• ScubaGuide
• ScubaReference
• ScubaScripting

Scripting

Commands

Note that many commands take IDs, such as layerID, collectionID, viewID, toolID, frameID, etc. These IDs are generated when the objects they refer to are created. As input, they must refer to valid objects. If they don't you'll receive an error. All IDs are integers.

AddSegmentationToSegVolReport structure

• Adds a structure to the list of structures to be reported on.

AddSegVolReportIntensityVolume volID

• Add an intensity volume to the segmentation volume report.

BeginValueRangeFillInView viewID sourceVolID roiID destVolID

• Begins a series of value range fills using the value ranges in sourceVolID to set values in destVolID. sourceVolID and destVolID are collectionIDs.

CaptureFrameToFile frameID fileName

• Make a screen capture of the frame.

ClearSegVolReport

• Clears all info in the segmentation volume report.

ConvertWindowToViewRAS viewID windowX windowY

• Returns the RAS coordinates of the input window coordinate. windowX and windowY should be integers.

CopyViewLayersToAllViewsInFrame frameID viewID

• Copies the layer settings in a view to all other views in a frame.

DeleteCollectionROI collectionID roiID

• Deletes an ROI for this collection.

DeleteDataCollection collectionID

• Delete a data collection.

DeleteLayer layerID

• Deletes a layer. Does not delete any data collections associated with it.

DoOneValueRangeFillInView viewID beginValueRange endValueRange fillValue

• Adds a single range to a series of value range fills. Must be between a call to BeginValueRangeFillInView and EndValueRangeFillInView. beginValueRange, endValueRange, and fillValueRange should be values appropriate for the volume you are editing.

DontUseROIInSegVolReport

• Don't use an ROI in the segmentation volume report.

EndValueRangeFillInView viewID

• Performs the series of value range fills specified by DoOneValueRangeFill.

ExportMarkersToControlPoints collectionID fileName

• Writes the markers to a control.dat file using a volume collection to transform them.

Flood2DMRIVolume layerID x y z toolID viewID type

• Floods the volume in a 2DMRIS layer at the input RAS point x, y, z (in RAS floating point coords), using the input tool and view for settings. Floods are of the following types: voxelEditingNew, voxelEditingErase, roiEditingSelect, roiEditingUnselect.

Get2DMRILayerBrightness layerID

• Returns the brightness for this layer.

Get2DMRILayerColorLUT layerID

• Returns the LUT id for this layer.

Get2DMRILayerContrast layerID

• Returns the contrast for this layer.

Get2DMRILayerColorMapMethod layerID

• Returns the color map method for this layer.

Get2DMRILayerDrawMIP layerID

• Returns the value of the property for drawingthe maximum intensity projection.

Get2DMRILayerDrawZeroClear layerID

• Returns the value of the property for drawingvalues of zero clear.

Get2DMRILayerEditableROI layerID

• Returns whether or not this layer's ROI is editable.

Get2DMRILayerHeatScaleMax layerID

• Returns the heat scale max value for the layer.

Get2DMRILayerHeatScaleMid layerID

• Returns the heat scale mid value for the layer.

Get2DMRILayerHeatScaleMin layerID

• Returns the heat scale min value for the layer.

Get2DMRILayerLevel layerID

• Returns the grayscale color level of the volume.

Get2DMRILayerMaxValue layerID

• Returns the maximum value of the volume.

Get2DMRILayerMaxVisibleValue layerID

• Returns the maximum value to be drawn.

Get2DMRILayerMinValue layerID

• Returns the minimum value of the volume.

Get2DMRILayerMinVisibleValue layerID

• Returns the minimum value to be drawn.

Get2DMRILayerROIOpacity layerID

• Returns the opacity of the ROI for a layer.

Get2DMRILayerSampleMethod layerID

• Returns the sample method for this layer.

Get2DMRILayerVolumeCollection layerID

• Returns the volume collection for this layer.

Get2DMRILayerWindow layerID

• Returns the grayscale window for this layer.

Get2DMRIRASCoordsFromIndex layerID x y z

• Returns a list of RAS coords converted from the input index coords. x, y, or z should be integer coordinates.

Get2DMRISLayerLineColor layerID

• Returns the line color for this layer as a list of red, green, and blue integers from 0-255.

