlerp.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dlerp.1", "source2": "mia-2dlerp.1", "unified_diff": "@@ -11,15 +11,15 @@\n .RS\n .IP \"\\-1 \\-\\-first=(required, input); io\"\n first input image \n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-2 \\-\\-second=(required, input); io\"\n second input image \n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output vector field\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-p \\-\\-positions=(required); vfloat\"\n image series positions (first, target, second)\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmultiimageregistration.1.gz", "source2": "./usr/share/man/man1/mia-2dmultiimageregistration.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmultiimageregistration.1", "source2": "mia-2dmultiimageregistration.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dmultiimageregistration \\-o <out\\-transform> [options] <PLUGINS:2dimage/fullcost>\n .SH DESCRIPTION\n .B mia\\-2dmultiimageregistration\n 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)\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-transform=(output, required); io\"\n+.IP \"\\-o \\-\\-out-transform=(required, output); io\"\n output transformation\n  For supported file types see PLUGINS:2dtransform/io\n .IP \"\\-l \\-\\-levels=3\"\n multi\\-resolution levels\n \n .IP \"\\-O \\-\\-optimizer=gsl:opt=gd,step=0.1\"\n Optimizer used for minimization\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmultiimageto3d.1.gz", "source2": "./usr/share/man/man1/mia-2dmultiimageto3d.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmultiimageto3d.1", "source2": "mia-2dmultiimageto3d.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dmultiimageto3d \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dmultiimageto3d\n This program is used to convert a 2D multi-image file to a 3D image.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input images\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmultiimagevar.1.gz", "source2": "./usr/share/man/man1/mia-2dmultiimagevar.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmultiimagevar.1", "source2": "mia-2dmultiimagevar.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dmultiimagevar \\-o <out\\-file> [options] <PLUGINS:2dimage/io>\n .SH DESCRIPTION\n .B mia\\-2dmultiimagevar\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image \n  For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz", "source2": "./usr/share/man/man1/mia-2dmyocard-icaseries.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyocard-icaseries.1", "source2": "mia-2dmyocard-icaseries.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B  mia\\-2dmyocard\\-icaseries \\-i <in\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dmyocard\\-icaseries\n 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.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-r \\-\\-references=(output); string\"\n File name base for the reference images. Image type and numbering scheme are taken from the input images.\n \n .IP \"\\-c \\-\\-save-cropped=(output); string\"\n save cropped set of the original set to this file, the image files will use the stem of the name as file name base\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyocard-segment.1.gz", "source2": "./usr/share/man/man1/mia-2dmyocard-segment.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyocard-segment.1", "source2": "mia-2dmyocard-segment.1", "unified_diff": "@@ -9,15 +9,15 @@\n This program is work in progress\n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output myocardial mask\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-f \\-\\-save-features=(output); string\"\n save ICA features to files with this name base\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-full.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-full.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-full.1", "source2": "mia-2dmyoica-full.1", "unified_diff": "@@ -17,15 +17,15 @@\n  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.\n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=\"\n 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.\n \n .IP \"   \\-\\-save-cropped=(output); string\"\n save cropped set to this file, the image files will use the stem of the name as file name base\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-nonrigid-parallel.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-nonrigid-parallel.1", "source2": "mia-2dmyoica-nonrigid-parallel.1", "unified_diff": "@@ -17,15 +17,15 @@\n This version of the program runs all registrations in parallel.\n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n 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.\n \n .IP \"   \\-\\-save-cropped=(output); string\"\n save cropped set to this file, the image files will use the stem of the name as file name base\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-nonrigid.1", "source2": "mia-2dmyoica-nonrigid.1", "unified_diff": "@@ -16,15 +16,15 @@\n \n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered fiels\n \n .IP \"   \\-\\-save-cropped=\"\n save cropped set to this file\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoica-nonrigid2.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoica-nonrigid2.1", "source2": "mia-2dmyoica-nonrigid2.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dmyoica\\-nonrigid2\n 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\n Special note to this implemnentation: the registration is always run from the original images to avoid the accumulation of interpolation errors.\n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered fiels\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoicapgt.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoicapgt.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoicapgt.1", "source2": "mia-2dmyoicapgt.1", "unified_diff": "@@ -43,15 +43,15 @@\n \n .IP \"\\-T \\-\\-rho-thresh=0.85\"\n correlation threshold for neighborhood analysis\n \n .RE\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n .IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=\"\n 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.\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyomilles.1.gz", "source2": "./usr/share/man/man1/mia-2dmyomilles.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyomilles.1", "source2": "mia-2dmyomilles.1", "unified_diff": "@@ -18,15 +18,15 @@\n \n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=\"\n file name base for registered files\n \n .IP \"   \\-\\-save-references=\"\n save synthetic reference images to this file base\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoperiodic-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoperiodic-nonrigid.1", "source2": "mia-2dmyoperiodic-nonrigid.1", "unified_diff": "@@ -14,18 +14,18 @@\n .UE\n .RE\n \n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered fiels\n \n .IP \"   \\-\\-save-references\"\n Save synthetic references to files refXXXX.v\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyopgt-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyopgt-nonrigid.1", "source2": "mia-2dmyopgt-nonrigid.1", "unified_diff": "@@ -18,15 +18,15 @@\n .SH OPTIONS\n .SS \n File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"\\-r \\-\\-registered=reg\"\n file name base for registered files, the image file type is the same as given in the input data set\n \n .RE\n .SS \n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoserial-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoserial-nonrigid.1", "source2": "mia-2dmyoserial-nonrigid.1", "unified_diff": "@@ -17,15 +17,15 @@\n .SH OPTIONS\n .SS \n File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output perfusion data set\n \n .IP \"\\-R \\-\\-registered=reg\"\n file name base for registered fiels\n \n .RE\n .SS \n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoseries-compdice.