Interface Document

The Document interface contains all properties and methods of objects of a FMR/VMR/AMR project (=document)

 

Public Methods

 

[more] PathName()
Gets the name of a project.
[more] PathName(string value)
Sets the name of a project.
[more] MapThreshold()
Gets the statistical threshold used in subsequent commands visualizing statistical maps.
[more] MapThreshold(number value)
Sets the statistical threshold used in subsequent commands visualizing statistical maps.
[more] MapClusterSize()
Valid only if objDocument is of type FMR or VMR.
[more] PixelSizeOfInplaneX()
Resolution of one pixel in x dimension [mm]
[more] PixelSizeOfInplaneY()
Resolution of one pixel in y dimension [mm]
[more] SliceThickness()
Get slice thickness without slice gap [mm]
[more] SliceThickness(number value)
Set slice thickness without slice gap [mm]
[more] GapThickness()
Get slice thickness without slice gap [mm]
[more] GapThickness(number value)
Set slice thickness without slice gap [mm]
[more] TR()
Gets TR of FMR project
[more] TR(number value)
Sets TR of fmr-project
[more] InterSliceTime()
Gets or set InterSliceTime of fmr-project
[more] TimeResolutionVerified()
Get flag ensuring that "TR" and "IST" are correct
[more] TimeResolutionVerified(number value)
Set flag ensuring that "TR" and "IST" are correct
[more] VoxelResolutionVerified([out, retval] number* value)
Get flag ensuring that pixel resolution values are correct
[more] VoxelResolutionVerified(number value)
Set flag ensuring that pixel resolution values are correct
[more] FileNameOfPreprocessdFMR()
Property of preprocessed fmr-project, generated by BrainVoyager; non-preprocessed fmr-project still exists
[more] StimulationProtocolResolution()
Gets time resolution of stimulation protocol in msec or volumes
[more] StimulationProtocolResolution(number value)
Sets time resolution of stimulation protocol in msec or volumes
[more] NrOfStimulationProtocolConditions()
Gets or sets the number of stimulation protocol conditions
[more] StimulationProtocolExperimentName()
Gets the experiment name as defined in the stimulation protocol
[more] StimulationProtocolExperimentName(string value)
Sets the experiment name in the stimulation protocol
[more] StimulationProtocolBackgroundColorR()
Gets the 'Red' dimension of stimulation protocol background color; value between 0 and 255.
[more] StimulationProtocolBackgroundColorR(number value)
Sets the 'Red' dimension of stimulation protocol background color; value between 0 and 255.
[more] StimulationProtocolBackgroundColorG()
Gets the 'Green' dimension of stimulation protocol background color; value between 0 and 255.
[more] StimulationProtocolBackgroundColorG(number value)
Sets the 'Green' dimension of stimulation protocol background color; value between 0 and 255.
[more] StimulationProtocolBackgroundColorB()
Gets the 'Blue' dimension of stimulation protocol background color; value between 0 and 255.
[more] StimulationProtocolBackgroundColorB(number value)
Sets the 'Blue' dimension of stimulation protocol background color; value between 0 and 255.
[more] StimulationProtocolTextColorR()
Gets the 'Red' dimension of stimulation protocol text color; value between 0 and 255.
[more] StimulationProtocolTextColorR(number value)
Sets the 'Red' dimension of stimulation protocol text color; value between 0 and 255.
[more] StimulationProtocolTextColorG()
Gets the 'Green' dimension of stimulation protocol text color; value between 0 and 255.
[more] StimulationProtocolTextColorG(number value)
Sets the 'Green' dimension of stimulation protocol text color; value between 0 and 255.
[more] StimulationProtocolTextColorB()
Gets the 'Blue' dimension of stimulation protocol text color; value between 0 and 255.
[more] StimulationProtocolTextColorB(number value)
Sets the 'Blue' dimension of stimulation protocol text color; value between 0 and 255.
[more] StimulationProtocolTimeCourseColorR()
Gets the 'Red' dimension of the stimulation protocol time course color; value between 0 and 255.
[more] StimulationProtocolTimeCourseColorR(number value)
Sets the 'Red' dimension of the stimulation protocol time course color; value between 0 and 255.
[more] StimulationProtocolTimeCourseColorG()
Gets the 'Green' dimension of the stimulation protocol time course color; value between 0 and 255.
[more] StimulationProtocolTimeCourseColorG(number value)
Sets the 'Green' dimension of the stimulation protocol time course color; value between 0 and 255.
[more] StimulationProtocolTimeCourseColorB()
Gets the 'Blue' dimension of the stimulation protocol time course color; value between 0 and 255.
[more] StimulationProtocolTimeCourseColorB(number value)
Sets the 'Blue' dimension of the stimulation protocol time course color; value between 0 and 255.
[more] StimulationProtocolTimeCourseThickness()
Gets thickness of line of response function
[more] StimulationProtocolTimeCourseThickness(number value)
Sets thickness of line of response function
[more] PositiveStatisticalValues()
Get whether positive values on overlay statistical map are shown
[more] PositiveStatisticalValues(number value)
Set whether positive values on overlay statistical map are shown
[more] NegativeStatisticalValues()
Get whether negative values on overlay statistical map are shown
[more] NegativeStatisticalValues(number value)
Set whether negative values on overlay statistical map are shown
[more] TwoSetContributionMaps()
Get whether the two set contribution maps option should be used (Overlay GLM contrasts dialog)
[more] TwoSetContributionMaps(number value)
Set whether relative contribution should be used.
[more] MatrixSizeX()
Gets number of columns of slice image matrix
[more] MatrixSizeY()
Gets number of rows of slice image matrix
[more] NrOfSlices()
Gets number of slices per volume (scan)
[more] NrOfSlices(number value)
Sets number of slices per volume (scan)
[more] NrOfVolumes()
Gets or sets number of volumes
[more] NrOfSkippedVolumes([out, retval] number* value)
Gets number of skipped volumes
[more] NrOfSkippedVolumes(number value)
Sets number of skipped volumes
[more] SeparationOfSubjectPredictors()
GLM-property
[more] SeparationOfStudyPredictors()
GLM-property
[more] ZTransformationOfStudies()
Get ZTransformationOfStudies; 1 -> time courses of runs have been z-transformed, 0 -> not.
[more] ZTransformationOfStudies(number value)
Set ZTransformationOfStudies; 1 -> time courses of runs have been z-transformed, 0 -> not.
[more] Save()
Saves a BrainVoyager project file using the current file name
[more] SaveAs(string SaveAsFileName)
Saves a BrainVoyager project file under a specifed file name.
[more] Close()
Closes a BrainVoyager project file.
[more] Remove()
Method Remove() is used to remove intermediate fmr-files while preprocessing.
[more] RefreshView()
Repaints the document's view which is a window showing an FMR, VMR or AMR project.
[more] SetCrossPosition( number x, number y, number z)
Sets the current voxel.
[more] SwitchToSurfaceModule()
Activates the Surface Module window.
[more] Show3DVolumeTools()
Shows the 3D Volume Tools dialog.
[more] Hide3DVolumeTools()
Hides the 3D Volume Tools dialog.
[more] LoadMesh(string MeshFileName)
Loads a surface mesh file.
[more] SaveSnapshotOfSurfaceWindow(string MeshFileName)
Makes a snapshot of the surface module window.
[more] AddMesh(string MeshFileName)
Reads a surface mesh file and adds it to the Surface Module window of the referenced VMR document.
[more] UpdateSurfaceWindow()
Repaints the Surface Module window which is a window showing one or more surface mesh files.
[more] SetViewpointPosition( number x, number y, number z)
Sets the 3D position of the viewpoint from which the scene in the Surface Module window is "seen".
[more] ViewpointTranslationX(int translX)
Move the viewing direction from which the scene in the Surface Module window is "seen" right or left.
[more] ViewpointTranslationY(int translY)
Move the viewing direction from which the scene in the Surface Module window is "seen" up or down.
[more] ViewpointTranslationZ(int translZ)
Move the viewing direction from which the scene in the Surface Module window is "seen" backward or forward.
[more] ViewpointRotationX(int rotX)
Rotate the viewing direction from which the scene in the Surface Module window around the X-axis (back to front in Talairach space) (in degrees (0-360)).
[more] ViewpointRotationY(int rotY)
Rotate the viewing direction from which the scene in the Surface Module window around the Y-axis (right to left in Talairach space) (in degrees (0-360)).
[more] ViewpointRotationZ(int rotZ)
Rotate the viewing direction from which the scene in the Surface Module window around the Z-axis (top to bottom in Talairach space) (in degrees (0-360)).
[more] SliceMeshAxial(number z)
Slices a surface mesh parallel to the XY-plane at the specified Z-level.
[more] SliceMeshCoronal(number y)
Slices a surface mesh parallel to the XZ-plane at the specified Y-level.
[more] SliceMeshSagittal(number x)
Slices a surface mesh parallel to the YZ-plane at the specified X-level.
[more] MeshSlicesOff()
Removes all activated slices from the current mesh.
[more] LoadViewingSettings(string FileNameVWP)
Restores surface module settings about the viewing position, angles, lightning conditions previously stored to disk.
[more] LoadGLM(string FileNameGLM)
Loads a file containg the results of a multiple regression (GLM) analysis.
[more] RunGLMFromProtocol()
Compute the General Linear Model with the linked protocol
[more] SaveGLM(string FileNameGLM)
Save the computed General Linear Model with the provided name
[more] ShowGLM()
Shows statistical map based on selected predictors of a GLM superimposed on (anatomical) reference images.
[more] SelectPredictorInSet1(number prednr)
Adds a predictor into set1 of two sets available for display of multiple regression (GLM) results.
[more] SelectPredictorInSet2(number prednr)
Adds a predictor into set2 of two sets available for display of multiple regression (GLM) results.
[more] SelectAllPredictors()
Selects all predictors of a multiple regression (GLM) result for display.
[more] DeselectAllPredictors()
Deselects all predictors of a multiple regression (GLM) result allowing to start a new predictor selection process.
[more] EnableTwoSetPredictorColours()
A flag is set to show the relative contribution of the combined variance explained by two sets of predictors in a multiple regression (GLM).