Get2DMRISLayerLineWidth layerID

• Returns the line width for this layer as an integer.

Get2DMRISLayerSurfaceCollection layerID

• Returns the surface collection for this layer.

Get2DMRISLayerVertexColor layerID

• Returns the vertex color for this layer as a list of red, green, and blue integers from 0-255.

Get2DMRISNearestVertexIndex layerID x y z

• Returns the index of the vertex closest to the input RAS coords and the distance to that vertex. x, y, and z should be floating point numbers.

Get2DMRISRASCoordsFromVertexIndex layerID vertexIndex

• Returns as a list of RAS coords the location of the vertex. vertexIndex should be an integer that's a valid index for the surface displayed by the layer.

GetCollectionRASBounds collectionID

• Return the bounds for this collection in RAS space. They will be returned as a list with six floating numbers: xmin, xmax, ymin, ymax, zmin, zmax.

GetCollectionLabel collectionID

• Return the label for this collection.

GetCollectionType collectionID

• Return the type for this layer.

GetColorLUTEntryLabel lutID entry

• Returns the label for an entry in an LUT. entry should be an integer index into the LUT.

GetColorLUTEntryRGB lutID entry

• Returns the rgb values (0-255) for an entry in an LUT. entry should be an integer index into the LUT.

GetColorLUTFileName lutID

• Returns the LUT file name for a transform.

GetColorLUTIDList

• Return a list of all colorLUTIDs.

GetColorLUTLabel lutID

• Returns the label for a color LUT.

GetColorLUTNumberOfEntries lutID

• Returns the number of entries in an LUT.

GetColumnOfViewInFrame frameID viewID

• Return the column of the view ID in a frame.

CycleCurrentViewInFrame frameID

• Selects the next view in a frame.

GetDataCollectionIDList

• Return a list of all collectionIDs.

GetFirstUnusedDrawLevelInView viewID

• Returns the first unused draw level.

GetLayerIDList

• Returns a list of all layerIDs.

GetLayerInViewAtLevel viewID level

• Returns the layer in a view at a given draw level. level should be an integer from 0 - 9.

GetLayerLabel layerID

• Return the label for this layer.

GetLayerMainDataCollection layerID

• Returns the collection ID of the main collection for this layer.

GetLayerOpacity layerID

• Return the opacity for this layer.

GetLayerReportInfo layerID

• Return whether or not a layer is reporting info.

GetLayerType layerID

• Return the type for this layer.

GetLevelReportInfoInView viewID level

• Returns whether a level in a view is reporting info. level should be an integer from 0 - 9.

GetLevelVisibilityInView viewID level

• Returns the visibility for a level in a view. level should be an integer from 0 - 9.

GetMainFrameID

• Returns the ID number of the main frame. This should be used whenever a frame ID is required.

GetNumberOfColsAtRowInFrame frameID row

• Return the number of columns in arow. row is an integer.

GetNumberOfRowsInFrame frameID

• Return the number of rows in a frame.

GetNumberOfViewMarkers

• Returns the number of view markers.

GetRASCoordsFromVolumeSurfaceRAS collectionID x y z

• Returns a list of RAS coords converted from the input surface RAS coords. This is for converting RAS points acquired from a surface that is associated with a volume and didn't generate coordinates with CRAS info. x, y, and z should be floating point numbers.

GetROIIDList

• Return a list of all ROIs.

GetROIIDListForCollection collectionID

• Returns a lit of roiIDs belonging to this collection.

GetRowOfViewInFrame frameID viewID

• Return the row of the view ID in a frame.

GetSelectedViewID frameID

• Return the viewID of the selected view.

GetSubjectDir

• Returns the path to the subject's data if the subject name was set.

GetSubjectName

• Returns the subject name if one was set.

GetSurfaceCollectionFileName collectionID

• Gets the file name for a given surface collection.

GetSurfaceDataToSurfaceTransformVolume collectionID

• If a surface collection is using a volume to get its data to surface transform, returns the volume's collection ID.

GetSurfaceUseRealRAS collectionID

• Returns whether or not a surface has its useRealRAS flag on.

GetToolBrush3D toolID

• Returns the current brush 3D of a tool.

GetToolBrushRadius toolID

• Gets the current brush radius of a tool.

GetToolBrushShape toolID

• Returns the current brush shape of a tool as a string: voxel, square or circle.