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoseries-compdice.1", "source2": "mia-2dmyoseries-compdice.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-2dmyoseries\\-compdice \\-1 <first> \\-2 <second> [options]\n .SH DESCRIPTION\n .B mia\\-2dmyoseries\\-compdice\n This program is used to evaluate the per-frame dice index of segmented regions of two image series\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-first=(required, input); string\"\n+.IP \"\\-1 \\-\\-first=(input, required); string\"\n first segmentation set\n \n-.IP \"\\-2 \\-\\-second=(required, input); string\"\n+.IP \"\\-2 \\-\\-second=(input, required); string\"\n second segmentation set\n \n .IP \"\\-k \\-\\-skip=2\"\n images to skip atthe begin of the series\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-2dmyoset-all2one-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dmyoset-all2one-nonrigid.1", "source2": "mia-2dmyoset-all2one-nonrigid.1", "unified_diff": "@@ -10,15 +10,15 @@\n .SH OPTIONS\n .SS \n File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input perfusion data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output perfusion data set\n \n .IP \"   \\-\\-out-filebase=reg\"\n file name basae for registered files, file type is deducted from the image file type in the input data set.\n \n .RE\n .SS \n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegcompare.1.gz", "source2": "./usr/share/man/man1/mia-2dsegcompare.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegcompare.1", "source2": "mia-2dsegcompare.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-2dsegcompare \\-i <in\\-file> \\-r <ref\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dsegcompare\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-r \\-\\-ref-file=(required, input); string\"\n+.IP \"\\-r \\-\\-ref-file=(input, required); string\"\n reference  segmentation set\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-ahmed.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-ahmed.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-ahmed.1", "source2": "mia-2dsegment-ahmed.1", "unified_diff": "@@ -13,15 +13,15 @@\n 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,\n .UE\n .RE\n \n  changes are: p=2, and exp\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n image to be segmented\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(output, required); io\"\n class probability images, the image type must support multiple images and floating point values\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-a \\-\\-no-of-classes=3\"\n number of classes\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-fuzzyw.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-fuzzyw.1", "source2": "mia-2dsegment-fuzzyw.1", "unified_diff": "@@ -852,15 +852,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -888,15 +888,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -1207,15 +1207,15 @@\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-local-cmeans.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-local-cmeans.1", "source2": "mia-2dsegment-local-cmeans.1", "unified_diff": "@@ -13,15 +13,15 @@\n Dunmore CJ, Wollny G, Skinner MM. (2018) MIA-Clustering: a novel method for segmentation of paleontological material. PeerJ 6:e4374.\n .UE\n .RE\n \n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n image to be segmented\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(output); io\"\n class label image based on merging local labels\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-G \\-\\-out-global-crisp=(output); io\"\n class label image based on global segmentation\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-local-kmeans.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-local-kmeans.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-local-kmeans.1", "source2": "mia-2dsegment-local-kmeans.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B  mia\\-2dsegment\\-local\\-kmeans \\-i <in\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dsegment\\-local\\-kmeans\n 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.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n image to be segmented\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(output); io\"\n class label image based on merging local labels\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-O \\-\\-out-file2=(output); io\"\n class label image based on classifying by using the interpolated class centers \n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz", "source2": "./usr/share/man/man1/mia-2dsegment-per-pixel-kmeans.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegment-per-pixel-kmeans.1", "source2": "mia-2dsegment-per-pixel-kmeans.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B  mia\\-2dsegment\\-per\\-pixel\\-kmeans \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dsegment\\-per\\-pixel\\-kmeans\n 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.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n image to be segmented\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-out-file=(output, required); io\"\n class label image based on merging local labels\n  For supported file types see PLUGINS:2dimage/io\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegmentcropbox.1.gz", "source2": "./usr/share/man/man1/mia-2dsegmentcropbox.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegmentcropbox.1", "source2": "mia-2dsegmentcropbox.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dsegmentcropbox \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dsegmentcropbox\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n .IP \"\\-p \\-\\-override-imagepath\"\n Instead of using the path of the image files as given in the segmentation set, assume the files are located in the current directory\n \n .IP \"\\-o \\-\\-out-file=(required, output); string\"\n output segmentation set\n"}]}, {"source1": "./usr/share/man/man1/mia-2dsegshiftperslice.1.gz", "source2": "./usr/share/man/man1/mia-2dsegshiftperslice.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dsegshiftperslice.1", "source2": "mia-2dsegshiftperslice.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dsegshiftperslice\n 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. \n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output segmentation set\n \n .IP \"\\-g \\-\\-image-file=crop\"\n output image filename base\n \n .IP \"\\-S \\-\\-shift=(required); string\"\n shift of segmentation \\- base name \n"}]}, {"source1": "./usr/share/man/man1/mia-2dseries-mincorr.1.gz", "source2": "./usr/share/man/man1/mia-2dseries-mincorr.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseries-mincorr.1", "source2": "mia-2dseries-mincorr.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dseries\\-mincorr\n Given a set of images of temporal sucession, this program evaluates the minimal correlation of the time-intensity curve between neighboring pixels.