[more] EnableTwoSetPredictorContrast()
Sets the status of a flag to show the contrast between two sets of predictors in a multiple regression (GLM).
[more] SliceTimeCorrection(number SliceSamplingType)
Most EPI sequences measure the slices of a functional volume in succession but one often would like to treat the data of one volume as if it were acquired at the same time, particularly in the context of event-related studies.
[more] SliceTimeCorrectionEx( number TR, number InterSliceTime, number SliceSamplingType, number SincInterpolation, string NewFMRFile, string NewSTCPrefix)
Most EPI sequences measure the slices of a functional volume in succession but one often would like to treat the data of one volume as if it were acquired at the same time, particularly in the context of event-related studies.
[more] TemporalSmoothingFD2D(number HighPass, number LowPass)
Filters in the frequency domain the time series of each voxel in the STC files of an FMR project.
[more] TemporalSmoothingFD2DEx( number HighPass, number LowPass, string NewFMRFile, string NewSTCPrefix)
Filters the time series of each voxel in the STC files of an FMR project.
[more] SpatialSmoothingFD2D( number HighPass, number LowPass)
Spatially filters each recorded image in the STC files of an FMR project in the frequency domain.
[more] SpatialSmoothingFD2DEx( number HighPass, number LowPass, string NewFMRFile, string NewSTCPrefix)
Spatially filters each recorded image in the STC files of an FMR project in the frequency domain.
[more] CreateVTC( string FMRFile, string 2D3DTRFFile, string ACPCTRFFile, string TALFile, string VTCFileName)
Transforms the time course data of an FMR project into a defined 3D space, typically Talairach space.
[more] CorrectMotion(int targetVolume)
Detects and corrects rigid-body motion within an FMR file.
[more] CorrectMotionTargetVolumeInOtherRun(str intraSessionRunName, int targetVolume)
Detects and corrects rigid-body motion within several runs.
[more] TemporalSmoothingFD3D( number HighPass, number LowPass)
Filters in the frequency domain the time series of each voxel in a VTC file.
[more] SpatialSmoothingFD3D( number HighPass, number LowPass)
Spatially filters each 3D volume of a VTC file in the frequency domain.
[more] TemporalSmoothingFD3DEx( number HighPass, number LowPass, string VTCFileNameIn, string VTCFileNameOut)
Filters the time series of each voxel in a VTC file.
[more] SpatialSmoothingFD3DEx( number HighPass, number LowPass, string VTCFileNameIn, string VTCFileNameOut)
Spatially filters each 3D volume of a VTC file in the frequency domain.
[more] LinkVTC( string VTCFileName, number LoadInMem)
Links a 3D time course file (VTC) to a 3D anatomical project (VMR).
[more] SetVoxelIntensity( int x, int y, int z, int value)
Sets the intensity value of the specified voxel in an VMR data set.
[more] GetVoxelIntensity( int x, int y, int z)
Gets the voxel intensity of the voxel specified by the coordinates
[more] SetLayoutRowsCols( number NrOfRows, number NrOfCols)
Defines a grid of rows and columns in which multiple images of an FMR or AMR project are shown.
[more] SetZoomLevel(number ZoomLevel)
Sets the zoom level of the view of a BrainVoyager project file (FMR, VMR, AMR).
[more] ConvertFuncToAMR(string AMRFileName)
Converts the first functional volume of an FMR project into an AMR file.
[more] LinkAMRFile(string AMRFileName)
Links a (pseudo-) anatomical AMR file to an FMR document.
[more] LinkStimulationProtocol(string ProtocolFileName)
Links a stimulation protocol PRT file to an FMR project or a 3D volume time course VTC file.
[more] BeginRecordingSurfaceWindowMovie(string AVIMovieFileName)
Starts recording every updated view in the Surface Module window and saves it to a movie file.
[more] EndRecordingSurfaceWindowMovie()
Stops recording Surface Module window movie and closes the movie file.
[more] ShowTimeCourseOfVoxel( number x, number y, number z, string TCWinName)
Shows a time course from a Region-Of-Interest of the currently linked VTC file.
[more] ShowTimeCourseOfVoxelEx( number x, number y, number z, string TCWinName, number SingleVoxel, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height, number NewWin, number AddWin)
Shows a time course from a Region-Of-Interest of the currently linked VTC file.
[more] MoveTimeCoursePlot( string TCWinName, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height)
Moves a previously created time course window to a new screen position and changes its width and height.
[more] CloseTimeCoursePlot(string TCWinName)
Closes a previously created time course window.
[more] CloseAllTimeCoursePlots()
Closes all previously created time course windows.
[more] ShowEventRelatedAverage( string TCWinName, string AVGFile)
Averages events as specified in an AVG file and shows the event-related averaging results in a window.
[more] ShowEventRelatedAverageEx( string TCWinName, string AVGFile, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height)
Averages events as specified in an AVG file and shows the event-related averaging results in a window.
[more] MoveEventRelatedAveragePlot( string TCWinName, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height)
Moves a previously created event-related averaging window to a new screen position and changes its width and height.
[more] CreateSphereMesh()
Creates a new spherical mesh which can be used to reconstruct the skin of a subject's head by iterative morphing.
[more] RemoveBridges(string SourceVMRFileName)
Remove topological errors named 'handles' or 'bridges' (object produced by puncturing a surface twice)
[more] RemoveBridgesEx( string SourceVMRFileName, int GreyMatterIntensity, int WhiteMatterIntensity, int GMWMThreshold)
Remove topological errors - extended version
[more] PrepareBoundaryReconstruction()
This option guarantees that the subsequent reconstruction process creates a valid 2D surface (eg, without moebius bands).
[more] ReconstructBoundary()
Creates a new triangle mesh by reconstructing the boundary of a segmented data set.
[more] MorphMesh( number NrOfIterations, number ScreenUpdateIterations, number SmoothTau, number VMRFindSurfTau, number VMRFindSurfValue, number SmoothingMode)
Morphs a created or loaded mesh; typical applications are surface smoothing or skin reconstruction.
[more] InflateMesh( number NrOfIterations, number ScreenUpdateIterations, number SmoothTau, string RefMesh)
Unfolds the sulci of a folded mesh representing the cortical sheet of a hemisphere.
[more] SaveMesh(string MeshFileName)
Saves a surface mesh file to disk.
[more] ReverseSliceOrder()
Reverse the order of the slices (*stc files) from ascending to descending
[more] UninterleaveSliceOrder()
Change the interleaved slices to continuous ascending or descending
[more] SpatialGaussianSmoothing( number FWHM, string UnitsFWHM)
Spatial Gaussian smoothing for FMR projects
[more] SpatialGaussianSmoothingEx( number FWHM, string UnitsFWHM, number InSpaceDomain, number In3D, string NewFMRFile, string NewSTCPrefix)
Spatial Gaussian smoothing for FMR projects - extended version
[more] TemporalGaussianSmoothing( number FWHM, string UnitsFWHM)
Temporal Gaussian smoothing
[more] TemporalGaussianSmoothingEx( number FWHM, string UnitsFWHM, number InTimeDomain, string NewFMRFile, string NewSTCPrefix)
Temporal Gaussian smoothing - extended version
[more] LinearTrendRemoval()
Remove linear drifts from the data
[more] LinearTrendRemovalEx( string NewFMRFile, string NewSTCPrefix)
Remove linear drifts from the data - extended version
[more] TemporalHighPassFilter( number HighPassValue, string UnitsHighPass)
Apply a HighPassFilter in the temporal domain; typically used with '2D' fmr files HighPassFiltered fmr file is saved under name <previous_name>_THP<nr>c.
[more] TemporalHighPassFilterEx( number HighPassValue, string UnitsHighPass, string NewFMRFile, string NewSTCPrefix)
Apply a HighPassFilter in the temporal domain; typically used with '2D' fmr files HighPassFiltered fmr file is saved under name <previous_name>_THP<nr>c.
[more] ClearStimulationProtocol()
Used to start a new stimulation protocol;
[more] AddCondition(string ConditionName)
Adds a condition to a stimulation protocol
[more] AddInterval( string ConditionName, number IntervalStart, number IntervalEnd)
Add an interval to a stimulation protocol.
[more] SetConditionColor( string ConditionName, number ColorR, number ColorG, number ColorB)
Sets the condition color in stimulation protocol.
[more] SaveStimulationProtocol(string StimulationProtocolFileName)
Save the created protocol.
[more] ClearDesignMatrix()
Create a design matrix.
[more] AddPredictor(string PredictorName)
Adds a predictor to a design matrix Example: 'docAddPredictor "RVF"'
[more] SetPredictorValuesFromCondition( string PredictorName, string ConditionName, number ValueForConditionIntervals)
Set predictor value for a condition in a design matrix.
[more] SetPredictorValues( string PredictorName, number IntervalStart, number IntervalEnd, number ValueForInterval)
Set any predictor value at any time point (interval) in a design matrix.
[more] ApplyHemodynamicResponseFunctionToPredictor(string PredictorName)
Apply the hemodynamic response function to a predictor in a design matrix Example: 'docApplyHemodynamicResponseFunctionToPredictor "RVF"'
[more] LoadSingleStudyGLMDesignMatrix(string DesignMatrixFileName)
Loads an existing design matrix.
[more] SaveSingleStudyGLMDesignMatrix(string DesignMatrixFileName)
Save the single study design matrix (reference time course, *rtc)
[more] ComputeSingleStudyGLM()
Run the single study GLM
[more] ClearContrast()
Clear contrast in design matrix
[more] SetContrastValue( string PredictorName, int ValueForContrastElement)
Define whether a predictor is included in the model Example: 'docSetContrastValue "RVF", -1'
[more] ClearMultiStudyGLMDefinition()
Clear/create multi study, multi subject GLM to specify study x predictor interaction effects
[more] AddStudyAndDesignMatrix( string StudyFileName, string DesignMatrixFileName)
Add subject study and design matrix to multi study, multi subject GLM
[more] ComputeMultiStudyGLM(string GLMFileName)
Run the multi study, multi subject GLM
[more] LoadMultiStudyGLMDefinitionFile(string MultiStudyGLMDefinitionFileName)
Loads an existing multi study, multi subject design matrix
[more] SaveMultiStudyGLMDefinitionFile(string MultiStudyGLMDefinitionFileName)
Saves a mulit study, multi subject design matrix

