||Up to TkMeditGuide||Back to [[../TkMeditScripting| TkMeditScripting]]||Continue to [[../TkMeditSampleScreenshotScript| TkMeditSampleScreenshotScript]]|| = Scripting = <> This section assumes you are familiar with Tcl and how to write basic scripts. Most of TkMedit's functions have Tcl bindings. As you have probably noticed, the interface is just a Tk/Tix window. You can look at the interface script, TkMedit.tcl, to see how most of the functionality is used. Following is a list of Tcl commands defined by TkMedit. You can use these commands in your own scripts and call them with the -tcl command line option to execute them on startup. TkMedit can run in a kind of batch mode in this fashion, altho it still requires X and has to be able to open its main window. You can also enter these script commands from the shell that TkMedit was launched in. You can use the Tcl source command to load a script file from the Tcl shell as well. This list is provided for reference. If you can figure out something that works, great, but it is not officially a feature of TkMedit. == Commands == Functions arguments are listed by their name followed by their arguments. Arguments in square brackets are optional. <> ''Average``Surface``Vertex``Positions'' '''''numberOfAverages''''' Averages the vertex positions of the Main surface '''numberOfAverages''' times. <> ''Clear``Selection'' Clears the current voxel selection. <> ''Clear``Undo``Volume'' Clears the undoable voxels. <> ''Debug``Print'' '''''string''''' Prints '''string''' to debugging output (either the {{{xdebug_TkMedit.txt}}} file or the screen). <> ''Export``Changed``Segmentation``Volume'' '''''volume [destinationDirectory]''''' Saves the segmentation '''volume''' in its original location (overwriting the original), or a new location if '''destinationDirectory''' is specified. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. The volume will be saved in COR format. <> ''Flip``Volume'' '''''xAxis yAxis zAxis''''' Flips the Main anatomical volume over an axis. Specify 0 or 1 for '''xAxis''', '''yAxis''', and '''zAxis''' to not flip or flip, respectively, on that axis. Axes are in anatomical index coordinate space. <> ''Get``Subject``Dir'' '''''volume''''' Returns the subject directory path. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. <> ''Get``Subject``Name'' '''''volume''''' Returns the subject name. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. <> ''Goto``Main``Vertex'' '''''vertexNumber''''' Sets the cursor to the location of the numbered vertex in the Main surface. '''vertexNumber''' should be between 0 and the number of vertices in the surface. <> ''Goto``Original``Vertex'' '''''vertexNumber''''' Sets the cursor to the location of the numbered vertex in the Original surface. '''vertexNumber''' should be between 0 and the number of vertices in the surface. <> ''Goto``Pial``Vertex'' '''''vertexNumber''''' Sets the cursor to the location of the numbered vertex in the Pial surface. '''vertexNumber''' should be between 0 and the number of vertices in the surface. <> ''Graph``Selected``Region'' Graphs the average timecourse for the selected voxels. <> ''Import``Surface``Annotation``To``Segmentation'' '''''surface annotationFileName colorTableFileName''''' Loads '''annotationFileName''' into a surface, creates a new segmentation volume, and goes through the surface, mapping a vertex location to a voxel in the segmentation volume. For each, it looks up a label value from the RGB color stored in the annotation value using '''colorTableFileName''' and sets the segmentation value to the label value. '''surface''' should be 0 for the Main surface, and 1 for the Aux surface. <> ''Load``Aux``Volume'' '''''volumeFileName''''' Loads '''volumeFileName''' as the Aux volume. <> ''Load``DTI``Volumes'' '''''vectorVolumeFileName intensityVolumeFileName redAxis greenAxis blueAxis''''' Loads a DTI volume using '''vectorVolumeFileName''' as the volume containing the vectors, and '''intensityVolumeFileName''' as the volume containing the scaling factor. The former should be a three frame volume and the latter should be a one frame volume. The '''redAxis''', '''greenAxis''', and '''blueAxis''' parameters should be x, y, or z, indicating which value