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-set=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-set=(output, required); io\"\n+.IP \"\\-o \\-\\-out-set=(required, output); io\"\n output image of minimal correlation\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=2\"\n skip images at beginning of series\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseries2dordermedian.1.gz", "source2": "./usr/share/man/man1/mia-2dseries2dordermedian.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseries2dordermedian.1", "source2": "mia-2dseries2dordermedian.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dseries2dordermedian \\-i <in\\-file> \\-o <out\\-file> [options] <PLUGINS:2dimage/filter>\n .SH DESCRIPTION\n .B mia\\-2dseries2dordermedian\n 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).\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n .IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image name\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n Skip files at the beginning\n@@ -364,15 +364,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -708,15 +708,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -734,15 +734,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -773,15 +773,15 @@\n .RE\n \n .RE\n .RE\n .RS 14\n .I\n input\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -796,25 +796,25 @@\n .TP 10\n .B maxflow\n This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: \n .P\n .RS 14\n .I\n sink-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the sink.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n .I\n source-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the source.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1003,15 +1003,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n seed image (bit valued).\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1184,15 +1184,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n@@ -1269,15 +1269,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:2dtransform/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriescorr.1.gz", "source2": "./usr/share/man/man1/mia-2dseriescorr.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriescorr.1", "source2": "mia-2dseriescorr.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dseriescorr \\-i <in\\-base> \\-o <outname> [options]\n .SH DESCRIPTION\n .B mia\\-2dseriescorr\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-base=(input, required); io\"\n+.IP \"\\-i \\-\\-in-base=(required, input); io\"\n input file name base\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-o \\-\\-outname=(required, output); io\"\n output file name to save the avarage per\\-pixel correlation\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-z \\-\\-horizontal=(output); io\"\n horiZontal correlation output file name\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriesgradMAD.1.gz", "source2": "./usr/share/man/man1/mia-2dseriesgradMAD.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriesgradMAD.1", "source2": "mia-2dseriesgradMAD.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dseriesgradMAD\n 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).\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n Skip files at the beginning\n \n .IP \"\\-e \\-\\-enlarge-boundary=5\"\n Enlarge cropbox by number of pixels\n@@ -833,15 +833,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -869,15 +869,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -1188,15 +1188,15 @@\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriesgradvariation.1.gz", "source2": "./usr/share/man/man1/mia-2dseriesgradvariation.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriesgradvariation.1", "source2": "mia-2dseriesgradvariation.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-2dseriesgradvariation \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dseriesgradvariation\n 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. \n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n Skip files at the beginning\n \n .IP \"\\-e \\-\\-enlarge-boundary=5\"\n Enlarge cropbox by number of pixels\n"}]}, {"source1": "./usr/share/man/man1/mia-2dserieshausdorff.1.gz", "source2": "./usr/share/man/man1/mia-2dserieshausdorff.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dserieshausdorff.1", "source2": "mia-2dserieshausdorff.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-2dserieshausdorff \\-i <in\\-file> \\-r <ref\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dserieshausdorff\n Get the per-slice Hausdorff distance of a segmentation with respect to a given reference segmentation set.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input segmentation set\n \n-.IP \"\\-r \\-\\-ref-file=(required, input); string\"\n+.IP \"\\-r \\-\\-ref-file=(input, required); string\"\n reference segmentation set\n \n .IP \"\\-k \\-\\-skip=0\"\n skip images at the beginning\n \n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz", "source2": "./usr/share/man/man1/mia-2dseriessmoothgradMAD.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dseriessmoothgradMAD.1", "source2": "mia-2dseriessmoothgradMAD.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-2dseriessmoothgradMAD \\-i <in\\-file> \\-o <out\\-file> [options] <PLUGINS:2dimage/filter>\n .SH DESCRIPTION\n .B mia\\-2dseriessmoothgradMAD\n 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)\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input segmentation set\n \n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-k \\-\\-skip=0\"\n Skip files at the beginning\n@@ -358,15 +358,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -702,15 +702,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -728,15 +728,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -767,15 +767,15 @@\n .RE\n \n .RE\n .RE\n .RS 14\n .I\n input\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -790,25 +790,25 @@\n .TP 10\n .B maxflow\n This filter implements the uses the max-flow min-cut algorithmfor image segmentation, supported parameters are: \n .P\n .RS 14\n .I\n sink-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the sink.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n .I\n source-flow\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Image of float type to define the per\\-pixel flow to the source.\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -997,15 +997,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n seed image (bit valued).\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1178,15 +1178,15 @@\n For supported plug-ins see PLUGINS:2dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n@@ -1263,15 +1263,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:2dtransform/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dstackfilter.1.gz", "source2": "./usr/share/man/man1/mia-2dstackfilter.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dstackfilter.1", "source2": "mia-2dstackfilter.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dstackfilter\n 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.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n 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\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-t \\-\\-type=(required); set\"\n output file type\n \n .RS 10\n .I\n@@ -856,15 +856,15 @@\n Intensity thresholding parameter: Pixels with intensities below this threshold will be set to zero, and also not used when evaluating mean and variation.