Documentation

The Document interface contains all properties and methods of objects of a FMR/VMR/AMR project (=document)
o PathName()
Gets the name of a project. Works with all three project types. This property keeps internally the full path plus file name of objDocument. If you specify a filename without a path, the current pathway is used to define the full file name. If you assign a new file name for this property and then save the document (see below), the dcoument is saved under the new name. An alternative method would be to call the SaveAs method.
 
Returns:
pathName

 

o PathName(string value)
Sets the name of a project. For more information: see get Pathname
 
Parameters:
pathname - Pathname of the project

 

o MapThreshold()
Gets the statistical threshold used in subsequent commands visualizing statistical maps. Valid only if objDocument is of type FMR or VMR. The method retrieves the value used by a document to threshold statistical maps.
 
Returns:
thresholdvalue (number)

 

o MapThreshold(number value)
Sets the statistical threshold used in subsequent commands visualizing statistical maps. Valid only if objDocument is of type FMR or VMR. The method sets the value used by a document to threshold statistical maps.
 
Parameters:
thresholdvalue -

 

o MapClusterSize()
Valid only if objDocument is of type FMR or VMR. The property sets or retrieves the cluster size used by objDocument to filter out all activated clusters which do not reach the statistical threshold when a map is visualized, i.e. by calling ShowGLM. The statistical threshold can be modified or inspected using the MapThreshold property.
 
Returns:
mapClusterSize in voxels (number)

 

o PixelSizeOfInplaneX()
Resolution of one pixel in x dimension [mm]
 
Returns:
x-Resolution
Since:
4.6

 

o PixelSizeOfInplaneY()
Resolution of one pixel in y dimension [mm]
 
Returns:
y-Resolution
Since:
4.6

 

o SliceThickness()
Get slice thickness without slice gap [mm]
 
Returns:
Slice thickness
Since:
4.6

 

o SliceThickness(number value)
Set slice thickness without slice gap [mm]
 
Parameters:
- SliceThickness in mm
Since:
4.6

 




o GapThickness()

Get slice thickness without slice gap [mm] 
 
Returns:
GapThickness in mm

 




o GapThickness(number value)

Set slice thickness without slice gap [mm] 
 
Parameters:
- GapThickness in mm

 




o TR()

Gets TR of FMR project 
 
Returns:
TR Time of Repetition in msec
Since:
4.6

 




o TR(number value)

Sets TR of fmr-project 
 
Parameters:
- TR Time of Repetition in msec
Since:
4.6

 




o InterSliceTime()

Gets or set InterSliceTime of fmr-project 
 
Returns:
Inter slice time (IST) in msec
Since:
4.6

 




o TimeResolutionVerified()

Get flag ensuring that "TR" and "IST" are correct 
 
Returns:
TimeResolutionVerified, boolean (0 or 1)
Since:
4.6

 




o TimeResolutionVerified(number value)

Set flag ensuring that "TR" and "IST" are correct 
 
Parameters:
- TimeResolutionVerified boolean (0 or 1)
Since:
4.6

 




o VoxelResolutionVerified([out, retval] number* value)

Get flag ensuring that pixel resolution values are correct 
 
Returns:
VoxelResolutionVerified boolean (0 or 1)
Since:
4.6

 




o VoxelResolutionVerified(number value)

Set flag ensuring that pixel resolution values are correct 
 
Parameters:
- VoxelResolutionVerified boolean (0 or 1)
Since:
4.6

 




o FileNameOfPreprocessdFMR()

Property of preprocessed fmr-project, generated by BrainVoyager; non-preprocessed fmr-project still exists 
 
Returns:
Filename of preprocessed FMR

 




o StimulationProtocolResolution()

Gets time resolution of stimulation protocol in msec or volumes 
 
Returns:
Volumes_or_msec, 1 = volumes, 2 = msec
Since:
4.2

 




o StimulationProtocolResolution(number value)

Sets time resolution of stimulation protocol in msec or volumes 
 
Parameters:
Volumes_or_msec - , 1 = volumes, 2 = msec
Since:
4.2

 




o NrOfStimulationProtocolConditions()

Gets or sets the number of stimulation protocol conditions 
 
Returns:
Number of conditions within run (integer)

 




o StimulationProtocolExperimentName()

Gets the experiment name as defined in the stimulation protocol 
 
Returns:
stimulation protocol experiment name

 




o StimulationProtocolExperimentName(string value)

Sets the experiment name in the stimulation protocol 
 
Parameters:
stimulation - protocol experiment name

 




o StimulationProtocolBackgroundColorR()

Gets the 'Red' dimension of stimulation protocol background color; value between 0 and 255. 
 
Returns:
red hue

 




o StimulationProtocolBackgroundColorR(number value)

Sets the 'Red' dimension of stimulation protocol background color; value between 0 and 255. 
 
Parameters:
redIntensity - intensity of red

 




o StimulationProtocolBackgroundColorG()

Gets the 'Green' dimension of stimulation protocol background color; value between 0 and 255. 
 
Returns:
greenIntensity intensity of green

 




o StimulationProtocolBackgroundColorG(number value)

Sets the 'Green' dimension of stimulation protocol background color; value between 0 and 255. 
 
Parameters:
greenIntensity - intensity of green

 




o StimulationProtocolBackgroundColorB()

Gets the 'Blue' dimension of stimulation protocol background color; value between 0 and 255. 
 
Returns:
blueIntensity intensity of blue

 




o StimulationProtocolBackgroundColorB(number value)

Sets the 'Blue' dimension of stimulation protocol background color; value between 0 and 255. 
 
Parameters:
blueIntensity - intensity of blue

 




o StimulationProtocolTextColorR()

Gets the 'Red' dimension of stimulation protocol text color; value between 0 and 255. 
 
Returns:
redIntensity intensity of red

 




o StimulationProtocolTextColorR(number value)

Sets the 'Red' dimension of stimulation protocol text color; value between 0 and 255. 
 
Parameters:
redIntensity - intensity of red

 




o StimulationProtocolTextColorG()

Gets the 'Green' dimension of stimulation protocol text color; value between 0 and 255. 
 
Returns:
greenIntensity intensity of green

 




o StimulationProtocolTextColorG(number value)

Sets the 'Green' dimension of stimulation protocol text color; value between 0 and 255. 
 
Parameters:
greenIntensity - intensity of green

 




o StimulationProtocolTextColorB()

Gets the 'Blue' dimension of stimulation protocol text color; value between 0 and 255. 
 
Returns:
blueIntensity intensity of blue

 




o StimulationProtocolTextColorB(number value)

Sets the 'Blue' dimension of stimulation protocol text color; value between 0 and 255. 
 
Parameters:
blueIntensity - intensity of blue

 




o StimulationProtocolTimeCourseColorR()

Gets the 'Red' dimension of the stimulation protocol time course color; value between 0 and 255. 
 
Returns:
redIntensity intensity of red

 




o StimulationProtocolTimeCourseColorR(number value)

Sets the 'Red' dimension of the stimulation protocol time course color; value between 0 and 255. 
 
Parameters:
redIntensity - intensity of red

 




o StimulationProtocolTimeCourseColorG()

Gets the 'Green' dimension of the stimulation protocol time course color; value between 0 and 255. 
 
Returns:
greenIntensity intensity of green

 




o StimulationProtocolTimeCourseColorG(number value)

Sets the 'Green' dimension of the stimulation protocol time course color; value between 0 and 255. 
 
Parameters:
greenIntensity - intensity of green

 




o StimulationProtocolTimeCourseColorB()

Gets the 'Blue' dimension of the stimulation protocol time course color; value between 0 and 255. 
 
Returns:
blueIntensity intensity of blue

 




o StimulationProtocolTimeCourseColorB(number value)

Sets the 'Blue' dimension of the stimulation protocol time course color; value between 0 and 255. 
 
Parameters:
blueIntensity - intensity of blue

 




o StimulationProtocolTimeCourseThickness()

Gets thickness of line of response function 
 
Returns:
Thickness in mm (number)

 




o StimulationProtocolTimeCourseThickness(number value)

Sets thickness of line of response function 
 
Parameters:
Thickness - in mm (number)

 




o PositiveStatisticalValues()

Get whether positive values on overlay statistical map are shown 
 
Returns:
value (boolean): 0 or 1

 




o PositiveStatisticalValues(number value)

Set whether positive values on overlay statistical map are shown 
 
Parameters:
value - (boolean): 0 or 1

 




o NegativeStatisticalValues()

Get whether negative values on overlay statistical map are shown 
 
Returns:
value (boolean): 0 or 1

 




o NegativeStatisticalValues(number value)

Set whether negative values on overlay statistical map are shown 
 
Parameters:
value - (boolean): 0 or 1

 




o TwoSetContributionMaps()

Get whether the two set contribution maps option should be used (Overlay GLM contrasts dialog) 
 
Returns:
value (number)

 




o TwoSetContributionMaps(number value)

Set whether relative contribution should be used. Example: 'doc.TwoSetContributionMaps = 1'. (Overlay GLM contrasts dialog) 
 
Parameters:
numericalValue - relative contribution indication

 




o MatrixSizeX()

Gets number of columns of slice image matrix 
 
Returns:
numberOfColumns

 




o MatrixSizeY()

Gets number of rows of slice image matrix 
 
Returns:
numberOfRows

 




o NrOfSlices()

Gets number of slices per volume (scan) 
 
Returns:
number of slices (number)

 




o NrOfSlices(number value)

Sets number of slices per volume (scan) 
 
Parameters:
number - of slices (number)

 




o NrOfVolumes()

Gets or sets number of volumes 
 
Returns:
Number of time points per pixel (data points, samples)

 




o NrOfSkippedVolumes([out, retval] number* value)

Gets number of skipped volumes 
 
Returns:
Number of skipped volumes (number)
Since:
4.6

 




o NrOfSkippedVolumes(number value)

Sets number of skipped volumes 
 
Parameters:
Number - of volumes skipped during project creation
Since:
4.6

 




o SeparationOfSubjectPredictors()

GLM-property 
 
Returns:
separationOfSubjectPredictorsOrNot 0 -> no, 1 -> for each study, 2 -> for each subject

 




o SeparationOfStudyPredictors()

GLM-property 
 
Returns:
separationOfStudyPredictorsOrNot 0 -> no, 1 -> for each study, 2 -> for each subject

 




o ZTransformationOfStudies()

Get ZTransformationOfStudies; 1 -> time courses of runs have been z-transformed, 0 -> not. GLM-file property. 
 
Returns:
Z-transformed or not (number)

 




o ZTransformationOfStudies(number value)

Set ZTransformationOfStudies; 1 -> time courses of runs have been z-transformed, 0 -> not. GLM-file property. 
 