GetToolEdgePathEdgeBias toolID

• Returns the bias for edges for the edge path tool.

GetToolEdgePathStraightBias toolID

• Returns the bias for straight paths for the edge path tool.

GetToolEraseVoxelValue toolID

• Gets the erase voxel value of a tool.

GetToolFlood3D toolID

• Gets the current flood 3D of a tool.

GetToolFloodFuzziness toolID

• Returns a tool flood's fuzziness.

GetToolFloodFuzzinessType toolID

• Returns the tool's fuzziness type: seed or gradient.

GetToolFloodMaxDistance toolID

• Returns a tool flood's max distance.

GetToolFloodSourceCollection toolID

• Gets the current flood source collection of a tool.

GetToolFloodStopAtPaths toolID

• Returns whether or not a tool flood will stop at paths.

GetToolFloodStopAtROIs toolID

• Returns whether or not a tool flood will stop at ROIs.

GetToolIDForFrame frameID

• Returns the ID of the tool for this frame.

GetToolMode toolID

• Gets the current mode of a tool. The returned string will be one of the tool modes supplied to SetToolMode.

GetToolNewVoxelValue toolID

• Gets the new voxel value of a tool.

GetToolOnlyBrushZero toolID

• Returns whether or not a brush is only affecting zero values.

GetToolOnlyFloodZero toolID

• Returns whether or not a flood is only affecting zero values.

GetToolTargetLayer toolID

• Gets the target layer of a tool. Returns a layerID.

GetTransformIDList

• Return a list of all transformIDs.

GetTransformLabel transformID

• Returns the label for a transform.

GetTransformRegistrationDest transformID

• Returns the id of the dest volume if the transform is being treated as a registration.

GetTransformRegistrationSource transformID

• Returns the id of the source volume if the transform is being treated as a registration.

GetTransformValues transformID

• Returns a list of transform values in column order.

GetUseVolumeDataToIndexTransform collectionID

• Returns whether or not a volume is using its Data to Index transform (usually RAS transform) in displaying data.

GetViewFlipLeftRightYZ viewID

• Returns the left-right flip flag for a view.

GetViewIDAtFrameLocation frameID windowX windowY

• Return the view ID at a window location. windowX and windowY should be integers.

GetViewIDFromFrameColRow frameID col row

• Return the viewID from a view at a certain location. col and row must be valid integers for the current view configuration.

GetViewInPlane viewID

• Returns the in plane in a view.

GetViewLockOnCursor viewID

• Returns whether or not a view is locked on the cursor.

GetViewLinkedStatus viewID

• Returns the linked status for a view.

GetViewRASCenter viewID

• Returns the view center as a list of x, y, and z RAS coordinates.

GetViewRASCursor

• Returns the cursor in RAS coords in a list of x y z coords.

GetViewThroughPlaneIncrement viewID throughPlane

• Returns the through plane movement increment for throughPlane. throughPlane should be x, y, or z.

GetViewTransform viewID

• Returns the transformID of a view's view to world transform.

GetViewZoomLevel viewID

• Returns the zoom level in a view.

GetVolumeAutosaveOn collectionID

• Returns whether or not autosave is on for this volume.

GetVolumeAverageValueInROI collectionID roiID

• Returns the average value of the voxels in an ROI in a volume.

GetVolumeCollectionFileName collectionID

• Returns the file name for a given volume collection.

GetVolumeHistogramInView viewID volID roiID numBins

• Returns a histogram of the volume that's visible in a view. Returns the format: {minBinValue binIncrement {binCount0 binCount1 .. binCountN}} where binCountN is numBins-1. volID is a collectionID. numBins is an integer.

GetVolumeStandardDeviationInROI collectionID roiID

• Returns the standard deviation of the voxels in an ROI in a volume.

GetVolumeSurfaceRASCoordsFromRAS collectionID x y z

• Returns a list of surface RAS coords converted from the input RAS coords. Thisis for converting RAS points acquired from a surface that is associated with a volume and didn't generate coordinates with CRAS info. x, y, and z should be floating point numbers.

ImportMarkersFromControlPoints collectionID fileName

• Imports markers from a control.dat file using a volume collection to transform them..

InvertTransform transformID

• Inverts a transform.