\n \n .RE\n .RE\n .RS 14\n .I\n varfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the variation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -892,15 +892,15 @@\n .TP 10\n .B medianmad\n 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: \n .P\n .RS 14\n .I\n madfile\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the median absolute deviation image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -1211,15 +1211,15 @@\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(output, required, io)\n+=(required, output, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:2dimage/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-2dtransform.1.gz", "source2": "./usr/share/man/man1/mia-2dtransform.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dtransform.1", "source2": "mia-2dtransform.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-2dtransform\n This program is used to deform a 2D image using a given transformation.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output image\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-t \\-\\-transformation=(input, required); io\"\n transformation file name\n  For supported file types see PLUGINS:2dtransform/io\n .IP \"\\-p \\-\\-interpolator=\"\n override the interpolator provided by the transformation\n"}]}, {"source1": "./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz", "source2": "./usr/share/man/man1/mia-2dtransformation-to-strain.1.gz", "unified_diff": null, "details": [{"source1": "mia-2dtransformation-to-strain.1", "source2": "mia-2dtransformation-to-strain.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-2dtransformation\\-to\\-strain \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-2dtransformation\\-to\\-strain\n Evaluate the Green strain tensor corresponding to a given 2D transformation for each grid point.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input transformation\n  For supported file types see PLUGINS:2dtransform/io\n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output Green's strain tensor\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dbrainextractT1.1.gz", "source2": "./usr/share/man/man1/mia-3dbrainextractT1.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dbrainextractT1.1", "source2": "mia-3dbrainextractT1.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-3dbrainextractT1\n 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.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image(s) to be segmented\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n brain mask\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-n \\-\\-no-of-classes=3\"\n number of classes\n \n .IP \"\\-w \\-\\-wm-class=2\"\n index of white matter\n"}]}, {"source1": "./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz", "source2": "./usr/share/man/man1/mia-3dcombine-mr-segmentations.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dcombine-mr-segmentations.1", "source2": "mia-3dcombine-mr-segmentations.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-3dcombine\\-mr\\-segmentations \\-i <in\\-file> \\-o <out\\-file> [options] <PLUGINS:3dimage/io>\n .SH DESCRIPTION\n .B mia\\-3dcombine\\-mr\\-segmentations\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input probability images. The number of mask images must correspond to the number of probability images given here.\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n output image that contains the labeling.\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz", "source2": "./usr/share/man/man1/mia-3dcost-translatedgrad.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dcost-translatedgrad.1", "source2": "mia-3dcost-translatedgrad.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-3dcost\\-translatedgrad \\-i <in\\-file> \\-r <ref\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-3dcost\\-translatedgrad\n Evaluate the cost gradient between two images and evaluate the transformation related gradient for it based on the given transformation model.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image \n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-r \\-\\-ref-file=(required, input); io\"\n+.IP \"\\-r \\-\\-ref-file=(input, required); io\"\n reference image \n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-file=(output, required); io\"\n output vector field \n  For supported file types see PLUGINS:3dtransform/io\n .IP \"\\-g \\-\\-gradimg-file=(output); io\"\n norm image of the spline transformed gradient\n"}]}, {"source1": "./usr/share/man/man1/mia-3dcost.1.gz", "source2": "./usr/share/man/man1/mia-3dcost.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dcost.1", "source2": "mia-3dcost.1", "unified_diff": "@@ -403,15 +403,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -717,15 +717,15 @@\n lower threshold for mask growing.\n \n .RE\n .RE\n .RS 14\n .I\n ref\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n reference image for mask region growing.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -798,15 +798,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -824,15 +824,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -851,15 +851,15 @@\n .TP 10\n .B mask\n 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: \n .P\n .RS 14\n .I\n input\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1241,15 +1241,15 @@\n For supported plug-ins see PLUGINS:3dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n@@ -1275,15 +1275,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:3dtransform/io\n \n .RE\n .RE\n .RS 14\n"}]}, {"source1": "./usr/share/man/man1/mia-3dcrispsegment.1.gz", "source2": "./usr/share/man/man1/mia-3dcrispsegment.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dcrispsegment.1", "source2": "mia-3dcrispsegment.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-3dcrispsegment \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-3dcrispsegment\n 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\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input class file, should contain multiple images with tissue class probabilities\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-file=(output, required); io\"\n output class label image\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-l \\-\\-label-offset=1\"\n label offset\n"}]}, {"source1": "./usr/share/man/man1/mia-3ddeform.1.gz", "source2": "./usr/share/man/man1/mia-3ddeform.1.gz", "unified_diff": null, "details": [{"source1": "mia-3ddeform.1", "source2": "mia-3ddeform.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B  mia\\-3ddeform \\-i <in\\-image> \\-o <out\\-image> \\-t <transformation> [options]\n .SH DESCRIPTION\n .B mia\\-3ddeform\n 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)\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-image=(input, required); io\"\n+.IP \"\\-i \\-\\-in-image=(required, input); io\"\n input image\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-image=(required, output); io\"\n transformed image\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-t \\-\\-transformation=(input, required); io\"\n+.IP \"\\-t \\-\\-transformation=(required, input); io\"\n transformation vector field\n  For supported file types see PLUGINS:3dvf/io\n .IP \"\\-p \\-\\-interpolator=bspline:d=3\"\n image interpolator kernel\n  For supported plugins see PLUGINS:1d/splinekernel\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-3ddistance.1.gz", "source2": "./usr/share/man/man1/mia-3ddistance.1.gz", "unified_diff": null, "details": [{"source1": "mia-3ddistance.1", "source2": "mia-3ddistance.1", "unified_diff": "@@ -12,15 +12,15 @@\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); string\"\n input image(s) that contain the source pixel mask\n \n .IP \"\\-r \\-\\-ref-file=(input, required); string\"\n reference mask to evaluate the distance from\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output file name\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dfield2norm.1.gz", "source2": "./usr/share/man/man1/mia-3dfield2norm.