in the vector volume corresponds to which color. <> ''Load``Functional``Overlay'' '''''volumeFileName registrationType [registrationFileName]''''' Loads a functional overlay volume from '''volumeFileName'''. You must also specify a '''registrationType''', which should be 0 to find a registration file in the same directory as the data, 1 to use an identity registration, and 2 to specify a file. If 2 is the '''registrationType''', use '''registrationFileName''' to specify the file. The overlay will be displayed in the graphics widnow. <> ''Load``Functional``Time``Course'' '''''volumeFileName registrationType [registrationFileName]''''' Loads a functional time course volume from '''volumeFileName'''. You must also specify a '''registrationType''', which should be 0 to find a registration file in the same directory as the data, 1 to use an identity registration, and 2 to specify a file. If 2 is the '''registrationType''', use '''registrationFileName''' to specify the file. The time course graph will be displayed in a separate window. <> ''Load``GCA'' '''''volumeFileName transformFileName''''' Loads a GCA volume from ''volumeFileName'' using the transform in '''transformFileName'''. <> ''Load``GCA``Renormalization'' '''''renormalizationVolumeFileName''''' Loads a GCA renormalization volume from '''renormalizationVolumeFileName'''. <> ''Load``Head``Pts'' '''''headPointsFileName transformFileName''''' Loads a head points array from '''headPointsFileName''' using the transform in '''transformFileName'''. <> ''Load``Label'' '''''labelFileName''''' Loads a label file from '''labelFileName'''. This will add the voxels in the label file to the selection. <> ''Load``Main``Surface'' '''''surface surfaceFileName''''' Loads a surface file from '''surfaceFileName'''. '''surface''' should be 0 for the Main surface, and 1 for the Aux surface. Note that this loads the main surface object, and will unload the Original or Pial surface configurations if they exist. <> ''Load``Original``Surface'' '''''surface surfaceFileName''''' Loads the Original vertex configuration from '''surfaceFileName''' into an existing surface. '''surface''' should be 0 for the Main surface, and 1 for the Aux surface. Note that the Main surface (that is, the Main Main or Aux Main) must already be loaded; this just loads in an alternate vertex configuration. <> ''Load``Pial``Surface'' '''''surface surfaceFileName''''' Loads the Pial vertex configuration from '''surfaceFileName''' into an existing surface. '''surface''' should be 0 for the Main surface, and 1 for the Aux surface. Note that the Main surface (that is, the Main Main or Aux Main) must already be loaded; this just loads in an alternate vertex configuration. <> ''Load``Segmentation``Volume'' '''''volume volumeFileName colorTableFileName''''' Loads a segmentation volume from '''volumeFileName''' using the color table in '''colorTableFileName'''. volume should be 0 for the Main volume, and 1 for the Aux volume. <> ''Load``Surface``Annotation'' '''''surface annotationFileName''''' Loads a surface annotation file from '''annotationFileName''' into a surface. '''surface''' should be 0 for the Main surface, and 1 for the Aux surface. This will color the vertices and edges of the surface display using the RGB annotation values. <> ''Load``Volume``Display``Transform'' '''''volume transformFileName''''' Loads a display transform from '''transformFileName''' for an anatomical volume. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. <> ''Load``Volume'' '''''volumeFileName''''' Loads '''volumeFileName''' as the Main volume. <> ''New``Control``Point'' Creates a new control point where the cursor is. <> ''New``Segmentation``Volume'' '''''volume fromAnatomicalVolume colorTableFileName''''' Creates a new segmentation volume based on one of the anatomical volumes using the color table in '''colorTableFileName'''. '''volume''' should be 0 for the Main segmentation volume, and 1 for the Aux segmentation volume, and '''fromAnatomicalVolume''' should be 0 for the Main anatomical volume, and 1 for the Aux anatomical volume. <> ''Overlay_``Restore``Registration'' Restores the functional overlay registration to the last saved value. <> ''Overlay_``Save``Registration'' Saves the current