Parameters:
Z-transformed - or not (number)

 




o Save()

Saves a BrainVoyager project file using the current file name 
 

 




o SaveAs(string SaveAsFileName)

Saves a BrainVoyager project file under a specifed file name. Saves the referenced document object objDocument to disk with the provided file name strFileName. 
 
Parameters:
filename -

 




o Close()

Closes a BrainVoyager project file. Closing a project file also deletes the associated objDocument. You can no longer invoke methods using the respective document variable. 
 

 




o Remove()

Method Remove() is used to remove intermediate fmr-files while preprocessing. Used for fmr-projects. Instead of calling "Close", we call "Remove" to close and delete the document from disk. This is useful if one wants not to keep intermediate preprocessing files. Syntax: "docFMR_2.Remove" 
 

 




o RefreshView()

Repaints the document's view which is a window showing an FMR, VMR or AMR project. Most document methods are defined to operate without updating the document's view. Use this method to refresh the respective document window to render the effect of an operation visible. 
 

 




o SetCrossPosition( number x, number y, number z)

Sets the current voxel. The current voxel is shown as the center of the red cross in the SAG, COR and TRA window. Valid only if objDocument is of type VMR. The method is executed independent of whether the red cross is turned on (visible) or off (invisible). To update the SAG, COR and TRA window, call RefreshView after execution of this method. 
 
Parameters:
x - in pixels
y
- in pixels
z
- in pixels

 




o SwitchToSurfaceModule()

Activates the Surface Module window. Valid only if objDocument is of type VMR. Each VMR project can call exactly one Surface Module window. If the Surface Module window has not been activated before, the window is created showing the 3D string "BrainVoyager". If the Surface Module window has been created, you can access surface-related document methods like LoadMesh. 
 

 




o Show3DVolumeTools()

Shows the 3D Volume Tools dialog. If the Surface Module window is shown maximized, this method also switches to the VMR window thereby hiding the Surface Module window. Valid only if objDocument is of type VMR. 
 

 




o Hide3DVolumeTools()

Hides the 3D Volume Tools dialog. Valid only if objDocument is of type VMR. 
 

 




o LoadMesh(string MeshFileName)

Loads a surface mesh file. Surface mesh file names have extension ".srf". Valid only if objDocument is of type VMR and if the Surface Module window for this VMR project has been created. The loaded mesh is not shown automatically in the Surface Module window. To update it, call the UpdateSurfaceWindow() method. 
 
Parameters:
MeshFileName - name of mesh file to load
Returns:
succeeded (boolean)

 




o SaveSnapshotOfSurfaceWindow(string MeshFileName)

Makes a snapshot of the surface module window. Valid only if objDocument is of type VMR and if the Surface Module window for this VMR project has been created. The image is saved with the by the user provided filename and extension specified in the 'Global preferences'. 
 
Parameters:
snapShotFileName -
Returns:
succeeded (boolean)

 




o AddMesh(string MeshFileName)

Reads a surface mesh file and adds it to the Surface Module window of the referenced VMR document. This method allows to compose scenes of surface meshes, i.e. loading the mesh file of the reconstructed head of a subject and adding the reconstructed meshes of the cortical hemispheres of that subject. Valid only if objDocument is of type VMR and if the Surface Module window for this VMR project has been created. The loaded mesh is not shown automatically in the Surface Module window. To update it, call the UpdateSurfaceWindow method. 
 
Parameters:
strMeshFileName -
Returns:
success (boolean)

 




o UpdateSurfaceWindow()

Repaints the Surface Module window which is a window showing one or more surface mesh files. Valid only if objDocument is of type VMR and if the Surface Module window for this VMR project has been created. Most surface-related document methods are defined to operate without updating the Surface Module window. Use this method to refresh this window to render the effect of an operation visible. 
 
Returns:
boolSuccess operationSucceeded

 




o SetViewpointPosition( number x, number y, number z)

Sets the 3D position of the viewpoint from which the scene in the Surface Module window is "seen". Valid only if objDocument is of type VMR and if the Surface Module window for this VMR project has been created. This method sets only the position of the viewpoint; use the method SetViewpointAngles to also set the viewing direction. To update the Surface Module window, call the RefreshSurfaceWindow method. 
 
Parameters:
intX - coordinate on x-axis
intY
- coordinate on y-axis
intZ
- coordinate on z-axis

 




o ViewpointTranslationX(int translX)

Move the viewing direction from which the scene in the Surface Module window is "seen" right or left. Valid only if objDocument is of type VMR and a mesh is loaded in the Surface Module window. To update the Surface Module window, call the UpdateSurfaceWindow method. The origin (0,0,0) of the space is in the middle so from the origin the surface object can be translated to the right (+) or to the left (-). 
 
Parameters:
intTranslationX - shift on the x axis

 




o ViewpointTranslationY(int translY)

Move the viewing direction from which the scene in the Surface Module window is "seen" up or down. Valid only if objDocument is of type VMR and a mesh is loaded in the Surface Module window. To update the Surface Module window, call the UpdateSurfaceWindow method. The origin (0,0,0) of the space is in the middle so from the origin the surface object can be translated upward (+) or downward (-). 
 
Parameters:
intTranslationY - shift on the y axis

 




o ViewpointTranslationZ(int translZ)

Move the viewing direction from which the scene in the Surface Module window is "seen" backward or forward. Valid only if objDocument is of type VMR and a mesh is loaded in the Surface Module window. To update the Surface Module window, call the UpdateSurfaceWindow method. The origin (0,0,0) of the space is in the middle so from the origin the surface object can be translated forward or backward. 
 
Parameters:
intTranslationZ - shift on the z axis

 




o ViewpointRotationX(int rotX)

Rotate the viewing direction from which the scene in the Surface Module window around the X-axis (back to front in Talairach space) (in degrees (0-360)). Valid only if objDocument is of type VMR and a mesh is loaded in the Surface Module window. To update the Surface Module window, call the UpdateSurfaceWindow method. 
 
Parameters:
intRotationXaxis -

 




o ViewpointRotationY(int rotY)

Rotate the viewing direction from which the scene in the Surface Module window around the Y-axis (right to left in Talairach space) (in degrees (0-360)). Valid only if objDocument is of type VMR and a mesh is loaded in the Surface Module window. To update the Surface Module window, call the UpdateSurfaceWindow method. 
 
Parameters:
intRotationYaxis -

 




o ViewpointRotationZ(int rotZ)

Rotate the viewing direction from which the scene in the Surface Module window around the Z-axis (top to bottom in Talairach space) (in degrees (0-360)). Valid only if objDocument is of type VMR and a mesh is loaded in the Surface Module window. To update the Surface Module window, call the UpdateSurfaceWindow method. 
 
Parameters:
intRotationZaxis -

 




o SliceMeshAxial(number z)

Slices a surface mesh parallel to the XY-plane at the specified Z-level. Valid only if objDocument is of type VMR and if a mesh has been loaded or created. The slice shows the data contained at that level in the respective VMR document. If multiple surface meshes are present, the method is applied to the current mesh. If a mesh is created or loaded/added, it automatically becomes the current mesh. To update the Surface Module window, call the RefreshSurfaceWindow method. 
 
Parameters:
intSlice -

 




o SliceMeshCoronal(number y)

Slices a surface mesh parallel to the XZ-plane at the specified Y-level. 
 
Parameters:
intSlice - slice shown in mesh Valid only if objDocument is of type VMR and if a mesh has been loaded or created. The slice shows the data contained at that level in the respective VMR document. If multiple surface meshes are present, the method is applied to the current mesh. If a mesh is created or loaded/added, it automatically becomes the current mesh. To update the Surface Module window, call the RefreshSurfaceWindow method.

 




o SliceMeshSagittal(number x)

Slices a surface mesh parallel to the YZ-plane at the specified X-level. Valid only if objDocument is of type VMR and if a mesh has been loaded or created. The slice shows the data contained at that level in the respective VMR document. If multiple surface meshes are present, the method is applied to the current mesh. If a mesh is created or loaded/added, it automatically becomes the current mesh. To update the Surface Module window, call the RefreshSurfaceWindow method. 
 
Parameters:
intSlice - Integer, indicates at which slice the mesh will be cut

 




o MeshSlicesOff()

Removes all activated slices from the current mesh. Valid only if objDocument is of type VMR and if a mesh has been loaded or created. If multiple surface meshes are present, the method is applied to the current mesh. If a mesh is created or loaded/added, it automatically becomes the current mesh. To update the Surface Module window, call the RefreshSurfaceWindow method. 
 

 




o LoadViewingSettings(string FileNameVWP)

Restores surface module settings about the viewing position, angles, lightning conditions previously stored to disk. Valid only if objDocument is of type VMR and and if the Surface Module window for this VMR project has been created. Viewpoint files possess the extension "vwp". To update the Surface Module window, call the RefreshSurfaceWindow method. 
 
Parameters:
strViewpointFileName - File with viewpoint settings to be loaded (*.vwp)

 




o LoadGLM(string FileNameGLM)

Loads a file containg the results of a multiple regression (GLM) analysis. Valid only if objDocument is of type FMR or VMR. If it is of type VMR, all three dimensions currently must be 256. The specified GLM file strGLMFileName is loaded into memory and can be shown superimposed on anatomical images by selecting predictors (i.e. using the SelectAllPredictors method) and then calling the ShowGLM method. During loading of the GLM, BrainVoyager also tries to find all VTC files referenced by the GLM file. 
 
Parameters:
FileNameGLM - Name of file to be loaded

 




o RunGLMFromProtocol()

Compute the General Linear Model with the linked protocol 
 

 




o SaveGLM(string FileNameGLM)

Save the computed General Linear Model with the provided name 
 
Parameters:
fileName -

 




o ShowGLM()

Shows statistical map based on selected predictors of a GLM superimposed on (anatomical) reference images. Valid only if objDocument is of type FMR or VMR. After performing or loading a GLM file, predictors can be selected and then shown as statistical maps on reference images of an FMR or VMR project. To select predictors, use one of the following methods: SelectAllPredictors, SelectPredictorInSet1, SelectPredictorInSet2. You can also deselect all currently selected predictors by using the DeselectAllPredictors method. To show a contrast between two predictor sets, select the desired predictors in set 1 and set 2 and make sure to call DisableTwoSetPredictorColours prior to the ShowGLM method. If you want to visualize the relative contribution of explained variance between two predictor sets, call EnableTwoSetPredictorColours prior to the ShowGLM method. 
 