IsSurfaceUsingDataToSurfaceTransformFromVolume collectionID

• Returns whether or not a surface collection is using a volume to get its data to surface transform.

IsTransformRegistration transformID

• Returns whether or not a transform is being treated as a registration.

LoadVolume fileName createLayer frameIDToAdd

• Loads a volume from fileName. createLayer should be 1 or 0 and specifies whether an appropriate layer will be created, and if so, frameIDToAdd should specify which frame to add the layer to in all views. createLayer should probably be 1 and frameIDToAdd should be a call to GetMainFrameID.

LoadVolumeFromFileName collectionID

• Loads the volume from the file name. The file name must have been set previously.

LoadSurface fileName createLayer frameIDToAdd

• Loads a surface from fileName. createLayer should be 1 or 0 and specifies whether an appropriate layer will be created, and if so, frameIDToAdd should specify which frame to add the layer to in all views. createLayer should probably be 1 and frameIDToAdd should be a call to GetMainFrameID.

LoadSurfaceFromFileName collectionID

• Loads the surface from the file name.

LoadSurfacePatch collectionID fileName

• Loads a patch into a surface.

LoadTransform fileName

• Loads a transform.

LoadTransformFromLTAFile transformID LTAFileName

• Loads an LTA from a file into an existing transform.

MakeDataCollection collectionType

• Make a new data collection of the given type and return the collectionID. collectionID should be a recognized collection type such as:

• Note that there are easier functions to use to load data, such as LoadVolume and LoadSurface. This is a low level function that creates a data collection but does not load any actual data nor create a layer.

MakeLayer layerType

• Makes a new layer of the given type and returns the layerID. layerID should be a recognized layer type such as:

• Note that there are easier functions to use to load data, such as LoadVolume and LoadSurface. This is a low level function that creates a layer but does not associate any data with it nor add it to any views.

MakeLayer layerType

• Makes a new layer of the given type and returns the layerID. layerID should be a recognized layer type such as:

• Note that there are easier functions to use to load data, such as LoadVolume and LoadSurface. This is a low level function that creates a layer but does not associate any data with it nor add it to any views.

MakeNewColorLUT

• Creates a new color LUT and returns its ID.

MakeNewTransform

• Creates a new transform and returns its ID.

MakeSegVolIntensityReport fnReport

• Make the intensity report from the segmentation volume report.

MakeSegVolReport fnReport

• Make the segmentation volume report.

MakeVolumeUsingTemplate collectionID templateCollectionID

• Makes a volume using an existing volume as a template. Given an existing volume, this initializes internal settings according to an existing template.

NewCollectionROI collectionID

• Makes a new ROI for this collection and returns the ID.

NewVolume templateID createLayer frameIDToAdd

• Creates a new volume based on an existing one. templateID is a collectionID for the volume to use as a template. createLayer should be 1 or 0 and specifies whether an appropriate layer will be created, and if so, frameIDToAdd should specify which frame to add the layer to in all views. createLayer should probably be 1 and frameIDToAdd should be a call to GetMainFrameID.

NewVolumeROIFromLabel collectionID fileName

• Creates an ROI from a label file and returns the ID of the new ROI.

PrintAllCommands

• Print all registered commands.

ReadPathFile fileName

• Read paths from a file.

RedrawFrame frameID

• Tells a frame to redraw without waiting for the next update event. Should be used in scripts to force a redraw before taking a screenshot.

RemoveAllLayersFromView viewID

• Remove all layers from a view.

RemoveLayerFromViewAtLevel viewID level

• Remove a layer from a view. level should be an integer from 0 - 9.

SaveSceneScript fileName

• Makes a script that can be used to reproduce the current view configuration.

SaveVolume collectionID

• Save volume with its file name.

SaveVolumeWithFileName collectionID fileName

• Save volume with a given file name.

SelectCollectionROI collectionID roiID

• Selects an ROI for this collection.

Set2DMRILayerBrightness layerID brightness

• Sets the brightness for this layer. brightness should be a floating point number from 0 to 1.

Set2DMRILayerColorLUT layerID lutID

• Sets the LUT for this layer.

Set2DMRILayerColorMapMethod layerID method

• Sets the color map method for this layer. method should be grayscale, heatScale, or lut.

Set2DMRILayerContrast layerID contrast

• Sets the contrast for this layer. contrast should be a floating point number from 0 to 30.