overlay registration. Overwrites previous file. <> ''Overlay_``Set``Condition'' '''''condition''''' Sets the functional overlay's current condition. '''condition''' must be with in the valid range of conditions. <> ''Overlay_``Set``Display``Flag'' '''''flag value''''' Sets a display flag for the functional overlay in the current display pane. '''value''' should be 0 or 1. '''flag''' should be one of the following, corresponding to an item in the View, Configure Overlay... dialog box: ||0||Truncate Negative Values|| ||1||Truncate Positive Values|| ||2||Reverse Phase|| ||3||Offset Values|| ||4||Ignore Threshold|| ||5||Grayscale Overlay|| ||6||Opaque Overlay|| <> ''Overlay_``Set``Registration``To``Identity'' Sets the functional overlay registration to the identity matrix. <> ''Overlay_``Set``Threshold'' '''''min mid slope''''' Sets the functional overlay threshold. '''min''' and '''mid''' should be valid functional values, and '''slope''' should a positive floating point number. <> ''Overlay_``Set``Time``Point'' '''''timePoint''''' Sets the functional overlay's current time point. '''timePoint''' must be with in the valid range of time points <> ''Overlay_``Set``Volume``Sample``Type'' '''''sampleType''''' Sets the functional overlay sampling method. '''sampleType''' should be 0 for nearest neighbor sampling and 1 for trilinear sampling. <> ''Quit``Medit'' Quits the program. <> ''Read``Cursor'' Reads a location from the {{{edit.dat}}} file and sets the cursor to that location. <> ''Read``Voxel``Labels'' '''''voxelLabelVolume1FileName voxelLabelVolume2FileName''''' Reads VLI volumes from '''voxelLabelVolume1FileName''' and '''voxelLabelVolume2FileName'''. <> ''Recompute``Segmentation'' '''''volume''''' Recomputes the Main or Aux segmentation volume based on the Main anatomical volume, the GCA volume, and the specified segmentation volume and its changed values. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. <> ''Redraw``All'' This schedules a redraw of the graphics window which will happen at the next update. It is best suited when a redraw does not need to happen until a series of script commands is finished. <> ''Redraw``Screen'' This forces an immediate redraw of the graphics window. This should be used when a script takes multiple screen captures in the middle of a loop. <> ''Restore``Head``Pts'' Restores the head points transformation to the original matrix. <> ''Restore``Previous``Segmentation'' '''''volume''''' Restores a segmentation volume to the state it was in before it was recomputed. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. <> ''Restore``Volume``From``Snapshot'' Restores the Main volume to the state it was in when the snapshot was taken. <> ''Rotate``Head``Pts'' '''''degrees axis''''' Rotates the head points orientation by '''degrees''' degrees over the x, y, or z axis. '''degrees''' can be a floating point number and '''axis''' should be x, y, or z. <> ''Rotate``Overlay``Registration'' '''''degrees axis''''' Rotates the functional overlay registration by '''degrees''' degrees over the x, y, or z axis. '''degrees''' can be a floating point number and '''axis''' should be x, y, or z. <> ''Rotate``Volume'' '''''axis degrees''''' Rotates the Main anatomical volume over the x, y, or z axis by '''degrees''' degrees. '''degrees''' can be a floating point number and '''axis''' should be x, y, or z. <> ''Save``GCA'' '''''volumeFileName''''' Saves the GCA volume as '''volumeFileName'''. <> ''Save``Label'' '''''labelFileName''''' Saves the current selection as a label file in '''labelFileName'''. <> ''Save``TIFF'' '''''imageFileName''''' Takes a screen shot of the graphics window and saves it as an TIFF file in '''imageFileName'''. <> ''Save``Segmentation``Volume'' '''''volume [destinationDirectory]''''' Saves the specified segmentation volume in its original location (overwriting the old file), or in a new location if '''destinationDirectory''' is specified. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. The volume will be saved in COR format. <> ''Save``Volume'' '''''volume''''' Saves the anatomical volume in its original location, overwriting the old file. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. The volume will be saved in COR format. <> ''Save``Volume``As'' '''''volume destinationDirectory''''' Saves the anatomical volume in '''destinationDirectory'''. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. The volume will be saved in COR format. <> ''Scale``Overlay``Registration'' '''''distance axis''''' Scales the functional overlay registration by '''distance''' over the x, y, or z axis. '''distance''' can be a floating point number and '''axis''' should be x, y, or z. <> ''Select``Voxels``By``Func``Value'' '''''compareType''''' Adds to the selection all contiguous voxels whose functional value pass the comparison with the value under the cursor. '''compareType''' should be one of the following: ||0||Greater than or equal to, or less than or equal to: If the value is positive, this will select all voxels whose value are greater than or equal to the value, and if negative, less than or equal to.|| ||1||Equal to: Values must be equal|| ||2||Greater than or equal to threshold minimum: This will select all voxels whose values are above the threshold minimum|| <> ''Send``Cursor'' Writes the location of the cursor to the {{{edit.dat}}} file, to be shared with tksurfer. <> ''Set``Brush``Info'' '''''brush low high new''''' Sets information about the anatomical Edit Voxel Tool shape. '''brush''' should be 2 or 3, for the brush associated with button 2 or 3. '''low''', '''high''', and '''new''' should be within the range of voxel values, and set the threshold and new values for the brush. <> ''Set``Brush``Info``To``Defaults'' Restores the brush info (see above) to the default values. <> ''Set``Brush``Shape'' '''''radius shape 3D''''' Sets the brush shape, which affects both edit tools and the Select Voxels tool. '''radius''' should be an integer greater than 0. '''shape''' should be 0 for circle, and 1 for square. '''3D''' should be 0 for in-plane edits only, and 1 for three dimensional editing. <> ''Set``Brush``Target'' '''''target''''' Sets the brush Edit Voxel Tool target. '''target''' should be 0 for the Main volume, and 1 for the Aux volume, and 2 for the Main and Aux volume. <> ''Set``Cursor'' '''''coordinateSpace x y z''''' Sets the cursor in the volume and moves the current slice to display it. '''coordinateSpace''' should be 0 for volume index space, 1 for RAS world space, 2 for surface RAS space, and 3 for (real, not MNI) Talairach space. '''x''', '''y''', and '''z''' can be floating point numbers. <> ''Set``Cursor``Color'' '''''r g b''''' Sets the display color for the cursor. '''r''', '''g''', and '''b''' should be floating point values from 0 to 1. <> ''Set``Cursor``Shape'' '''''shape''''' Sets the display shape for the cursor. '''shape''' should be 0 for crosshair and 1 for diamond. <> ''Set``Cursor``To``Center``Of``Selection'' Sets the cursor location to the center of the current selection, changing the view appropriately. <> ''Set``DTI``Alpha'' '''''alpha''''' Sets the opacity alpha for the DTI overlay. '''alpha''' should be a floating point number between 0 and 1. <> ''Set``Display``Config'' '''''numberOfColumns numberOfRows linkPolicy''''' Sets the number of rows and columns of display panes in the graphics window. Calling this function will configure the panes in default orientations and slice numbers. '''numberOfCols''' and '''numberOfRows''' should be between 1 and 4. '''linkPolicy''' should be one of the following: ||0||None: Normal link policy; cursor actions in other panes don't affect each other.|| ||1||Cursor: Changing the cursor in one pane will set the cursor in other panes. Zoom levels are linked. Orientation changes are linked. When the display is set to this configuration, all panes are set to different orientations around the cursor.|| ||2||Slice: Changing the slice number in one view will change all other views by the same amount. Cursor changes are not linked. Zoom levels are linked. Orientation changes are linked. When the display is first set to this configuration, all panes are set to the same orientation but to different slices.