 




o SelectPredictorInSet1(number prednr)

Adds a predictor into set1 of two sets available for display of multiple regression (GLM) results. Valid only if objDocument is of type FMR or VMR. and a GLM has been run or loaded from disk. You can put more than one predictor into set1 by calling the method repeatedly. Set1 is the standard set for showing the explained variance of a subset of the full model, i.e. one or more predictors. If you want to show contrasts or the relative contribution of explained variance between two sets of predictors, you must use the SelectPredictorInSet2 method in addition to the present method. The set of selected predictors produces a statistical map which represents the amount of variance explained by the selected partial model. After selecting the predictors, call the ShowGLM method to visualize the resulting statistical map. The generated statistical map is internally stored in a VMP (volume map) data set which you can save to disk (currently only interactively using the Analysis->Overlay maps->Save 3D Map... menu item). 
 
Parameters:
prednr - Number of the predictor to be selected in set 1

 




o SelectPredictorInSet2(number prednr)

Adds a predictor into set2 of two sets available for display of multiple regression (GLM) results. Valid only if objDocument is of type FMR or VMR. and a GLM has been run or loaded from disk. You can put more than one predictor into set2 by calling the method repeatedly. Set2 can only be used in addition to set1 in order to show contrasts between two sets of predictors or to show the relative contribution of the combined variance explained by the two sets of predictors. After selecting predictors, call the ShowGLM method to visualize the resulting statistical map. The generated statistical map is internally stored in a VMP (volume map) data set which you can save to disk (currently only interactively using the Analysis->Overlay maps->Save 3D Map... menu item). 
 
Parameters:
prednr - Number of the predictor to be selected in set 2

 




o SelectAllPredictors()

Selects all predictors of a multiple regression (GLM) result for display. Valid only if objDocument is of type FMR or VMR. and a GLM has been run or loaded from disk. Selecting all predictors produces a statistical map which is identical to the overall multiple R value, i.e. the amount of variance explained by the full model. After selecting the predictors, call the ShowGLM method to visualize the resulting statistical map. The generated statistical map is internally stored in a VMP (volume map) data set which you can save to disk (currently only interactively using the Analysis->Overlay maps->Save 3D Map... menu item). 
 

 




o DeselectAllPredictors()

Deselects all predictors of a multiple regression (GLM) result allowing to start a new predictor selection process. Valid only if objDocument is of type FMR or VMR. and a GLM has been run or loaded from disk. Deselect all predictors before defining a new statistical map using the SelectPredictorInSet1 and/or SelectPredictorInSet2 method. 
 

 




o EnableTwoSetPredictorColours()

A flag is set to show the relative contribution of the combined variance explained by two sets of predictors in a multiple regression (GLM). Valid only if objDocument is of type FMR or VMR. and a GLM has been run or loaded from disk. The flag set internally by this method has only an effect if predictors are selected into both set1 and set2 using the SelectPredictorInSet1 and SelectPredictorInSet2 method. In this case, the relative contribution of the combined explained variance in the time series of each voxel is visualized. 
 

 




o EnableTwoSetPredictorContrast()

Sets the status of a flag to show the contrast between two sets of predictors in a multiple regression (GLM). Valid only if objDocument is of type FMR or VMR. and a GLM has been run or loaded from disk. The flag set internally by this method has only an effect if predictors are selected into both set1 and set2 using the SelectPredictorInSet1 and SelectPredictorInSet2 method. In this case, the contrast between the two sets of predictors is computed, i.e. how much variance is explained by predictor set 1 over and above the variance explained by predictor set 2. 
 

 




o SliceTimeCorrection(number SliceSamplingType)

Most EPI sequences measure the slices of a functional volume in succession but one often would like to treat the data of one volume as if it were acquired at the same time, particularly in the context of event-related studies. Using linear interpolation, the present method resamples the time series for the different slices in such a way that the resulting slice time courses can be treated as if they were obtained simultaneously. Valid only if objDocument is of type FMR. Slice time correction can only be done in FMR projects because these projects contain the time series data separated with respect to the individually measured slices (STC files); this information is lost in VTC files after spatial transformation. Slices typically are scanned ascending (i.e., slice 1, slice 2, slice 3 ...) or interleaved (i.e., slice 1, slice 3, slice 5 .. slice 2, slice 4, slice 6 ...). If your data had been scanned interleaved, specify "1" as the third argument, if it had been scanned ascending, specify "0". The first two parameters are necessary to perform the correct resampling of the data. While the TR value should be easily obtained from the scanner protocol or from a file header, the inter slice time might be more difficult to get. If scanning ran continously, i..e. if there is no pause between scanning the last slice of volume N and the first slice of volume N+1, then you can simply divide the TR value by the number of slices per volume to get the inter slice time. If scanning ran not continously, you must either get the information about the duration of acquiring all slices or the duration of the pause between volumes. An alternative possibility (used by our group) is to read slice trigger pulses from the scanner measuring the time point when each slice is scanned; by subtracting, for example the time point of slice 1 from the time point of slice 2 results in the inter slice time. The resulting corrected data is automatically saved to disk. The names for the new FMR project and the new STC prefix is determined as in the GUI version, i.e., if the FMR project "cg_objects.fmr" is used, the resulting new file on disk will be "cg_objects_pp.fmr". In addition, a set of new STC files, actuallly containing the time series data, is stored to disk. If, for example, the prefix in the source FMR project was "slice-" (referencing file slice-1.stc, slice-2.stc etc.), the STC prefix of the new FMR file will be "slice_pp-". If you do not want to use this implicit naming scheme, you might want to use the method SliceTimeCorrectionEx which allows to specify the name of the resulting FMR project and STC prefix. 
 
Parameters:
sliceSamplingType - 0 -> Ascending
1 -> Ascending-Interleaved
2 -> Ascending-Interleaved2
10 -> Descending
11 -> Desc-Interleaved
12 -> Descending-Interleaved2

 




o SliceTimeCorrectionEx( number TR, number InterSliceTime, number SliceSamplingType, number SincInterpolation, string NewFMRFile, string NewSTCPrefix)

Most EPI sequences measure the slices of a functional volume in succession but one often would like to treat the data of one volume as if it were acquired at the same time, particularly in the context of event-related studies. Using linear interpolation, the present method resamples the time series for the different slices in such a way that the resulting slice time courses can be treated as if they were obtained simultaneously. Valid only if objDocument is of type FMR. The method operates identical as the SliceTimeCorrection version. In addition to the specification of the intTR, intInterSliceTime and intSliceSamplingType, the name of the resulting FMR project (strNewFMRFileName) and the resulting STC prefix (strNewSTCPrefix) must be specified. 
 
Parameters:
intTR -
intInterSliceTime
-
intSliceSamplingType
-
numberSincInterpolation
-
strNewFMRFileName
-
strNewSTCPrefix
-

 




o TemporalSmoothingFD2D(number HighPass, number LowPass)

Filters in the frequency domain the time series of each voxel in the STC files of an FMR project. Can be used to remove linear and non-linear drifts (high-pass) and/or to smooth the time series (low-pass). Valid only if objDocument is of type FMR. The high- and low pass values are interpreted in cycles per length of the time course measured in volumes. A high pass value of "3" removes frequency components below 3 cycles within the time series. A low pass value equal to or greater than half the length of the time series will have no effect (Nyquist theorem), i.e. the low-pass filter is turned off. If the time series data, for example, contains 256 measurements, then a low pass value of 128 or greater lets everything pass, i.e. it has no effect and is turned off. In the GUI version, BrainVoyager sets the default value of the low pass to one-third of the lenght of the time series which proved to produce good results, i..e. it results in slightly smoothed time series. It is, however, recommended, not to use low pass filtering at all when preprocessing data sets from event-related designs. This is also the reason, why low pass filtering is turned off in the GUI version (2D Data Preprocessing dialog) as default. The resulting filtered data is automatically saved to disk. The names for the new FMR project and the new STC prefix is determined as in the GUI version, i.e., if the FMR project "cg_objects.fmr" is used, the resulting new file on disk will be "cg_objects_pp.fmr". In addition, a set of new STC files, actually containing the time series data, is stored to disk. If, for example, the prefix in the source FMR project was "slice-" (referencing file slice-1.stc, slice-2.stc etc.), the STC prefix of the new FMR file will be "slice_pp-". If you do not want to use this implicit naming scheme, you might want to use the method TemporalSmoothingFD2DEx which allows to specify the name of the resulting FMR project and STC prefix. 
 
Parameters:
HighPass - value
LowPass
- value

 




o TemporalSmoothingFD2DEx( number HighPass, number LowPass, string NewFMRFile, string NewSTCPrefix)

Filters the time series of each voxel in the STC files of an FMR project. Can be used to remove linear and non-linear drifts (high-pass) and/or to smooth the time series (low-pass). Valid only if objDocument is of type FMR. The method operates identical as the TemporalSmoothingFD2D version. In addition to the specification of the high-pass and low pass filter values, the name of the resulting FMR project (strNewFMRFileName) and the resulting STC prefix (strNewSTCPrefix) must be specified. 
 
Parameters:
HighPass -
LowPass
-
NewFMRFile
-
NewSTCPrefix
-

 




o SpatialSmoothingFD2D( number HighPass, number LowPass)

Spatially filters each recorded image in the STC files of an FMR project in the frequency domain. Valid only if objDocument is of type FMR. The high- and low pass values are interpreted in cycles per spatial dimension measured in voxels (i.e. matrix size). In the rare case of a non-square matrices, the largest dimension is chosen as reference. A low pass value equal to or greater than half of the dimension (i.e. > 32 in the case of a 64 x 64 matrix) lets everyghing pass, it will have no effect (Nyquist theorem). In the GUI version (2D Data Preprocessing dialog), BrainVoyager sets the default value of the low pass filter to half of this value (i.e. 16 in case of a 64 x 64 matrix, 32 in case of a 128 x 128 matrix) which produces a modest spatial smoothing roughly equal to spatial smoothing with a FWHM of 4mm in the spatial domain. In the GUI version, the low-pass filter is turned off completely for 64 x 64 matrices and is only turned on by greater matrices. The high-pass filter is also turned off in the GUI version since such a spatial filter is not useful in the context of fMRI data analysis. To turn the high-pass filter off, specify "1" as the intHighPass argument. The resulting filtered data is automatically saved to disk. The names for the new FMR project and the new STC prefix is determined as in the GUI version, i.e., if the FMR project "cg_objects.fmr" is used, the resulting new file on disk will be "cg_objects_pp.fmr". In addition, a set of new STC files, actually containing the smoothed data, is stored to disk. If, for example, the prefix in the source FMR project was "slice-" (referencing file slice-1.stc, slice-2.stc etc.), the STC prefix of the new FMR file will be "slice_pp-". If you do not want to use this implicit naming scheme, you might want to use the method SpatialSmoothingFD2DEx which allows to specify the name of the resulting FMR project and STC prefix. 
 