Set2DMRILayerDrawMIP layerID drawMIP

• Sets property for drawing the maximum intensity projection. drawMIP should be 1 or 0.

Set2DMRILayerDrawZeroClear layerID drawClear

• Sets property for drawingvalues of zero clear. drawClear should be 1 or 0.

Set2DMRILayerEditableROI layerID editable

• Specify whether or not this layer's ROI is editable. editable should be 1 or 0.

Set2DMRILayerHeatScaleMax layerID value

• Sets the heat scale max value for the layer. value should be a value in the range of the volume belonging to the layer.

Set2DMRILayerHeatScaleMid layerID value

• Sets the heat scale mid value for the layer. value should be a value in the range of the volume belonging to the layer.

Set2DMRILayerHeatScaleMin layerID value

• Sets the heat scale min value for the layer. value should be a value in the range of the volume belonging to the layer.

Set2DMRILayerLevel layerID level

• Sets the grayscale color level for the layer. level should be a floating value from 0 to 1.

Set2DMRILayerMaxVisibleValue layerID value

• Sets the maximum value to be drawn.values of zero clear. value should be a value in the range of the volume belonging to the layer.

Set2DMRILayerMinVisibleValue layerID value

• Sets the minimum value to be drawn.values of zero clear. value should be a value in the range of the volume belonging to the layer.

Set2DMRILayerROIOpacity layerID opacity

• Sets the opacity of the ROI for a layer. opacity should be from 0 to 1.

Set2DMRILayerSampleMethod layerID method

• Sets the sample method for this layer. method should be nearest, trilinear, or sinc.

Set2DMRILayerVolumeCollection layerID collectionID

• Sets the volume collection for this layer.

Set2DMRISLayerLineColor layerID red green blue

• Sets the line color for this layer. red, green, and blue should be 0-255 integers.

Set2DMRISLayerLineWidth layerID width

• Sets the line width for this layer. width should be an integer.

Set2DMRISLayerSurfaceCollection layerID collectionID

• Sets the surface collection for this layer.

Set2DMRISLayerVertexColor layerID red green blue

• Sets the vertex color for this layer. red, green, and blue should be 0-255 integers.

Set2DMRILayerWindow layerID window

• Sets the grayscale window for the layer. window should be a floating value from 0 to 1.

SetCollectionLabel collectionID label

• Set the label for a collection.

SetColorLUTFileName lutID fileName

• Set the LUT file name for a colorLUT.

SetColorLUTLabel lutID label

• Set the label for a color LUT. labe should be a string.

SetCursorFromEditDatFile

• Reads a cursor from a subject's edit.dat file if it exists and the subject name has been set.

SetCursorFromSurfaceVertexIndex layerID vertexNumber

• Sets the cursor to a vertex in a surface. The layer should be one displaying a surface, and vertexNumber should be a valid vertx index in the layer's surface.

SetCursorFromVolumeIndexCoords collectionID x y z

• Converts the given MRI index coordinate to RAS and sets the cursor from that, converting in the volume referenced by collectionID. x, y, and z should be integers.

SetDataTransform collectionID transformID

• Set the data to world transform for a data collection.

SetFrameViewConfiguration frameID configuration

• Sets a frame's view configuration. Supported configurations, where each number is the number of columns in a row: c1 c22 c44 c13.

SetLayerInViewAtLevel viewID layerID level

• Sets the layer in a view at a given draw level. Higher draw levels will draw later. level should be an integer from 0 - 9.

SetLayerLabel layerID label

• Set the label for a layer.

SetLayerOpacity layerID opacity

• Set the opacity for this layer. opacity should be a float from 0 to 1.

SetLayerReportInfo layerID report

• Set whether or not a layer should report info. report should be 1 or 0.

SetLevelReportInfoInView viewID level reportInfo

• Sets the flag for reporting info for a level in a view. level should be an integer from 0 - 9. reportInfo should be 1 or 0.

SetLevelVisibilityInView viewID level visibility

• Sets the visibility for a level in a view. level should be an integer from 0 - 9. visibility should be 1 or 0.

SetNumberOfViewMarkers numMarkers

• Sets the number of view markers.

SetROIForSegVolReport volID roiID

• Set the volume and ROI to use in the segmentation volume report.

