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| 1 | .\"·DO·NOT·MODIFY·THIS·FILE!··It·was·generated·by·help2man·1.47.8. | 1 | .\"·DO·NOT·MODIFY·THIS·FILE!··It·was·generated·by·help2man·1.47.8. |
| 2 | .TH·PYSURFER·"1"·"June·2018"·"pysurfer·0.7"·"User·Commands" | 2 | .TH·PYSURFER·"1"·"June·2018"·"pysurfer·0.7"·"User·Commands" |
| 3 | .SH·NAME | 3 | .SH·NAME |
| 4 | pysurfer·\-·visualize·cortical·surface·reconstruction·from·Freesurfer | 4 | pysurfer·\-·visualize·cortical·surface·reconstruction·from·Freesurfer |
| 5 | .SH·DESCRIPTION | 5 | .SH·DESCRIPTION |
| 6 | usage:·pysurfer·subject_id·hemisphere·surface·[options] | 6 | Unable·to·init·server:·Could·not·connect:·Connection·refused |
| | 7 | Traceback·(most·recent·call·last): |
| | 8 | .IP |
| | 9 | File·"debian/python\-surfer/usr/bin/pysurfer",·line·9,·in·<module> |
| | 10 | .IP |
| | 11 | from·surfer._commandline·import·parser |
| | 12 | .IP |
| | 13 | File·"/build/pysurfer\-0.7/surfer/__init__.py",·line·1,·in·<module> |
| | 14 | .TP |
| | 15 | from·.viz·import·Brain,·TimeViewer |
| | 16 | #·noqa |
| | 17 | .IP |
| | 18 | File·"/build/pysurfer\-0.7/surfer/viz.py",·line·13,·in·<module> |
| | 19 | .IP |
| | 20 | from·mayavi·import·mlab |
| | 21 | .IP |
| | 22 | File·"/usr/lib/python2.7/dist\-packages/mayavi/mlab.py",·line·27,·in·<module> |
| | 23 | .IP |
| | 24 | from·mayavi.tools.camera·import·view,·roll,·yaw,·pitch,·move |
| | 25 | .IP |
| | 26 | File·"/usr/lib/python2.7/dist\-packages/mayavi/tools/camera.py",·line·25,·in·<module> |
| | 27 | .IP |
| | 28 | from·.engine_manager·import·get_engine |
| | 29 | .IP |
| | 30 | File·"/usr/lib/python2.7/dist\-packages/mayavi/tools/engine_manager.py",·line·12,·in·<module> |
| | 31 | .IP |
| | 32 | from·mayavi.preferences.api·import·preference_manager |
| | 33 | .IP |
| | 34 | File·"/usr/lib/python2.7/dist\-packages/mayavi/preferences/api.py",·line·4,·in·<module> |
| | 35 | .IP |
| | 36 | from·.preference_manager·import·preference_manager |
| | 37 | .IP |
| | 38 | File·"/usr/lib/python2.7/dist\-packages/mayavi/preferences/preference_manager.py",·line·29,·in·<module> |
| | 39 | .IP |
| | 40 | from·traitsui.api·import·View,·Group,·Item |
| | 41 | .IP |
| | 42 | File·"/usr/lib/python2.7/dist\-packages/traitsui/api.py",·line·36,·in·<module> |
| | 43 | .IP |
| | 44 | from·.editors.api·import·ArrayEditor |
| | 45 | .IP |
| | 46 | File·"/usr/lib/python2.7/dist\-packages/traitsui/editors/__init__.py",·line·23,·in·<module> |
| | 47 | .IP |
| | 48 | from·.api·import·ArrayEditor |
| | 49 | .IP |
| | 50 | File·"/usr/lib/python2.7/dist\-packages/traitsui/editors/api.py",·line·19,·in·<module> |
| | 51 | .IP |
| | 52 | from·.code_editor·import·CodeEditor |
| | 53 | .IP |
| | 54 | File·"/usr/lib/python2.7/dist\-packages/traitsui/editors/code_editor.py",·line·36,·in·<module> |
| | 55 | .IP |
| | 56 | class·ToolkitEditorFactory·(·EditorFactory·): |
| | 57 | .IP |
| | 58 | File·"/usr/lib/python2.7/dist\-packages/traitsui/editors/code_editor.py",·line·48,·in·ToolkitEditorFactory |
| | 59 | .IP |
| | 60 | mark_color·=·Color(·0xECE9D8·) |
| | 61 | .IP |