|| <> ''Set``Display``Flag'' '''''flag value''''' Sets a display flag for the current display pane. '''flag''' should be an index number below, '''value''' should be 0 or 1. flag should be one of the following, corresponding to an item in the View menu: ||1||Aux Volume|| ||2||Anatomical Volume|| ||3||Cursor|| ||4||Main Surface|| ||5||Original Surface|| ||6||Pial Surface|| ||7||Interpolate Surface Vertices|| ||8||Surface Vertices|| ||9||Control Points|| ||10||Selection|| ||11||Functional Overlay|| ||12||Functional Color Scale Bar|| ||13||Mask to Functional Overlay|| ||14||Mask Overlay to Aux Volume|| ||15||Segmentation Volume Overlay|| ||16||Aux Segmentation Volume|| ||17||Segmentation Label Volume Count|| ||18||DTI Overlay|| ||20||Focus Frame|| ||21||Undoable Voxels|| ||22||Axes|| ||23||Maximum Intensity Porjection|| ||24||Head Points|| ||25||Verbose GCA Dump|| <> ''Set``Flood``Select``Params'' '''''3D sourceVolume fuzziness distance''''' Sets the parameters for the flood select part of the Select Voxels tool. '''3D''' should be 0 or 1. '''sourceVolume''' should be 0 for the Main anatomical volume, 1 for the Aux anatomical volume, 2 for the Main segmentation volume, and 3 for the Aux segmentation volume. '''fuzziness''' and '''distance''' should be floating point numbers. <> ''Set``Func``Overlay``Alpha'' '''''alpha''''' Sets the opacity alpha for the functional overlay. '''alpha''' should be a floating point number between 0 and 1. <> ''Set``GCA``Display``Status'' '''''displayIntermediateResults''''' Sets the display status for GCA operations. '''displayIntermediateResults''' should be 0 or 1. <> ''Set``Linked``Cursor``Flag'' '''''linked''''' Sets cursor linking on or off. '''linked''' should be 0 or 1. <> ''Set``Orientation'' '''''orientation''''' Sets the orientation of the current display pane. '''orientation''' should be 0 for coronal, 1 for horizontal, or 2 for sagittal. <> ''Set``Seg``Brush``Info'' '''''newValue 3D sourceVolume fuzziness distance''''' Sets the parameters for the Edit Segmentation tool, both brush and fill parameters. '''newValue''' should be a valid index in the currently loaded color table. '''3D''' should be 0 or 1. '''sourceVolume''' should be 0 for the Main anatomical volume, 1 for the Aux anatomical volume, 2 for the Main segmentation volume, and 3 for the Aux segmentation volume. '''fuzziness''' and '''distance''' should be floating point numbers. <> ''Set``Segmentation``Alpha'' '''''alpha''''' Sets the opacity alpha for the segmentation overlay. '''alpha''' should be a floating point number between 0 and 1. <> ''Set``Selected``Head``Point``Label'' '''''label''''' Sets the label for the currently selected head point. '''label''' should be a string. <> ''Set``Slice'' '''''sliceNumber''''' Sets the slice number in the currently selected display pane for the anatomical volume. Note that this may trigger updates in other panes due to cursor linking. '''sliceNumber''' should be within the valid range of volume index coordinates. <> ''Set``Surface``Distance``At``Cursor'' Copies the current surface distance value into the Main surface vertex nearest the cursor. <> ''Set``Surface``Line``Color'' '''''surface set r g b''''' Sets the surface line color. '''surface''' should be 0 for the Main surface, and 1 for the Aux surface. '''set''' should be 0 for Main, 1 for Original, and 2 for Pial. '''r''', '''g''', and '''b''' should be floating numbers from 0 to 1. <> ''Set``Surface``Line``Width'' '''''surface set width''''' Sets the surface line width. '''surface''' should be 0 for the Main surface, and 1 for the Aux surface. '''set''' should be 0 for Main, 1 for Original, and 2 for Pial. '''width''' should be an integer. <> ''Set``Tool'' '''''tool''''' Sets the currently active tool. '''tool''' should be 0 for Navigate, 1 for Select Voxels, 2 for Edit Voxels, 3 for Edit Segmentation, or 4 for Edit Control Points. <> ''Set``Volume``Brightness``Contrast'' '''''volume brightness contrast''''' Sets the brightness and contrast values for a volume. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. '''brightness''' should be a floating point number from 0 to 1 (0 is brighter than 1) and '''contrast''' should be a floating point number from 0 to 30. <> ''Set``Volume``Color``Scale'' '''''volume brightness contrast min max''''' Sets the color (grayscale, really) scale for a volume. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. '''brightness''' should be a floating point number from 0 to 1 (0 is brighter than 1) and '''contrast''' should be a floating point number from 0 to 30. '''min''' and '''max''' define the values for black and white and should be valid numbers in the voxel value range. <> ''Set``Volume``Min``Max'' '''''volume min max''''' Sets the color (grayscale, really) scale for a volume. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. '''min''' and '''max''' define the values for black and white and should be valid numbers in the voxel value range. <> ''Set``Volume``Resample``Method'' '''''volume method''''' Sets the resampling method for an anatomical volume. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. '''method''' should be 0 for RAS and 1 for slice. <> ''Set``Volume``Sample``Type'' '''''volume sampleType''''' Sets the sampling method for an anatomical volume. '''volume''' should be 0 for the Main volume, and 1 for the Aux volume. '''sampleType''' should be 0 for nearest neighbor, 1 for trilinear, and 2 for sinc. <> ''Set``Zoom``Center'' '''''x y z''''' Sets the zoom center of the current display pane, changing the visible area without setting the cursor. '''x''', '''y''', and '''z''' should be integers in the anatomical index space. <> ''Set``Zoom``Level'' '''''level''''' Sets the zoom level of the current display pane. '''level''' should be an integer from 1 to 128. <> ''Show``Nearest``Interpolated``Main``Vertex'' Sets the cursor to the point of the nearest interpolated vertex on the Main surface configuration. <> ''Show``Nearest``Interpolated``Original``Vertex'' Sets the cursor to the point of the nearest interpolated vertex on the Original surface configuration. <> ''Show``Nearest``Interpolated``Pial``Vertex'' Sets the cursor to the point of the nearest interpolated vertex on the Pial surface configuration. <> ''Show``Nearest``Main``Vertex'' Sets the cursor to the point of the vertex on the Main surface configuration. <> ''Show``Nearest``Original``Vertex'' Sets the cursor to the point of the vertex on the Original surface configuration. <> ''Show``Nearest``Pial``Vertex'' Sets the cursor to the point of the vertex on the Pial surface configuration. <> ''Smart``Cut``At``Cursor'' Performs a smart cut operation at the current cursor location. <> ''Smooth``Functional``Overlay'' '''''sigma''''' Smooths the functional overlay volume with given sigma. sigma should be a floating point number. <> ''Snapshot``Volume'' Saves the state of the Main anatomical volume so it can be restored later. <> ''Threshold``Volume'' '''''thresholdValue direction newValue''''' Performs a thresholding operation on the Main anatomical volume. '''thresholdValue''' is the value above or below which all values will be set to '''newValue''', and both must be valid anatomical values. '''direction''' should be 0 for below, or 1 for above. <> ''Time``Course_``Print``Selection``RangeToFile'' '''''fileName''''' Prints information about the averaged time course values over all time points for the selected voxels to a text file '''fileName'''. <> ''Time``Course_``Set``Display``Flag'' '''''flag value''''' Sets a display flag for the functional time course. '''value''' should be 0 or 1. '''flag''' should be one of the following, corresponding to an item in the View, Configure Time Course... dialog box: ||7||Open Graph Window|| ||8||Offset Values|| ||9||Show Prestim Offset|| <> ''Time``Course_``Set``Num``Pre``Stim``Points'' '''''numPoints''''' Sets the number of pre-stim time points in the time course volume to '''numPoints'''. <> ''Time``Course_``Set``Time``Resolution'' '''''resolution''''' Sets the time resolution of the time course volume to '''resolution'''. <> ''Translate``Head``Pts'' '''''distance axis''''' Translates the head points orientation by '''distance''' units over the x, y, or z axis. '''axis''' can be x, y, or z. <> ''Undo``Last``Edit'' Performs and undo. <> ''Unload``All``Surfaces'' Unloads the Main and Aux surface. <> ''UnloadGCA'' Unloads the GCA volume. <> ''Unload``Surface'' '''''surface''''' Unloads a surface. '''surface''' should be 0 for the Main surface, or 1 for the Aux surface. <> ''Unload``Volume'' '''''volume''''' Unloads an anatomical volume. '''volume''' should be 0 for the Main volume, or 1 for the Aux volume. <> ''Unload``Volume``Display``Transform'' '''''volume''''' Unloads an