SetSegVolReportLUT lutID

• Set the LUT in the segmentation volume report.

SetSegVolReportSegmentation segID

• Set the segmentation volume in the segmentation volume report.

SetSelectedViewID frameID viewID

• Sets the select view in a frame.

SetSurfaceCollectionFileName collectionID fileName

• Sets the file name for a given surface collection.

SetSurfaceDataToSurfaceTransformFromVolume collectionID volumeID

• Gets the data to surface transform from a volume.

SetSurfaceDataToSurfaceTransformToDefault collectionID

• Sets the data to surface transform for a surface to the default, which will be ../mri/orig or identity.

SetToolBrush3D toolID 3D

• Sets the current brush 3D of a tool. 3D is either 1 or 0.

SetToolBrushRadius toolID radius

• Sets the current brush radius of a tool. radius should be a floating point number.

SetToolBrushShape toolID shape

• Sets the current brush shape of a tool. shape should be voxel, square or circle.

SetToolEdgePathEdgeBias toolID bias

• Sets the bias for edges for the edge path tool. bias is a floating point number from 0 to 1.

SetToolEdgePathStraightBias toolID bias

• Sets the bias for straight paths for the edge path tool. bias is a floating point number from 0 to 1.

SetToolEraseVoxelValue toolID value

• Sets the erase voxel value of a tool.

SetToolFlood3D toolID 3D

• Sets the current flood 3D of a tool. 3D is either 1 or 0.

SetToolFloodFuzziness toolID fuzziness

• Specify a tool flood's fuzziness. fuzziness is a floating point number.

SetToolFloodFuzzinessType toolID type

• Sets the tool's fuzziness type. type should be seed or gradient.

SetToolFloodMaxDistance toolID distance

• Specify a tool flood's max distance. distance is a floating point number.

SetToolFloodSourceCollection toolID collectionID

• Sets the current flood source collection of a tool.

SetToolFloodStopAtPaths toolID stop

• Specify whether a tool flood should stop at paths. stop is either 1 or 0.

SetToolFloodStopAtROIs toolID stop

• Specify whether a tool flood should stop at ROIs. stop is either 1 or 0.

SetToolMode toolID mode

• Sets the current mode of a tool. mode should be one of the following:

SetToolNewVoxelValue toolID value

• Sets the new voxel value of a tool. value is a float.

SetToolOnlyBrushZero toolID onlyZero

• Specify whether the brush should only affect zero values..

SetToolOnlyFloodZero toolID onlyZero

• Specify whether the flood should only affect zero values. onlyZero is 1 or 0.

SetToolTargetLayer toolID layerID

• Sets the target layer of a tool.

SetTransformLabel transformID label

• Set the label for a transform. label should be a string.

SetTransformValues transformID listOfValues

• Sets the values of a transform. listOfValues should be a list of 16 values in column order.

SetUseVolumeDataToIndexTransform collectionID use

• Use or don't use the volume's Data to Index transform (usually RAS transform) in displaying data. use should be 1 or 0.

SetViewFlipLeftRightYZ viewID flip

• Set the left-right flip flag for a view. flip should be 1 or 0.

SetViewInPlane viewID inPlane

• Sets the in plane in a view. inPlane should be one of the following: x y z

SetViewLinkedStatus viewID linked

• Set the linked status for a view.

SetViewLockOnCursor viewID lock

• Set a view to keep its view locked on the cursor. lock should be 1 or 0.

SetViewRASCenter viewID x y z

• Sets the view center. x, y, and z should be floating point numbers in world RAS coordinates.

SetViewRASCursor x y z

• Sets the cursor in RAS coords. x, y, and z are floating point numbers.

SetViewStateToLayerBounds viewID layerID

• Sets the view so that the layer's data completely fills the view.

SetViewThroughPlaneIncrement viewID throughPlane increment

• Set the amount that using the through plane movement keys will increment or decrement the through plane RAS value. throughPlane should be x, y, or z. increments should be a floating point number.

SetViewTransform viewID transformID

• Set the view to world transform for a view.

SetViewZoomLevel viewID zoomLevel

• Sets the zoom level in a view. zoomLevel should be a floating point number. 1 is normal zoom, 0-1 is zoomed out, and 1+ is zoomed in.