Parameters:
HighPass -
LowPass
-

 




o SpatialSmoothingFD2DEx( number HighPass, number LowPass, string NewFMRFile, string NewSTCPrefix)

Spatially filters each recorded image in the STC files of an FMR project in the frequency domain. Valid only if objDocument is of type FMR. The method operates identical as the SpatialSmoothingFD2D version. In addition to the specification of the high-pass and low pass filter values, the name of the resulting FMR project (strNewFMRFileName) and the resulting STC prefix (strNewSTCPrefix) must be specified. 
 
Parameters:
HighPass -
LowPass
-
NewFMRFile
-
NewSTCPrefix
-

 




o CreateVTC( string FMRFile, string 2D3DTRFFile, string ACPCTRFFile, string TALFile, string VTCFileName)

Transforms the time course data of an FMR project into a defined 3D space, typically Talairach space. The result of this transformation is a VTC file. Valid only if objDocument is of type VMR. FMR projects contain functional data in the originally recorded slices without any knowledge about where these slices are located with respect to a 3D reference frame, i.e. Talairach space. Transforming the functional data in Talairach space allows to analyze data from the same subject across different scanner sessions as well as to analyze data coming from different subjects. The resulting 4D VTC file consists of a series of 3D volumes aligned in stereotactic space. The file is saved to disk under the name strFileVTC entered as the last parameter. The first parameter strFileFMR specifies the FMR project whose functional data should be transformed in 3D space (the functional data actually resides in STC files which are referenced by the FMR project). The spatial transformation into Talairach space is controlled by three files which must exist prior to calling this method. The strFile2D3DTRF is responsible to align the stack of 2D slices at the correct position of a 3D VMR data set which is typically recorded in the same session as the functional data. If this is the case, the alignment can be done automatically based on the header information of the functional and anatomical data sets (assuming no or only minimal motion between the two data sets). The automatic alignment is currently only possible for Siemens IMA and DICOM files but should be available soon also for Philips and GE scanners (for further information, contact Brain Innovation). If the necessary header information is not available, the alignment has to be performed interactively within BrainVoyager. If the functional data has been registered with a 3D VMR data set, the further alignment information can be obtained from anatomical transformations. The 3D data set to which the functional data has been aligned can be rotated into the AC-PC plane. If you have already once rotated a 3D data set of the same subject into the AC-PC plane, you can use BrainVoyager's automatic 3D-3D alignment routine to do this step. In both cases, a TRF file is produced which transforms the source 3D data set into the AC-PC plane. Since the functional data should undergo exactly the same transformation, you must enter the obtained file as the strFileACPCTRFF file for the present method. The AC-PC plane space is not Talairach space. The final step is to apply a non-linear scaling operation to bring the data in stereotactic space. This is done for the 3D VMR data set in AC-PC space and results in a TAL file. In order to apply the same transformation to the functional data, enter the obtained file as the strFileCerebrumTAL file. 
 
Parameters:
strFileFMR - Name of FMR file to be transformed
strFile2D3DTRF
- *.trf file
strFileACPCTRFF
-
strFileCerebrumTAL
-
strFileVTC
- Name of the 4D VTC file to be created and saved

 




o CorrectMotion(int targetVolume)

Detects and corrects rigid-body motion within an FMR file. The target volume provided by the user serves as the reference to which all other volumes are aligned. This version uses the default settings as shown in the GUI version (FMR Data Preprocessing): trilinear interpolation to perform the rigid-body translation/rotation, a reduced data set (every second voxel in each dimension = one eighth of a full volume = 12.5%), a maximum of 100 iterations to fit a volume to the reference, creation of pre- and post AVI movie files and a standard log file. The new file name is based on the name of the FMR file prior to starting the filter and adds a suing describing the preprocessing performed. If, for example, the name of the FMR file was "cg_objects.fmr", the new name will be "cg_objects_3DMC.fmr". The added suing "_3DMC" describes that motion correction (MC) has been performed in 3D (3DMC), i.e. fitting 3 translation and 3 rotation parameters. All 3D preprocessing steps add such descriptive suings which makes it easy to get the information about the sequence of steps which has been performed to produce a particular FMR file. 
 
Parameters:
intTargetVolume - Volume of FMR file to align to

 




o CorrectMotionTargetVolumeInOtherRun(str intraSessionRunName, int targetVolume)

Detects and corrects rigid-body motion within several runs. This intra-session alignment method makes it possible to align all volumes of all runs in a session to the same targetvolume. This version uses the default settings as shown in the GUI version (FMR Data Preprocessing): trilinear interpolation to perform the rigid-body translation/rotation, a reduced data set (every second voxel in each dimension = one eighth of a full volume = 12.5%), a maximum of 100 iterations to fit a volume to the reference, creation of pre- and post AVI movie files and a standard log file. The new file name is based on the name of the FMR file prior to starting the filter and adds a suing describing the preprocessing performed. If, for example, the name of the FMR file was "cg_objects.fmr", the new name will be "cg_objects_3DMC.fmr". The added suing "_3DMC" describes that motion correction (MC) has been performed in 3D (3DMC), i.e. fitting 3 translation and 3 rotation parameters. All 3D preprocessing steps add such descriptive suings which makes it easy to get the information about the sequence of steps which has been performed to produce a particular FMR file. The intra-session alignment is integrated in the 3D motion correction step by specifying to which target volume and target run the data should be aligned. The target run should be the one, which is closest in time to the recorded 3D data set to minimize the effect of motion across scans. If a session, for example, started with a 3D data set followed by three runs, run 1, run 2 and run 3, 3D motion correction in the first run would proceed as in the 3DMotionCorrection() method by selecting a target volume i.e. volume 1 (default). For run 2, the same target volume in run 1 is specified aligning th data of run 2 directly with run 1. The same is specified for run 3, i.e. the data are directly aligned to the target volume in run 1. This procedure ensures that all volumes in all runs are aligned to the very same target volume. Note that the described strategy works only if all runs have been recorded with the same nominal slice positions. If slice positions have been changed across runs, intra-session alignment can be achieved by using coregistration. 
 
Parameters:
strIntraSessionRun - Name of the FMR file to align all runs and volumes to
intTargetVolume
- Volume of FMR file to align to

 




o TemporalSmoothingFD3D( number HighPass, number LowPass)

Filters in the frequency domain the time series of each voxel in a VTC file. Can be used to remove linear and non-linear drifts (high-pass) and/or to smooth the time series (low-pass). Valid only if objDocument is of type VMR and if a VTC file has been linked. If the VTC file is referenced but not in memory, BrainVoyager will load the VTC file prior to running the temporal filter. A high pass value of "3" removes frequency components below 3 cycles within the time series. A low pass value equal to or greater than half the length of the time series will have no effect (Nyquist theorem), i.e. the low-pass filter is turned off. If the time series data, for example, contains 256 measurements, then a low pass value of 128 or greater lets everything pass, i.e. it has no effect and is turned off. In the GUI version, BrainVoyager sets the default value of the low pass to one-third of the length of the time series which proved to produce good results, i..e. it results in slightly smoothed time series. It is, however, recommended, not to use low pass filtering at all when preprocessing data sets from event-related designs. This is also the reason, why low pass filtering is turned off in the GUI version (3D Data Preprocessing dialog). As in the GUI version, the temporal filter produces a new VTC file which is saved to disk automatically under a new file name. The new file name is based on the name of the linked VTC file prior to starting the filter and adds a suing describing the preprocessing performed. If, for example, the name of the linked VTC file was "cg_objects_SC_3DMC.vtc", the new name will be "cg_objects_SC_3DMC_FTS-3-126.vtc". The added suing "_FTS-3-126" describes that temporal smoothing (TS) has been performed in the frequency domain (FTS) using a high-pass filter of "3" and a low-pass filter of "126". All 3D preprocessing steps add such descriptive suings which makes it easy to get the information about the sequence of steps which has been performed to produce a particular VTC file. If you do not want to use the implicit naming scheme, you might want to use the method TemporalSmoothingFD3DEx which allows to specify the source VTC file and the target VTC file. Note also that the resulting VTC file is linked automatically to objDocument which allows to run a cascade of preprocessing commands without having to link intermediate files. 
 
Parameters:
HighPass - Interpreted in cycles per length of the time course measured in volumes
LowPass
- interpreted in cycles per length of the time course measured in volumes

 




o SpatialSmoothingFD3D( number HighPass, number LowPass)

Spatially filters each 3D volume of a VTC file in the frequency domain. Valid only if objDocument is of type VMR and if a VTC file has been linked. If the VTC file is referenced but not in memory, BrainVoyager will load the VTC file prior to running the spatial filter. Since there are three spatial dimensions, the largest dimension is chosen as reference. Since VTC files normally are in Talairach space, the largest dimension is the YTAL-dimension corresponding to 174 mm or 174 voxels in a 1mm3 VMR data set (for details about the dimensions of VTC files, see chapter "BrainVoyager File Formats"). Since the functional data in VTC files consists typically of 3mm3 voxels, this results in a value of 174/3 = 58 when measured in voxels. A low pass value equal to or greater than half of this value (> 26) lets everything pass, it will have no effect (Nyquist theorem). In the GUI version (3D Data Preprocessing dialog), BrainVoyager sets the default value of the low pass filter to roughly half of this value (14) which produces a modest spatial smoothing roughly equal to spatial smoothing with a FWHM of 4mm in the spatial domain. In the GUI version the high-pass filter is turned off since it is not useful in the context of fMRI data analysis. To turn the high-pass filter off, specify "1" as the intHighPass value. As in the GUI version, the spatial filter produces a new VTC file which is saved to disk automatically under a new file name. The new file name is based on the name of the linked VTC file prior to starting the filter and adds a suing describing the preprocessing performed. If, for example, the name of the linked VTC file was "cg_objects_SC_3DMC.vtc", the new name will be "cg_objects_SC_3DMC_FSS-1-14.vtc". The added suing "_FSS-1-14" describes that spatial smoothing (SS) has been performed in the frequency domain (FSS) using a high-pass filter of "1" and a low-pass filter of "14". All 3D preprocessing steps add such descriptive suings which makes it easy to get the information about the sequence of steps which has been performed to produce a particular VTC file. If you do not want to use the implicit naming scheme, you might want to use the method SpatialSmoothingFD3DEx which allows to specify the source VTC file and the target VTC file. Note also that the resulting VTC file is linked automatically to objDocument which allows to run a cascade of preprocessing commands without having to link intermediate files. 
 