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dfield2norm.1", "source2": "mia-3dfield2norm.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-3dfield2norm \\-i <in\\-vectorfield> \\-o <out\\-image> [options]\n .SH DESCRIPTION\n .B mia\\-3dfield2norm\n This program converts a 3d vector field to an image of its voxel-wise norm.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-vectorfield=(input, required); io\"\n+.IP \"\\-i \\-\\-in-vectorfield=(required, input); io\"\n input vector field\n  For supported file types see PLUGINS:3dvf/io\n .IP \"\\-o \\-\\-out-image=(output, required); io\"\n output image comprising the per voxel norm of each image\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-3dfluid.1.gz", "source2": "./usr/share/man/man1/mia-3dfluid.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dfluid.1", "source2": "mia-3dfluid.1", "unified_diff": "@@ -14,18 +14,18 @@\n .UE\n .RE\n \n  It uses SSD as the sole registration criterion.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-image=(input, required); io\"\n+.IP \"\\-i \\-\\-in-image=(required, input); io\"\n input image\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-r \\-\\-ref-image=(input, required); io\"\n+.IP \"\\-r \\-\\-ref-image=(required, input); io\"\n reference image \n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-transformation=(required, output); io\"\n output transformation comprising the registering transformation field\n  For supported file types see PLUGINS:3dtransform/io\n .IP \"\\-d \\-\\-out-image=(output); io\"\n save deformed image\n"}]}, {"source1": "./usr/share/man/man1/mia-3dfuzzysegment.1.gz", "source2": "./usr/share/man/man1/mia-3dfuzzysegment.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dfuzzysegment.1", "source2": "mia-3dfuzzysegment.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-3dfuzzysegment \\-i <in\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-3dfuzzysegment\n This program runs a combined fuzzy c-means clustering and B-field correction to facilitate a 3D segmentation of 3D image\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image(s) to be segmenetd\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-c \\-\\-cls-file=(output); io\"\n output class probability images. Note, the used file format must support multible images (best is to use vista)\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-b0-file=(output); io\"\n image corrected for intensity non\\-uniformity\n"}]}, {"source1": "./usr/share/man/man1/mia-3dgetsize.1.gz", "source2": "./usr/share/man/man1/mia-3dgetsize.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dgetsize.1", "source2": "mia-3dgetsize.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-3dgetsize \\-i <in\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-3dgetsize\n Write the dimensions of the input 3D image to stdout.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dimagecombine.1.gz", "source2": "./usr/share/man/man1/mia-3dimagecombine.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dimagecombine.1", "source2": "mia-3dimagecombine.1", "unified_diff": "@@ -14,15 +14,15 @@\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-2 \\-\\-image2=(required, input); io\"\n input image  2 to be combined\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-c \\-\\-combiner=(required); factory\"\n combiner operation\n  For supported plugins see PLUGINS:3dimage/combiner\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image file\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dimagefilter.1.gz", "source2": "./usr/share/man/man1/mia-3dimagefilter.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dimagefilter.1", "source2": "mia-3dimagefilter.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-3dimagefilter \\-i <in\\-file> \\-o <out\\-file> [options] <PLUGINS:3dimage/filter>\n .SH DESCRIPTION\n .B mia\\-3dimagefilter\n This program is used to filter and convert gray scale 3D images.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image(s) that have been filtered\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n@@ -264,15 +264,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -578,15 +578,15 @@\n lower threshold for mask growing.\n \n .RE\n .RE\n .RS 14\n .I\n ref\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n reference image for mask region growing.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -659,15 +659,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -685,15 +685,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -712,15 +712,15 @@\n .TP 10\n .B mask\n 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: \n .P\n .RS 14\n .I\n input\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1102,28 +1102,28 @@\n For supported plug-ins see PLUGINS:3dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1136,15 +1136,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:3dtransform/io\n \n .RE\n .RE\n .RS 14\n"}]}, {"source1": "./usr/share/man/man1/mia-3dimagefilterstack.1.gz", "source2": "./usr/share/man/man1/mia-3dimagefilterstack.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dimagefilterstack.1", "source2": "mia-3dimagefilterstack.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-3dimagefilterstack\n 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. \n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output file name base, numbers are added accorfing to the input file pattern, and the file  extension is added according to the 'type' option.\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-t \\-\\-type=(required); set\"\n output file type\n \n .RS 10\n .I\n@@ -1134,15 +1134,15 @@\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-3disosurface-from-stack.1.gz", "source2": "./usr/share/man/man1/mia-3disosurface-from-stack.1.gz", "unified_diff": null, "details": [{"source1": "mia-3disosurface-from-stack.1", "source2": "mia-3disosurface-from-stack.1", "unified_diff": "@@ -6,18 +6,18 @@\n .B  mia\\-3disosurface\\-from\\-stack \\-i <in\\-image> \\-o <out\\-mesh> [options]\n .SH DESCRIPTION\n .B mia\\-3disosurface\\-from\\-stack\n This program is used to extract an iso-surface from the input gray scale image given as slices.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-image=(required, input); string\"\n+.IP \"\\-i \\-\\-in-image=(input, required); string\"\n input image filename pattern\n \n-.IP \"\\-o \\-\\-out-mesh=(output, required); string\"\n+.IP \"\\-o \\-\\-out-mesh=(required, output); string\"\n output mesh\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3disosurface-from-volume.1.gz", "source2": "./usr/share/man/man1/mia-3disosurface-from-volume.1.gz", "unified_diff": null, "details": [{"source1": "mia-3disosurface-from-volume.1", "source2": "mia-3disosurface-from-volume.1", "unified_diff": "@@ -9,15 +9,15 @@\n This program is used to extract an iso-surface from the input gray scale image by using marching thetrahedra.