anatomical volume display transform. '''volume''' should be 0 for the Main volume's transform, or 1 for the Aux volume's transform. <> ''Write``Control``Point``File'' Writes the control points to the control.dat file. This is done automatically when adding a new point, but not when removing a point. <> ''Write``Head``Points``File'' Writes the head points file. This overwrites the previous file. <> ''Write``Head``Points``Transform'' Writes the head points transform file. This overwrites the previous file. <> ''Write``Surface``Values'' '''''surface valueFileName''''' Writes the a surface's vertex values to a value file '''valueFileName'''. '''surface''' should be 0 for the Main surface, or 1 for the Aux surface. == Index == [[#AverageSurfaceVertexPositions|AverageSurfaceVertexPositions]] === Anatomical === [[#FlipVolume|FlipVolume]] [[#LoadAuxVolume|LoadAuxVolume]] [[#LoadVolume|LoadVolume]] [[#LoadVolumeDisplayTransform|LoadVolumeDisplayTransform]] [[#RestoreVolumeFromSnapshot|RestoreVolumeFromSnapshot]] [[#RotateVolume|RotateVolume]] [[#SaveVolume|SaveVolume]] [[#SaveVolumeAs|SaveVolumeAs]] [[#SetVolumeBrightnessContrast|SetVolumeBrightnessContrast]] [[#SetVolumeColorScale|SetVolumeColorScale]] [[#SetVolumeMinMax|SetVolumeMinMax]] [[#SetVolumeResampleMethod|SetVolumeResampleMethod]] [[#SetVolumeSampleType|SetVolumeSampleType]] [[#SmartCutAtCursor|SmartCutAtCursor]] [[#SnapshotVolume|SnapshotVolume]] [[#ThresholdVolume|ThresholdVolume]] [[#UndoLastEdit|UndoLastEdit]] [[#UnloadVolume|UnloadVolume]] [[#UnloadVolumeDisplayTransform|UnloadVolumeDisplayTransform]] === DTI === [[#LoadDTIVolumes|LoadDTIVolumes]] [[#SetDTIAlpha|SetDTIAlpha]] [[#Editing|Editing]] [[#ClearUndoVolume|ClearUndoVolume]] [[#FlipVolume|FlipVolume]] [[#RestoreVolumeFromSnapshot|RestoreVolumeFromSnapshot]] [[#RotateVolume|RotateVolume]] [[#SetBrushInfo|SetBrushInfo]] [[#SetBrushInfoToDefaults|SetBrushInfoToDefaults]] [[#SetBrushShape|SetBrushShape]] [[#SetBrushTarget|SetBrushTarget]] [[#SetSegBrushInfo|SetSegBrushInfo]] [[#SetTool|SetTool]] [[#SmartCutAtCursor|SmartCutAtCursor]] [[#SnapshotVolume|SnapshotVolume]] [[#ThresholdVolume|ThresholdVolume]] [[#UndoLastEdit|UndoLastEdit]] === Functional === [[#GraphSelectedRegion|GraphSelectedRegion]] [[#LoadFunctionalOverlay|LoadFunctionalOverlay]] [[#LoadFunctionalTimeCourse|LoadFunctionalTimeCourse]] [[#Overlay_RestoreRegistration|Overlay_RestoreRegistration]] [[#Overlay_SaveRegistration|Overlay_SaveRegistration]] [[#Overlay_SetCondition|Overlay_SetCondition]] [[#Overlay_SetDisplayFlag|Overlay_SetDisplayFlag]] [[#Overlay_SetRegistrationToIdentity|Overlay_SetRegistrationToIdentity]] [[#Overlay_SetThreshold|Overlay_SetThreshold]] [[#Overlay_SetTimePoint|Overlay_SetTimePoint]] [[#Overlay_SetVolumeSampleType|Overlay_SetVolumeSampleType]] [[#RotateOverlayRegistration|RotateOverlayRegistration]] [[#ScaleOverlayRegisgtration|ScaleOverlayRegisgtration]] [[#SelectVoxelsByFuncValue|SelectVoxelsByFuncValue]] [[#SetFuncOverlayAlpha|SetFuncOverlayAlpha]] [[#SmoothFunctionalOverlay|SmoothFunctionalOverlay]] [[#TimeCourse_PrintSelectionRangeToFile|TimeCourse_PrintSelectionRangeToFile]] [[#TimeCourse_SetDisplayFlag|TimeCourse_SetDisplayFlag]] [[#TimeCourse_SetNumPreStimPoints|TimeCourse_SetNumPreStimPoints]] [[#TimeCourse_SetTimeResolution|TimeCourse_SetTimeResolution]] === Control Points === [[#NewControlPoint|NewControlPoint]] [[#WriteControlPointFile|WriteControlPointFile]] === GCA === [[#LoadGCA|LoadGCA]] [[#LoadGCARenormalization|LoadGCARenormalization]] [[#SaveGCA|SaveGCA]] [[#SetGCADisplayStatus|SetGCADisplayStatus]] [[#UnloadGCA|UnloadGCA]] === Head Points === [[#LoadHeadPts|LoadHeadPts]] [[#RestoreHeadPts|RestoreHeadPts]] [[#RotateHeadPts|RotateHeadPts]] [[#SetSelectedHeadPointLabel|SetSelectedHeadPointLabel]] [[#TranslateHeadPts|TranslateHeadPts]] [[#TranslateOverlayRegisgtration|TranslateOverlayRegisgtration]] [[#WriteHeadPointsFile|WriteHeadPointsFile]] [[#WriteHeadPointsTransform|WriteHeadPointsTransform]] === I/O === [[#LoadAuxVolume|LoadAuxVolume]] [[#LoadDTIVolumes|LoadDTIVolumes]] [[#LoadFunctionalOverlay|LoadFunctionalOverlay]] [[#LoadFunctionalTimeCourse|LoadFunctionalTimeCourse]] [[#LoadGCA|LoadGCA]] [[#LoadGCARenormalization|LoadGCARenormalization]] [[#LoadHeadPts|LoadHeadPts]] [[#LoadLabel|LoadLabel]] [[#LoadMainSurface|LoadMainSurface]] [[#LoadOriginalSurface|LoadOriginalSurface]] [[#LoadPialSurface|LoadPialSurface]] [[#LoadSegmentationVolume|LoadSegmentationVolume]] [[#LoadSurfaceAnnoation|LoadSurfaceAnnoation]] [[#LoadVolume|LoadVolume]] [[#LoadVolumeDisplayTransform|LoadVolumeDisplayTransform]] [[#ReadCursor|ReadCursor]] [[#ReadVoxelLabels|ReadVoxelLabels]] [[#SaveGCA|SaveGCA]] [[#SaveLabel|SaveLabel]] [[#SaveRGB|SaveRGB]] [[#SaveSegmentationVolume|SaveSegmentationVolume]] [[#SaveVolume|SaveVolume]] [[#SaveVolumeAs|SaveVolumeAs]] [[#UnloadAllSurfaces|UnloadAllSurfaces]] [[#UnloadGCA|UnloadGCA]] [[#UnloadSurface|UnloadSurface]] [[#UnloadVolume|UnloadVolume]] [[#UnloadVolumeDisplayTransform|UnloadVolumeDisplayTransform]] [[#WriteControlPointFile|WriteControlPointFile]] [[#WriteHeadPointsFile|WriteHeadPointsFile]] [[#WriteHeadPointsTransform|WriteHeadPointsTransform]] [[#WriteSurfaceValues|WriteSurfaceValues]] === Misc === [[#DebugPrint|DebugPrint]] [[#QuitMedit|QuitMedit]] [[#SaveRGB|SaveRGB]] [[#SetTool|SetTool]] === Selection === [[#ClearSelection|ClearSelection]] [[#LoadLabel|LoadLabel]] [[#SaveLabel|SaveLabel]] [[#SetCursorToCenterOfSelection|SetCursorToCenterOfSelection]] [[#SetFloodSelectParams|SetFloodSelectParams]] === Surface === [[#AverageSurfaceVertexPositions|AverageSurfaceVertexPositions]] [[#GotoMainVertex|GotoMainVertex]] [[#GotoOriginalVertex|GotoOriginalVertex]] [[#GotoPialVertex|GotoPialVertex]] [[#LoadMainSurface|LoadMainSurface]] [[#LoadOriginalSurface|LoadOriginalSurface]] [[#LoadPialSurface|LoadPialSurface]] [[#LoadSurfaceAnnoation|LoadSurfaceAnnoation]] [[#SetSurfaceDistanceAtCursor|SetSurfaceDistanceAtCursor]] [[#SetSurfaceLineColor|SetSurfaceLineColor]] [[#SetSurfaceLineWidth|SetSurfaceLineWidth]] [[#ShowNearestInterpolatedMainVertex|ShowNearestInterpolatedMainVertex]] [[#ShowNearestInterpolatedOriginalVertex|ShowNearestInterpolatedOriginalVertex]] [[#ShowNearestInterpolatedPialVertex|ShowNearestInterpolatedPialVertex]] [[#ShowNearestMainVertex|ShowNearestMainVertex]] [[#ShowNearestOriginalVertex|ShowNearestOriginalVertex]] [[#ShowNearestPialVertex|ShowNearestPialVertex]] [[#UnloadAllSurfaces|UnloadAllSurfaces]] [[#UnloadSurface|UnloadSurface]] [[#WriteSurfaceValues|WriteSurfaceValues]] === Segmentation === [[#ExportChangedSegmentationVolume|ExportChangedSegmentationVolume]] [[#GetSubjectDir|GetSubjectDir]] [[#GetSubjectName|GetSubjectName]] [[#ImportSurfaceAnnotationToSegmentation|ImportSurfaceAnnotationToSegmentation]] [[#LoadSegmentationVolume|LoadSegmentationVolume]] [[#NewSegmentationVolume|NewSegmentationVolume]] [[#ReadVoxelLabels|ReadVoxelLabels]] [[#RecomputeSegmentation|RecomputeSegmentation]] [[#RestorePreviousSegmentation|RestorePreviousSegmentation]] [[#SaveSegmentationVolume|SaveSegmentationVolume]] [[#SetSegmentationAlpha|SetSegmentationAlpha]] [[#UndoLastEdit|UndoLastEdit]] === Viewing === [[#ReadCursor|ReadCursor]] [[#RedrawAll|RedrawAll]] [[#RedrawScreen|RedrawScreen]] [[#SendCursor|SendCursor]] [[#SetCursor|SetCursor]] [[#SetCursorColor|SetCursorColor]] [[#SetCursorShape|SetCursorShape]] [[#SetDTIAlpha|SetDTIAlpha]] [[#SetDisplayConfig|SetDisplayConfig]] [[#SetDisplayFlag|SetDisplayFlag]] [[#SetFuncOverlayAlpha|SetFuncOverlayAlpha]] [[#SetLinkedCursorFlag|SetLinkedCursorFlag]] [[#SetOrientation|SetOrientation]] [[#SetSegmentationAlpha|SetSegmentationAlpha]] [[#SetSlice|SetSlice]] [[#SetSurfaceLineColor|SetSurfaceLineColor]] [[#SetSurfaceLineWidth|SetSurfaceLineWidth]] [[#SetVolumeBrightnessContrast|SetVolumeBrightnessContrast]] [[#SetVolumeColorScale|SetVolumeColorScale]] [[#SetVolumeMinMax|SetVolumeMinMax]] [[#SetVolumeResampleMethod|SetVolumeResampleMethod]] [[#SetVolumeSampleType|SetVolumeSampleType]] [[#SetZoomCenter|SetZoomCenter]] [[#SetZoomLevel|SetZoomLevel]] [[#ShowNearestInterpolatedMainVertex|ShowNearestInterpolatedMainVertex]] [[#ShowNearestInterpolatedOriginalVertex|ShowNearestInterpolatedOriginalVertex]] [[#ShowNearestInterpolatedPialVertex|ShowNearestInterpolatedPialVertex]] [[#ShowNearestMainVertex|ShowNearestMainVertex]] [[#ShowNearestOriginalVertex|ShowNearestOriginalVertex]] [[#ShowNearestPialVertex|ShowNearestPialVertex]] [[#TimeCourse_SetDisplayFlag|TimeCourse_SetDisplayFlag]]