SetVolumeAutosaveOn collectionID on

• Set whether or not autosave is on for this volume. on should be 1 or 0.

SetVolumeCollectionFileName collectionID fileName

• Sets the file name for a given volume collection. This does not actually load the volume.

TreatTransformAsNative transformID

• If a transform was set to be treated as a registration, this restores it to normal.

TreatTransformAsRegistration transformID sourceVolumeID destVolumeID

• Treats a transform as a tkregistration between two volumes, getting the necessary geometry information from them to register them.. sourceVolumeID and destVolumeID are collectionIDs.

UpdateFrame frameID

• Forces a redraw of the given frame.

WriteCursorToEditDatFile

• Writes the cursor location to a subject's edit.dat file if it exists and the subject name has been set.

WritePathFile fileName

• Write paths to a file.

WriteVolumeROIsToSegmentation collectionID fileName

• Writes a series of structure ROIs to a segmentation volume. This will write all of the ROIs in the collection that are marked as structure ROIs to a new segmentation volume.

WriteVolumeROIToLabel collectionID roiID fileName

• Writes an ROI to a label file. Must provide the collectionID that the ROI is associated with; if the ROI doesn't match the collection, you'll receive an error.

Index

Loading Data

NewVolume LoadVolume LoadSurface LoadTransform

Frames

GetMainFrameID UpdateFrame RedrawFrame SetFrameViewConfiguration GetViewIDFromFrameColRow GetSelectedViewID SetSelectedViewID GetNumberOfRowsInFrame GetNumberOfColsAtRowInFrame GetViewIDAtFrameLocation GetColumnOfViewInFrame GetRowOfViewInFrame CopyViewLayersToAllViewsInFrame GetToolIDForFrame CycleCurrentViewInFrame CaptureFrameToFile

Views

SaveSceneScript ConvertWindowToViewRAS

View State

SetViewInPlane GetViewInPlane SetViewZoomLevel GetViewZoomLevel SetViewRASCenter GetViewRASCenter SetViewStateToLayerBounds SetViewLinkedStatus GetViewLinkedStatus SetViewLockOnCursor GetViewLockOnCursor SetViewTransform GetViewTransform SetViewFlipLeftRightYZ GetViewFlipLeftRightYZ SetViewThroughPlaneIncrement GetViewThroughPlaneIncrement

Draw Levels

SetLayerInViewAtLevel GetLayerInViewAtLevel RemoveAllLayersFromView RemoveLayerFromViewAtLevel SetLevelVisibilityInView GetLevelVisibilityInView SetLevelReportInfoInView GetLevelReportInfoInView GetFirstUnusedDrawLevelInView

Cursor

SetViewRASCursor GetViewRASCursor SetCursorFromSurfaceVertexIndex SetCursorFromVolumeIndexCoords SetCursorFromEditDatFile WriteCursorToEditDatFile

Markers

SetNumberOfViewMarkers GetNumberOfViewMarkers ExportMarkersToControlPoints ImportMarkersFromControlPoints

Paths

WritePathFile ReadPathFile

Layers

GetLayerIDList MakeLayer DeleteLayer SetLayerLabel GetLayerLabel GetLayerType GetLayerOpacity SetLayerOpacity GetLayerReportInfo SetLayerReportInfo GetLayerMainDataCollection

2DMRI Layer

Set2DMRILayerVolumeCollection Get2DMRILayerVolumeCollection Set2DMRILayerColorMapMethod Get2DMRILayerColorMapMethod Set2DMRILayerSampleMethod Get2DMRILayerSampleMethod Set2DMRILayerBrightness Get2DMRILayerBrightness Set2DMRILayerContrast Get2DMRILayerContrast Set2DMRILayerMinLevel Get2DMRILayerMinLevel Set2DMRILayerMinWindow Get2DMRILayerMinWindow Set2DMRILayerColorLUT Get2DMRILayerColorLUT Set2DMRILayerDrawZeroClear Get2DMRILayerDrawZeroClear Set2DMRILayerDrawMIP Get2DMRILayerDrawMIP Set2DMRILayerMinVisibleValue Get2DMRILayerMinVisibleValue Set2DMRILayerMaxVisibleValue Get2DMRILayerMaxVisibleValue Get2DMRILayerMinValue Get2DMRILayerMaxValue Get2DMRILayerHeatScaleMin Set2DMRILayerHeatScaleMin Get2DMRILayerHeatScaleMid Set2DMRILayerHeatScaleMid Get2DMRILayerHeatScaleMax Set2DMRILayerHeatScaleMax Set2DMRILayerROIOpacity Get2DMRILayerROIOpacity Set2DMRILayerEditableROI Get2DMRILayerEditableROI Get2DMRIRASCoordsFromIndex Flood2DMRIVolume