\n .SH OPTIONS\n .SS File-IO\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output mesh\n  For supported file types see PLUGINS:mesh/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dlandmarks-transform.1.gz", "source2": "./usr/share/man/man1/mia-3dlandmarks-transform.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dlandmarks-transform.1", "source2": "mia-3dlandmarks-transform.1", "unified_diff": "@@ -5,21 +5,21 @@\n .SH SYNOPSIS\n .B  mia\\-3dlandmarks\\-transform \\-i <in\\-file> \\-o <out\\-file> \\-t <transformation> [options]\n .SH DESCRIPTION\n .B mia\\-3dlandmarks\\-transform\n 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).\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input landmark set\n  For supported file types see PLUGINS:3dlandmarklist/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output landmark set\n  For supported file types see PLUGINS:3dlandmarklist/io\n-.IP \"\\-t \\-\\-transformation=(input, required); io\"\n+.IP \"\\-t \\-\\-transformation=(required, input); io\"\n transformation file\n  For supported file types see PLUGINS:3dtransform/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dlerp.1.gz", "source2": "./usr/share/man/man1/mia-3dlerp.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dlerp.1", "source2": "mia-3dlerp.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-3dlerp \\-1 <first> \\-2 <second> \\-o <out\\-file> \\-p <positions> [options]\n .SH DESCRIPTION\n .B mia\\-3dlerp\n merge two images by linear combination.\n .SH OPTIONS\n .RS\n-.IP \"\\-1 \\-\\-first=(input, required); io\"\n+.IP \"\\-1 \\-\\-first=(required, input); io\"\n first input image \n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-2 \\-\\-second=(input, required); io\"\n+.IP \"\\-2 \\-\\-second=(required, input); io\"\n second input image \n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n linearly interpolated image\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-p \\-\\-positions=(required); vfloat\"\n image series positions (first, target, second)\n"}]}, {"source1": "./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-3dmany2one-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dmany2one-nonrigid.1", "source2": "mia-3dmany2one-nonrigid.1", "unified_diff": "@@ -7,15 +7,15 @@\n .SH DESCRIPTION\n .B mia\\-3dmany2one\\-nonrigid\n This program runs the non-rigid registration of an image series by registereing all images to a user-selected reference.\n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input perfusion data set\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-file=(output); io\"\n file name for registered files\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS \n@@ -429,15 +429,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -743,15 +743,15 @@\n lower threshold for mask growing.\n \n .RE\n .RE\n .RS 14\n .I\n ref\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n reference image for mask region growing.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -824,15 +824,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -850,15 +850,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -877,15 +877,15 @@\n .TP 10\n .B mask\n 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: \n .P\n .RS 14\n .I\n input\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1267,15 +1267,15 @@\n For supported plug-ins see PLUGINS:3dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n@@ -1301,15 +1301,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:3dtransform/io\n \n .RE\n .RE\n .RS 14\n"}]}, {"source1": "./usr/share/man/man1/mia-3dmaskseeded.1.gz", "source2": "./usr/share/man/man1/mia-3dmaskseeded.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dmaskseeded.1", "source2": "mia-3dmaskseeded.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-3dmaskseeded \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-3dmaskseeded\n 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. \n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output image(s) that have been filtered\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-s \\-\\-seed=[0,0,0]\"\n seed point\n \n .IP \"\\-n \\-\\-neighborhood=6n\"\n neighborhood shape\n"}]}, {"source1": "./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz", "source2": "./usr/share/man/man1/mia-3dnonrigidreg-alt.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dnonrigidreg-alt.1", "source2": "mia-3dnonrigidreg-alt.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-3dnonrigidreg\\-alt \\-o <out\\-transform> [options] <PLUGINS:3dimage/fullcost>\n .SH DESCRIPTION\n .B mia\\-3dnonrigidreg\\-alt\n 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)\n .SH OPTIONS\n .RS\n-.IP \"\\-o \\-\\-out-transform=(required, output); io\"\n+.IP \"\\-o \\-\\-out-transform=(output, required); io\"\n output transformation\n  For supported file types see PLUGINS:3dtransform/io\n .IP \"\\-l \\-\\-levels=3\"\n multi\\-resolution levels\n \n .IP \"\\-O \\-\\-optimizer=gsl:opt=gd,step=0.1\"\n Optimizer used for minimization\n@@ -1268,15 +1268,15 @@\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n"}]}, {"source1": "./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz", "source2": "./usr/share/man/man1/mia-3dprealign-nonrigid.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dprealign-nonrigid.1", "source2": "mia-3dprealign-nonrigid.1", "unified_diff": "@@ -14,15 +14,15 @@\n .UE\n .RE\n \n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input images following the naming pattern nameXXXX.ext\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n file name base for registered files given as C\\-format string\n  For supported file types see PLUGINS:3dimage/io\n .IP \"   \\-\\-save-references\"\n Save synthetic references to files refXXXX.v\n@@ -470,15 +470,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -784,15 +784,15 @@\n lower threshold for mask growing.\n \n .RE\n .RE\n .RS 14\n .I\n ref\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n reference image for mask region growing.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -865,15 +865,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -891,15 +891,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -918,15 +918,15 @@\n .TP 10\n .B mask\n 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: \n .P\n .RS 14\n .I\n input\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1308,15 +1308,15 @@\n For supported plug-ins see PLUGINS:3dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(input, required, string)\n+=(required, input, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n@@ -1342,15 +1342,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(input, required, io)\n+=(required, input, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:3dtransform/io\n \n .RE\n .RE\n .RS 14\n"}]}, {"source1": "./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz", "source2": "./usr/share/man/man1/mia-3dpropose-boundingbox.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dpropose-boundingbox.1", "source2": "mia-3dpropose-boundingbox.1", "unified_diff": "@@ -6,15 +6,15 @@\n .B  mia\\-3dpropose\\-boundingbox \\-i <in\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-3dpropose\\-boundingbox\n 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.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n@@ -271,15 +271,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -585,15 +585,15 @@\n lower threshold for mask growing.