Parameters:
HighPass - interpreted in cycles per spatial dimension measured in voxels
LowPass
- interpreted in cycles per spatial dimension measured in voxels

 




o TemporalSmoothingFD3DEx( number HighPass, number LowPass, string VTCFileNameIn, string VTCFileNameOut)

Filters the time series of each voxel in a VTC file. Can be used to remove linear and non-linear drifts (high-pass) and/or to smooth the time series (low-pass). Valid only if objDocument is of type VMR. The method operates identical as the TemporalSmoothingFD3D version. In addition to the specification of the high-pass and low pass filter values, the source VTC file (strVTCFileNameIn) and a file name for the resulting VTC file (strVTCFileNameOut) must be specified. The source VTC file will be linked to objDocument and loaded into memory prior to temporal smoothing. The filtered file will be saved to disk under the specified "Out" file name. The resulting VTC file is linked automatically to objDocument. 
 
Parameters:
intHighPass -
intLowPass
-
strVTCFileNameIn
-
strVTCFileNameOut
-

 




o SpatialSmoothingFD3DEx( number HighPass, number LowPass, string VTCFileNameIn, string VTCFileNameOut)

Spatially filters each 3D volume of a VTC file in the frequency domain. Valid only if objDocument is of type VMR. The method operates identical as the SpatialSmoothingFD3D version. In addition to the specification of the high-pass and low pass filter values, the source VTC file (strVTCFileNameIn) and a file name for the resulting VTC file (strVTCFileNameOut) must be specified. The source VTC file will be linked to objDocument and loaded into memory prior to spatial smoothing. The filtered file will be saved to disk under the specified "Out" file name. The resulting VTC file is linked automatically to objDocument. 
 
Parameters:
intHighPass -
intLowPass
-
strVTCFileNameIn
-
strVTCFileNameOut
-

 




o LinkVTC( string VTCFileName, number LoadInMem)

Links a 3D time course file (VTC) to a 3D anatomical project (VMR). Valid only if objDocument is of type VMR. The VMR and VTC file must be in the same space, normally Talairach space. After linking the VTC file, statistical tests can be performed across the data set and time courses and event-related averages can be shown. If the second parameter is set to "1", the VTC file is load into working memory, if it is set to "0", a file reference is created and used to access the file when necessary. 
 
Parameters:
VTCFileName -
LoadInMemory
- Boolean, to be 0 (load in memory) or 1 (create reference file)

 




o SetVoxelIntensity( int x, int y, int z, int value)

Sets the intensity value of the specified voxel in an VMR data set. (In User's Guide known as 'SetVoxelValue') Valid only if objDocument is of type VMR. Intensity values in VMR files are stored in bytes. The values for intIntensity should be in the range of 10 - 245 since the colors indices below 10 and above 245 are reserved for the Windows system palette. The range of values normally interpreted as grey scale is from 10 to 225. To update the SAG, COR and TRA window, call RefreshView after execution of this method. Note that the method is quite slow, i.e. it is not appropriate to use this method to loop across all data points. If you want to work efficiently with VMR files, you should follow the method described in the topics "A simple C++ program" and "An easy C++ program". The method has been developed mainly for internal use, i.e. to test the speed of data access using scripts. If in a later release a so called in-process COM server is provided (basically BrainVoyager as a DLL), the speed might be as fast as with using C++. If this turns out to be the case, we will provide further methods for setting and retrieving intensity and dimension values from VMR files. 
 
Parameters:
intX -
intY
-
intZ
-
intIntensity
-

 




o GetVoxelIntensity( int x, int y, int z)

Gets the voxel intensity of the voxel specified by the coordinates 
 
Parameters:
x - axis coordinate
y
- axis coordinate
z
- axis coordinate
Returns:
intensity of voxel at specified coordinate (integer)

 




o SetLayoutRowsCols( number NrOfRows, number NrOfCols)

Defines a grid of rows and columns in which multiple images of an FMR or AMR project are shown. Only valid if objDocument is of type FMR or AMR. If an FMR project is saved, the current layout is stored with the file; when the file is reloaded, the previously stored layout (number of rows and columns) is used to display the project's images. This kind of persistence is not supported by AMR files. 
 
Parameters:
Rows -
Cols
-

 




o SetZoomLevel(number ZoomLevel)

Sets the zoom level of the view of a BrainVoyager project file (FMR, VMR, AMR). Valid for all document types: objDocument can be a VMR, FMR or AMR project. If an FMR project is saved, the current zoom level is stored with the file; when the file is reloaded, the previously stored zoom level is used to display the project's images. This kind of persistence is not supported by AMR and VMR files. Zoom level range: 1 to 10 (1 = slice resolution) 
 
Parameters:
Zoomlevel -

 




o ConvertFuncToAMR(string AMRFileName)

Converts the first functional volume of an FMR project into an AMR file. Valid only if objDocument is of type FMR. This method is useful to produce a "pseudo-anatomical" representation within the same space as the functional data. When short TR's are used (i.e. in event-related paradigms), the first measurement of the functional slices produces images with high T1-saturation, i.e. high signal level and good tissue contrast. The high signal drops rapidly with further measurements reaching a steady state. Since this signal change presents a problem for showing and analyzing time series data, the first few measurements are normally not read in when creating an FMR project. Because of good tissue contrast, It is, however, desirable to use the very first measurement as the images on which statistical maps should be shown. This is where the present method is useful: create an FMR project of the first volume only, then apply the method to produce a respective AMR file which can then be linked to the "real" FMR file containing the full time series data (except the very first measurements). Another advantage of using a pseudo-AMR file is that spatial smoothing does not change the AMR so that the anatomical location of functional clusters can be better visualized. Another possibility to obtain a pseudo-AMR file would be to create an AMR project from the images of the first functional volume. Although this is possible, the presented method is recommended since it produces an FMR file which can be transformed to a VTC file of the first volume. This again can be used in stereotactic space to show statistical maps not only on T1-weighted data sets but also on the original EPI data. The method corresponds to the function invoked by the Options->Convert func to AMR menu item. The transformation uses all default settings of the Rescale Images dialog which appears in the GUI version: the AMR will transform the original FMR slices (of the first volume) to a resolution of 256 x 256, it uses bilinear interpolation, it does not invert the intensity values and it does not invert the background. A method which allows to specify these settings will be provided shortly (ConvertFuncToAMREx). 
 
Parameters:
AMRFileName - Name of the amr-file to be created

 




o LinkAMRFile(string AMRFileName)

Links a (pseudo-) anatomical AMR file to an FMR document. Valid only if objDocument is of type FMR. To establish a permanent link to the AMR file, save the FMR file using the Save method. 
 
Parameters:
AMRFileName - Name of amr-file to be linked

 




o LinkStimulationProtocol(string ProtocolFileName)

Links a stimulation protocol PRT file to an FMR project or a 3D volume time course VTC file. Valid only if objDocument is a) of type FMR or b) of type VMR and if a VTC file has been linked. In the latter case, the specified stimulation protocol is linked to the VTC file. To establish a permanent link, save the FMR project or the VTC file. 
 
Parameters:
stimulationProtocolFileName - String, expects path from root, including extension of stimulationprotocol (*.prt)

 




o BeginRecordingSurfaceWindowMovie(string AVIMovieFileName)

Starts recording every updated view in the Surface Module window and saves it to a movie file. Valid only if objDocument is of type VMR and if the Surface Module window for this VMR project has been created. The method must be completed by a matching call to EndRecordingSurfaceWindowMovie, otherwise the movie file can not be used. The "grabbed" frames are stored in a movie file with the provided filename which should have the extension ".avi" since it is stored in Microsoft's format. Note, that the frames are stored uncompressed, i.e. each pixel of each frame is stored using 3 bytes (RGB values). This means that movie files become very large. Use the NewMainWindowSize method to reduce the size of the main window and thus also the size of the Surface Module window. You might use other software to compress the saved movie further, i.e. by converting the uncompressed AVI into GIF animation files. Any command that updates the Surface Module window will result in grabbing the windows content as a frame which is saved in the file. In most cases this will be triggered by the RefreshSurfaceWindow method. 
 
Parameters:
strMovieFileName -

 




o EndRecordingSurfaceWindowMovie()

Stops recording Surface Module window movie and closes the movie file. Valid only if objDocument is of type VMR and if the Surface Module window for this VMR project has been created. The method should be the matching call to an earlier call of the BeginRecordingSurfaceWindowMovie method. The present method closes the opened AVI file properly. If it is omitted, the movie file can not be used. 
 

 




o ShowTimeCourseOfVoxel( number x, number y, number z, string TCWinName)

Shows a time course from a Region-Of-Interest of the currently linked VTC file. Valid only if objDocument is of type VMR. A VTC file must be linked to the VMR. The voxel is specified by system coordinates intX, intY and intZ. The name for the window (strTimeCourseWindowName) can be used to move the window to a new position using the MoveTimeCoursePlot method and to close the window using the CloseTimeCoursePlot method. The function behaves exactly like clicking with the right mouse button at a position in the VMR viewing window. If no statistical map (VMP) has been computed, a ROI Time Course window appears showing the time course of the respective voxel. If a map has been computed, the ROI Time Course window shows the time course of the Region-Of-Interest to which the selected voxel belongs. No window will appear in the latter case if the specified voxel does not hit a "hot" voxel. You can control this behavior by using the ShowTimeCourseOfVoxelEx method. 
 