| | 62 | File·"/usr/lib/python2.7/dist\-packages/traits/traits.py",·line·522,·in·__call__ |
| | 63 | .IP |
| | 64 | return·self.maker_function(·*args,·**metadata·) |
| | 65 | .IP |
| | 66 | File·"/usr/lib/python2.7/dist\-packages/traits/traits.py",·line·1236,·in·Color |
| | 67 | .IP |
| | 68 | return·ColorTrait(·*args,·**metadata·) |
| | 69 | .IP |
| | 70 | File·"/usr/lib/python2.7/dist\-packages/traitsui/toolkit_traits.py",·line·7,·in·ColorTrait |
| | 71 | .IP |
| | 72 | return·toolkit().color_trait(·*args,·**traits·) |
| | 73 | .IP |
| | 74 | File·"/usr/lib/python2.7/dist\-packages/traitsui/toolkit.py",·line·117,·in·toolkit |
| | 75 | .IP |
| | 76 | _toolkit·=·_import_toolkit(·toolkit_name·) |
| | 77 | .IP |
| | 78 | File·"/usr/lib/python2.7/dist\-packages/traitsui/toolkit.py",·line·51,·in·_import_toolkit |
| | 79 | .IP |
| | 80 | return·__import__(·name,·globals=globals(),·level=1·).toolkit |
| | 81 | .IP |
| | 82 | File·"/usr/lib/python2.7/dist\-packages/traitsui/wx/__init__.py",·line·26,·in·<module> |
| | 83 | .IP |
| | 84 | import·toolkit |
| | 85 | .IP |
| | 86 | File·"/usr/lib/python2.7/dist\-packages/traitsui/wx/toolkit.py",·line·35,·in·<module> |
| | 87 | .IP |
| | 88 | _app·=·wx.App(redirect=False) |
| | 89 | .IP |
| | 90 | File·"/usr/lib/python2.7/dist\-packages/wx\-3.0\-gtk3/wx/_core.py",·line·8628,·in·__init__ |
| | 91 | .IP |
| | 92 | self._BootstrapApp() |
| | 93 | .IP |
| | 94 | File·"/usr/lib/python2.7/dist\-packages/wx\-3.0\-gtk3/wx/_core.py",·line·8196,·in·_BootstrapApp |
| | 95 | .IP |
| | 96 | return·_core_.PyApp__BootstrapApp(*args,·**kwargs) |
| 7 | .PP | 97 | .PP |
| 8 | PySurfer·is·a·package·for·visualization·and·interaction·with·cortical | 98 | SystemError:·wxEntryStart·failed,·unable·to·initialize·wxWidgets!··(Is·DISPLAY·set·properly?) |
| 9 | surface·representations·of·neuroimaging·data·from·Freesurfer. | |
| 10 | .PP | |
| 11 | The·command\-line·program·pysurfer·is·designed·to·largely·replicate | |
| 12 | Freesufer's·tksurfer·command\-line·interface·in·the·format·and·style | |
| 13 | of·arguments·it·accepts,·and,·like·tksurfer,·invoking·it·will·initialize | |
| 14 | a·visualization·in·an·external·window·and·begin·an·IPython·session·in·the | |
| 15 | terminal,·through·which·the·visualization·can·be·manipulated. | |
| 16 | .PP | |
| 17 | The·visualization·interface·is·exposed·through·methods·on·the·`brain' | |
| 18 | variable·that·will·exist·in·IPython·namespace·when·the·program·finishes | |
| 19 | loading.·Please·see·the·PySurfer·documentation·for·more·information | |
| 20 | about·how·to·interact·with·the·Brain·object. | |
| 21 | .SS·"positional·arguments:" | |
| 22 | .TP | |
| 23 | subject_id | |
| 24 | subject·id·as·in·subjects·dir | |
| 25 | .TP | |
| 26 | hemi | |
| 27 | hemisphere·to·load | |
| 28 | .TP | |
| 29 | surf | |
| 30 | surface·mesh·(e.g.·'pial',·'inflated') | |
| 31 | .SS·"optional·arguments:" | |
| 32 | .TP | |
| 33 | \fB\-h\fR,·\fB\-\-help\fR | |
| 34 | show·this·help·message·and·exit | |
| 35 | .TP | |
| 36 | \fB\-morphometry\fR·MEAS | |
| 37 | load·morphometry·file·(e.g.·thickness,·curvature) | |
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