\n \n .RE\n .RE\n .RS 14\n .I\n ref\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n reference image for mask region growing.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -666,15 +666,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -692,15 +692,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -719,15 +719,15 @@\n .TP 10\n .B mask\n 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: \n .P\n .RS 14\n .I\n input\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1109,15 +1109,15 @@\n For supported plug-ins see PLUGINS:3dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n@@ -1143,15 +1143,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:3dtransform/io\n \n .RE\n .RE\n .RS 14\n"}]}, {"source1": "./usr/share/man/man1/mia-3dsegment-ahmed.1.gz", "source2": "./usr/share/man/man1/mia-3dsegment-ahmed.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dsegment-ahmed.1", "source2": "mia-3dsegment-ahmed.1", "unified_diff": "@@ -14,18 +14,18 @@\n .UE\n .RE\n \n  changes are: p=2, and exp\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n image to be segmented\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-c \\-\\-class-file=(required, output); io\"\n+.IP \"\\-c \\-\\-class-file=(output, required); io\"\n class probability images, the image type must support multiple images and floating point values\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-b \\-\\-out-file=(output); io\"\n 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.\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n"}]}, {"source1": "./usr/share/man/man1/mia-3dseries-track-intensity.1.gz", "source2": "./usr/share/man/man1/mia-3dseries-track-intensity.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dseries-track-intensity.1", "source2": "mia-3dseries-track-intensity.1", "unified_diff": "@@ -7,18 +7,18 @@\n .SH DESCRIPTION\n .B mia\\-3dseries\\-track\\-intensity\n This program tracks the intensity of a pixel at the given coordinates.\n .SH OPTIONS\n .SS \n File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input perfusion data set\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n file name for output intensity slopes\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dtransform.1.gz", "source2": "./usr/share/man/man1/mia-3dtransform.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dtransform.1", "source2": "mia-3dtransform.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-3dtransform\n Transform a 3D image by applying a given 3D transformation.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image\n  For supported file types see PLUGINS:3dimage/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n transformed image\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-t \\-\\-transformation=(input, required); io\"\n transformation file\n  For supported file types see PLUGINS:3dtransform/io\n .IP \"\\-p \\-\\-interpolator=\"\n override the interpolator provided by the transformation\n"}]}, {"source1": "./usr/share/man/man1/mia-3dtransform2vf.1.gz", "source2": "./usr/share/man/man1/mia-3dtransform2vf.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dtransform2vf.1", "source2": "mia-3dtransform2vf.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-3dtransform2vf \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-3dtransform2vf\n Create a 3D vector field from a given transformation. The output vector field will have the dimesions as given in the transformation description.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); io\"\n+.IP \"\\-i \\-\\-in-file=(required, input); io\"\n input transformation \n  For supported file types see PLUGINS:3dtransform/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output vector field \n  For supported file types see PLUGINS:3dvf/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-3dvf2transform.1.gz", "source2": "./usr/share/man/man1/mia-3dvf2transform.1.gz", "unified_diff": null, "details": [{"source1": "mia-3dvf2transform.1", "source2": "mia-3dvf2transform.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-3dvf2transform\n 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.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(input, required); io\"\n input transformation \n  For supported file types see PLUGINS:3dvf/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output vector field \n  For supported file types see PLUGINS:3dtransform/io\n .IP \"\\-k \\-\\-imgkernel=bspline:d=3\"\n image interpolator kernel which is used when the transformation is applied to an image\n  For supported plugins see PLUGINS:1d/splinekernel\n .IP \"\\-b \\-\\-imgboundary=mirror\"\n Boundary condition applied when the transformation is used to transform an image\n"}]}, {"source1": "./usr/share/man/man1/mia-cmeans.1.gz", "source2": "./usr/share/man/man1/mia-cmeans.1.gz", "unified_diff": null, "details": [{"source1": "mia-cmeans.1", "source2": "mia-cmeans.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-cmeans \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-cmeans\n This Program reads a histogram from stdin and evaluates a cmeans classification of the intensity values into the given number of classes.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input file name containing the histogram\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output file name to store probabilities\n \n .IP \"\\-n \\-\\-nclasses=3\"\n number of classes to partition into\n \n .IP \"\\-m \\-\\-max-iter=100\"\n maximum number of iterations\n"}]}, {"source1": "./usr/share/man/man1/mia-filenumberpattern.1.gz", "source2": "./usr/share/man/man1/mia-filenumberpattern.1.gz", "unified_diff": null, "details": [{"source1": "mia-filenumberpattern.1", "source2": "mia-filenumberpattern.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-filenumberpattern \\-i <in\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-filenumberpattern\n This program is used to extract a extract the number pattern for file012312.ext type file names.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input image example name\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-labelsort.1.gz", "source2": "./usr/share/man/man1/mia-labelsort.1.gz", "unified_diff": null, "details": [{"source1": "mia-labelsort.1", "source2": "mia-labelsort.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-labelsort \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-labelsort\n 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.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input file name containing the histogram\n \n-.IP \"\\-o \\-\\-out-file=(output, required); string\"\n+.IP \"\\-o \\-\\-out-file=(required, output); string\"\n output file name to store probabilities\n \n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-mesh-deformable-model.1.gz", "source2": "./usr/share/man/man1/mia-mesh-deformable-model.1.gz", "unified_diff": null, "details": [{"source1": "mia-mesh-deformable-model.1", "source2": "mia-mesh-deformable-model.1", "unified_diff": "@@ -6,21 +6,21 @@\n .B  mia\\-mesh\\-deformable\\-model \\-i <in\\-file> \\-o <out\\-file> \\-r <ref\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-mesh\\-deformable\\-model\n This program runs a deformable model to adapt a mesh to an iso-value within a given image. <FIXME: Reference>\n .SH OPTIONS\n .SS File I/O\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input mesh to be adapted\n  For supported file types see PLUGINS:mesh/io\n-.IP \"\\-o \\-\\-out-file=(required, output); io\"\n+.IP \"\\-o \\-\\-out-file=(output, required); io\"\n output mesh that has been deformed\n  For supported file types see PLUGINS:mesh/io\n-.IP \"\\-r \\-\\-ref-file=(required, input); io\"\n+.IP \"\\-r \\-\\-ref-file=(input, required); io\"\n reference image\n  For supported file types see PLUGINS:3dimage/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n@@ -301,15 +301,15 @@\n .TP 10\n .B combiner\n 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: \n .P\n .RS 14\n .I\n image\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second image that is needed in the combiner.