2DMRIS Layer

Set2DMRISLayerSurfaceCollection Get2DMRISLayerSurfaceCollection Set2DMRISLayerLineColor Get2DMRISLayerLineColor Set2DMRISLayerVertexColor Get2DMRISLayerVertexColor Set2DMRISLayerLineWidth Get2DMRISLayerLineWidth Get2DMRISRASCoordsFromVertexIndex Get2DMRISNearestVertexIndex

ROIs

GetROIIDList GetROIIDListForCollection NewVolumeROIFromLabel DeleteCollectionROI NewCollectionROI SelectCollectionROI WriteVolumeROIsToSegmentation WriteVolumeROIToLabel GetVolumeAverageValueInROI GetVolumeStandardDeviationInROI

Color LUTs

GetColorLUTIDList MakeNewColorLUT SetColorLUTLabel GetColorLUTLabel SetColorLUTFileName GetColorLUTFileName GetColorLUTNumberOfEntries GetColorLUTEntryLabel GetColorLUTEntryRGB IsColorLUTEntryValid

Transforms

GetTransformIDList MakeNewTransform SetTransformLabel GetTransformLabel SetTransformValues GetTransformValues LoadTransformFromLTAFile InvertTransform TreatTransformAsRegistration TreatTransformAsNative IsTransformRegistration GetTransformRegistrationSource GetTransformRegistrationDest

Data Collections

GetDataCollectionIDList MakeDataCollection DeleteDataCollection GetCollectionRASBounds

Volumes

SetUseVolumeDataToIndexTransform GetUseVolumeDataToIndexTransform SetVolumeAutosaveOn GetVolumeAutosaveOn GetRASCoordsFromVolumeSurfaceRAS GetVolumeSurfaceRASCoordsFromRAS GetVolumeAverageValueInROI GetVolumeStandardDeviationInROI

Segmentation Volume Report

ClearSegVolReport SetSegVolReportSegmentation AddSegVolReportIntensityVolume SetROIForSegVolReport DontUseROIInSegVolReport SetSegVolReportLUT AddSegmentationToSegVolReport MakeSegVolReport MakeSegVolIntensityReport

Volume Histogram

GetVolumeHistogramInView BeginValueRangeFillInView DoOneValueRangeFillInView EndValueRangeFillInView

Surfaces

SetSurfaceCollectionFileName LoadSurfaceFromFileName GetSurfaceCollectionFileName SetSurfaceDataToSurfaceTransformFromVolume SetSurfaceDataToSurfaceTransformToDefault IsSurfaceUsingDataToSurfaceTransformFromVolume GetSurfaceDataToSurfaceTransformVolume LoadSurfacePatch GetSurfaceUseRealRAS

Tools

SetToolMode GetToolMode SetToolTargetLayer GetToolTargetLayer SetToolNewVoxelValue GetToolNewVoxelValue SetToolEraseVoxelValue GetToolEraseVoxelValue SetToolOnlyBrushZero GetToolOnlyBrushZero SetToolBrushRadius GetToolBrushRadius SetToolBrushShape GetToolBrushShape SetToolBrush3D GetToolBrush3D SetToolFloodStopAtPaths GetToolFloodStopAtPaths SetToolFloodStopAtROIs GetToolFloodStopAtROIs SetToolFloodFuzziness GetToolFloodFuzziness SetToolFloodMaxDistance GetToolFloodMaxDistance SetToolFlood3D GetToolFlood3D SetToolFloodSourceCollection SetToolFloodFuzzinessType GetToolFloodFuzzinessType GetToolFloodSourceCollection SetToolOnlyFloodZero GetToolOnlyFloodZero SetToolEdgePathStraightBias GetToolEdgePathStraightBias SetToolEdgePathEdgeBias GetToolEdgePathEdgeBias

Miscellaneous

GetSubjectName GetSubjectDir PrintAllCommands