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -615,15 +615,15 @@\n lower threshold for mask growing.\n \n .RE\n .RE\n .RS 14\n .I\n ref\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n reference image for mask region growing.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .RS 14\n@@ -696,15 +696,15 @@\n .TP 10\n .B labelmap\n Image filter to remap label id's. Only applicable to images with integer valued intensities/labels., supported parameters are: \n .P\n .RS 14\n .I\n map\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n Label mapping file.\n \n .RE\n .RE\n .TP 10\n .B labelscale\n@@ -722,15 +722,15 @@\n .TP 10\n .B load\n Load the input image from a file and use it to replace the current image in the pipeline., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n name of the input file to load from..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -749,15 +749,15 @@\n .TP 10\n .B mask\n 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: \n .P\n .RS 14\n .I\n input\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n second input image file name.\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1139,28 +1139,28 @@\n For supported plug-ins see PLUGINS:3dimage/shape\n \n .RE\n .RE\n .RS 14\n .I\n seed\n-=(required, input, string)\n+=(input, required, string)\n .RS 2\n seed input image containing the lables for the initial regions.\n \n .RE\n .RE\n .TP 10\n .B tee\n Save the input image to a file and also pass it through to the next filter, supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, output, io)\n+=(output, required, io)\n .RS 2\n name of the output file to save the image too..\n For supported file types see PLUGINS:3dimage/io\n \n .RE\n .RE\n .TP 10\n@@ -1173,15 +1173,15 @@\n .TP 10\n .B transform\n Transform the input image with the given transformation., supported parameters are: \n .P\n .RS 14\n .I\n file\n-=(required, input, io)\n+=(input, required, io)\n .RS 2\n Name of the file containing the transformation..\n For supported file types see PLUGINS:3dtransform/io\n \n .RE\n .RE\n .RS 14\n"}]}, {"source1": "./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz", "source2": "./usr/share/man/man1/mia-meshdistance-to-stackmask.1.gz", "unified_diff": null, "details": [{"source1": "mia-meshdistance-to-stackmask.1", "source2": "mia-meshdistance-to-stackmask.1", "unified_diff": "@@ -11,15 +11,15 @@\n .RS\n .IP \"\\-i \\-\\-in-mesh=(input, required); io\"\n input mesh\n  For supported file types see PLUGINS:mesh/io\n .IP \"\\-r \\-\\-ref-mask=(input, required); io\"\n reference binary mask\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-mesh=(required, output); io\"\n+.IP \"\\-o \\-\\-out-mesh=(output, required); io\"\n output mesh\n  For supported file types see PLUGINS:mesh/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-meshfilter.1.gz", "source2": "./usr/share/man/man1/mia-meshfilter.1.gz", "unified_diff": null, "details": [{"source1": "mia-meshfilter.1", "source2": "mia-meshfilter.1", "unified_diff": "@@ -10,15 +10,15 @@\n    'mia-plugin-help mesh/filter'\n from the command line\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); io\"\n input mesh to be filtered\n  For supported file types see PLUGINS:mesh/io\n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output mesh that have been filtered\n  For supported file types see PLUGINS:mesh/io\n .RE\n .SS Help & Info\n .RS\n .IP \"\\-V \\-\\-verbose=warning\"\n verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:\n"}]}, {"source1": "./usr/share/man/man1/mia-multihist.1.gz", "source2": "./usr/share/man/man1/mia-multihist.1.gz", "unified_diff": null, "details": [{"source1": "mia-multihist.1", "source2": "mia-multihist.1", "unified_diff": "@@ -5,18 +5,18 @@\n .SH SYNOPSIS\n .B  mia\\-multihist \\-i <in\\-file> \\-o <out\\-histogram> [options]\n .SH DESCRIPTION\n .B mia\\-multihist\n This program evaluates the histogram over a series of 2D images\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); io\"\n+.IP \"\\-i \\-\\-in-file=(input, required); io\"\n input image(s) to be filtered\n  For supported file types see PLUGINS:2dimage/io\n-.IP \"\\-o \\-\\-out-histogram=(required, output); string\"\n+.IP \"\\-o \\-\\-out-histogram=(output, required); string\"\n output file name\n \n .IP \"   \\-\\-min=0\"\n minimum of histogram range\n \n .IP \"   \\-\\-max=65535\"\n maximum of histogram range\n"}]}, {"source1": "./usr/share/man/man1/mia-raw2image.1.gz", "source2": "./usr/share/man/man1/mia-raw2image.1.gz", "unified_diff": null, "details": [{"source1": "mia-raw2image.1", "source2": "mia-raw2image.1", "unified_diff": "@@ -5,15 +5,15 @@\n .SH SYNOPSIS\n .B  mia\\-raw2image \\-i <in\\-file> \\-o <out\\-file> \\-s <size> [options]\n .SH DESCRIPTION\n .B mia\\-raw2image\n This program is used to convert raw data to a 2D file format.\n .SH OPTIONS\n .RS\n-.IP \"\\-i \\-\\-in-file=(input, required); string\"\n+.IP \"\\-i \\-\\-in-file=(required, input); string\"\n input file name\n \n .IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name\n  For supported file types see PLUGINS:2dimage/io\n .IP \"\\-r \\-\\-repn=ubyte\"\n input pixel type \n"}]}, {"source1": "./usr/share/man/man1/mia-raw2volume.1.gz", "source2": "./usr/share/man/man1/mia-raw2volume.1.gz", "unified_diff": null, "details": [{"source1": "mia-raw2volume.1", "source2": "mia-raw2volume.1", "unified_diff": "@@ -8,15 +8,15 @@\n .B mia\\-raw2volume\n This program is used to convert raw data into 3D images with apropriate metadata.\n .SH OPTIONS\n .RS\n .IP \"\\-i \\-\\-in-file=(required, input); string\"\n input file name\n \n-.IP \"\\-o \\-\\-out-file=(output, required); io\"\n+.IP \"\\-o \\-\\-out-file=(required, output); io\"\n output file name\n  For supported file types see PLUGINS:3dimage/io\n .IP \"\\-r \\-\\-repn=ubyte\"\n input pixel type \n \n .RS 10\n .I\n"}]}, {"source1": "./usr/share/man/man1/mia-wavelettrans.1.gz", "source2": "./usr/share/man/man1/mia-wavelettrans.1.gz", "unified_diff": null, "details": [{"source1": "mia-wavelettrans.1", "source2": "mia-wavelettrans.1", "unified_diff": "@@ -6,18 +6,18 @@\n .B  mia\\-wavelettrans \\-i <in\\-file> \\-o <out\\-file> [options]\n .SH DESCRIPTION\n .B mia\\-wavelettrans\n This program runs the a column-wise discret wavelet forward transform on the data given by an input text file.\n .SH OPTIONS\n .SS File-IO\n .RS\n-.IP \"\\-i \\-\\-in-file=(required, input); string\"\n+.IP \"\\-i \\-\\-in-file=(input, required); string\"\n input data set\n \n-.IP \"\\-o \\-\\-out-file=(required, output); string\"\n+.IP \"\\-o \\-\\-out-file=(output, required); string\"\n output data set\n \n .IP \"\\-s \\-\\-save-wave=(output); string\"\n base name of the output files that will store the wavelet coefficients as matrix\n \n .RE\n .SS Help & Info\n"}]}]}]}]}]}