Parameters:
x - x axis coordinate
y
- y axis coordinate
z
- z axis coordinate
strTimeCourseWindowName
-

 




o ShowTimeCourseOfVoxelEx( number x, number y, number z, string TCWinName, number SingleVoxel, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height, number NewWin, number AddWin)

Shows a time course from a Region-Of-Interest of the currently linked VTC file. Valid only if objDocument is of type VMR. A VTC file must be linked to the VMR. In contrast to the ShowTimeCourseOfVoxel version, this function allows to specify whether the invoked time course window shows the time course of a single voxel (boolSingleVoxel = 1) or of a functional cluster (boolSingleVoxel = 0). In the latter case, a statistical map has to be present and the specified voxel must hit a "hot" (significant) voxel. This version allows to specify the position of the invoked ROI Time Course window on screen as well as its width and height (see MoveTimeCoursePlot method). The position is specified with respect to the left corner (intXPos = 0, intYPos = 0) of the corresponding VMR window. If boolNewTCWindow is set to "1" (or "True"), a new ROI Time Course window is invoked for the specified time course. If this parameter is set to "0" (or "False"), a new window is only shown if no ROI Time Course window has been invoked previously for the corresponding VMR document. If there is already a ROI Time Course window, the last parameter specifies whether the time course shown in the existing window is replaced (boolAddToWindow = 0) by the new one or whether it is added to the existing window (boolAddToWindow = 1). 
 
Parameters:
intX -
intY
-
intZ
-
strTCWindowName
-
boolSingleVoxel
-
intXPos
-
intYPos
-
intWidth
-
intHeight
-
boolNewTCWindow
-
boolAddToWindow
-

 




o MoveTimeCoursePlot( string TCWinName, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height)

Moves a previously created time course window to a new screen position and changes its width and height. Valid only if objDocument is of type VMR. The window name (strTCWindowName) refers to the name specified when the ROI Time Course window has been created using the ShowTimeCourseOfVoxel or ShowTimeCourseOfVoxelEx method. The referred window is moved to a new position and gets width intWidth and height intHeight. The position is specified with respect to the left corner (intXPos = 0, intYPos = 0) of the corresponding VMR window. 
 
Parameters:
strTCWindowName -
intXPos
-
intYPos
-
intWidth
-
intHeight
-

 




o CloseTimeCoursePlot(string TCWinName)

Closes a previously created time course window. Valid only if objDocument is of type VMR. The window name (strTCWindowName) refers to the name specified when the ROI Time Course window has been created using the ShowTimeCourseOfVoxel or ShowTimeCourseOfVoxelEx method. 
 

 




o CloseAllTimeCoursePlots()

Closes all previously created time course windows. Valid only if objDocument is of type VMR. All ROI Time Course windows previously created with the ShowTimeCourseOfVoxel or ShowTimeCourseOfVoxelEx method are closed at once. 
 

 




o ShowEventRelatedAverage( string TCWinName, string AVGFile)

Averages events as specified in an AVG file and shows the event-related averaging results in a window. Valid only if objDocument is of type VMR or FMR. A ROI Time Course window must be created with the ShowTimeCourseOfVoxel or ShowTimeCourseOfVoxelEx method before the ShowEventRelatedAverage method can be used. The event-related averaging runs across time courses at the ROI of the corresponding time course window. The position and size of the created window can be controlled by using the ShowEventRelatedAverageEx method. 
 
Parameters:
strTimeCourseWindowName - The window name (strTimeCourseWindowName) refers to the name specified when the ROI Time Course window has been created
strAVGFileName
-

 




o ShowEventRelatedAverageEx( string TCWinName, string AVGFile, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height)

Averages events as specified in an AVG file and shows the event-related averaging results in a window. Valid only if objDocument is of type VMR or FMR. A ROI Time Course window must be created with the ShowTimeCourseOfVoxel or ShowTimeCourseOfVoxelEx method before the ShowEventRelatedAverageEx method can be used. The window name (strTimeCourseWindowName) refers to the name specified when the ROI Time Course window has been created. The event-related averaging runs across time courses at the ROI of the corresponding time course window. The position and size of the created window can be controlled by specifying values for the intXPos, intYPos, intWidth and intHeight parameters. The position is specified with respect to the left corner (intXPos = 0, intYPos = 0) of the corresponding ROI Time Course (RTC) window. If a AVG window has been invoked and if a new ROI (voxel) for the corresponding RTC window is specified, the event-related averaging will be performed for the new ROI and the AVG window will be updated automatically. 
 
Parameters:
strTimeCourseWindowName -
strAVGFileName
-
intXPos
-
intYPos
-
intWidth
-
intHeight
-

 




o MoveEventRelatedAveragePlot( string TCWinName, number tc_win_x, number tc_win_y, number tc_win_width, number tc_win_height)

Moves a previously created event-related averaging window to a new screen position and changes its width and height. Valid only if objDocument is of type VMR. The window name (strTCWindowName) refers to the name specified when the ROI Time Course (RTC) window to which the event-related averaging (AVG) window is linked has been created. The referred AVG window is moved to a new position and gets width intWidth and height intHeight. The position is specified with respect to the left corner (intXPos = 0, intYPos = 0) of the corresponding RTC window. The AVG window is closed when the linked RTC window is closed with the CloseTimeCoursePlot method. 
 
Parameters:
strTCWindowName -
intXPos
-
intYPos
-
intWidth
-
intHeight
-

 




o CreateSphereMesh()

Creates a new spherical mesh which can be used to reconstruct the skin of a subject's head by iterative morphing. Valid only if objDocument is of type VMR and the Surface Module window has been invoked using the SwitchToSurfaceModule method. Any meshes in the surface module are deleted when this function is executed. The created sphere possesses a standard mesh resolution (20480 vertices), a radius of 140 mm and it is centred at the midpoint of the underlying VMR data set. 
 

 




o RemoveBridges(string SourceVMRFileName)

Remove topological errors named 'handles' or 'bridges' (object produced by puncturing a surface twice) Used to reconstruct the boundaries of a segmented VMR file, producing a mesh representation. The goal is to reduce the genus of the object as much as possible. 
 
Parameters:
sourceVMRFileName - Name of segmented VMR file

 




o RemoveBridgesEx( string SourceVMRFileName, int GreyMatterIntensity, int WhiteMatterIntensity, int GMWMThreshold)

Remove topological errors - extended version Used to reconstruct the boundaries of a segmented VMR file, producing a mesh representation. The goal is to reduce the genus of the object as much as possible. 
 
Parameters:
sourceVMRFileName - Name of segmented VMR file
GreyMatterIntensity
- - average intensity of gray matter (value between - and 225)
WhiteMatterIntensity
- - average intensity of white matter (value between - and 225)
GMWMThreshold
- - value indicating the value separating between white and gray

 




o PrepareBoundaryReconstruction()

This option guarantees that the subsequent reconstruction process creates a valid 2D surface (eg, without moebius bands). This step is a necessary prerequisite of cortex reconstruction, to prevent a nonorientable surface. 
 

 




o ReconstructBoundary()

Creates a new triangle mesh by reconstructing the boundary of a segmented data set. A typical application is the reconstruction of the cortical sheet from a segmented hemisphere. Valid only if objDocument is of type VMR and the Surface Module window has been invoked using the SwitchToSurfaceModule method. Any meshes in the surface module are deleted when this function is executed. The new mesh is created by tesselation of the outer boundary of a segmented VMR data set. The initial surface representation shows the voxelated nature of the underlying segmented data set. To remove this, the triangle mesh can be smoothed by using the MorphMesh method. 
 

 




o MorphMesh( number NrOfIterations, number ScreenUpdateIterations, number SmoothTau, number VMRFindSurfTau, number VMRFindSurfValue, number SmoothingMode)

Morphs a created or loaded mesh; typical applications are surface smoothing or skin reconstruction. Valid only if objDocument is of type VMR and and at least one mesh is present in the Surface Module window. If multiple meshes exist, morphing is applied to the current mesh. Individual morphing steps producing small changes can be repeated as specified by the intNrOfIterations parameter. The screen is not necessarily updated after each morphing step but after several steps as specified by the intUpdateScreen parameter. The changes performed by a single morphing step are controlled by several forces. The smoothing force is specified by the floatSmoothFactor which typically has values between 0.05 and 0.8. Another force is the surface finding force which is specified by the intFindSurfFactor parameter which typically has values between 0.0 and 0.5. The surface finding force lets a vertex move in the direction of its normal vector until it finds an intensity value in the underlying VMR data set as specified by the intFindIntensity parameter. The surface finding force can be turned off by specifying a intFindSurfFactor of '0.0' or by setting the boolSmoothingMode parameter to 'True'. 
 
Parameters:
intNrOfIterations - number of sequential morphing steps
intUpdateScreen
- Specifies number of morphing steps after which the screen has to be updated
floatSmoothFactor
- Smoothing force
floatFindSurfFactor
- Surface finding force
intFindIntensity
- Intensity value at which a moving vertex has to stop
boolSmoothingMode
-

 




o InflateMesh( number NrOfIterations, number ScreenUpdateIterations, number SmoothTau, string RefMesh)

Unfolds the sulci of a folded mesh representing the cortical sheet of a hemisphere. During the inflation process, the hemisphere grows because the surface area is kept constant with respect to a linked reference mesh. Valid only if objDocument is of type VMR and and at least one mesh is present in the Surface Module window. If multiple meshes exist, the inflation process is applied to the current mesh. This is a specialized version of mesh morphing using only the smoothing force. 
 
Parameters:
intNrOfIterations - Individual morphing steps producing small changes can be repeated as specified by the intNrOfIterations parameter.
intUpdateScreen
- The screen is not necessarily updated after each morphing step but after several steps as specified by the intUpdateScreen parameter.
floatSmoothFactor
- The smoothing force is specified by the floatSmoothFactor which typically has values between 0.3 and 0.8 for inflation.
strReferenceMesh
- In the strReferenceMesh parameter, a mesh is specified which is used for the computation of the reference surface area. This mesh is typically the same mesh used at the start of the inflation process.

 




o SaveMesh(string MeshFileName)

Saves a surface mesh file to disk. Surface mesh file names have extension ".srf". Valid only if objDocument is of type VMR and at least one mesh is present in the Surface Module window. If multiple meshes exist, the current mesh is saved. The last loaded or created mesh automatically gets the "current" status. The current mesh can be specified interactively by using the "Select Mesh icon"; a script command for this purpose will be added in a later release. 
 
Parameters:
strMeshFileName -
Returns:
operationSucceeded (boolean)

 




o ReverseSliceOrder()

Reverse the order of the slices (*stc files) from ascending to descending 
 

 




o UninterleaveSliceOrder()

Change the interleaved slices to continuous ascending or descending 
 

 




o SpatialGaussianSmoothing( number FWHM, string UnitsFWHM)

Spatial Gaussian smoothing for FMR projects Spatial smoothing uses a 3D gaussian kernel. The width of the kernel can be specified in millimeters or pixels. Note that the millimeter specification is only correct if the "voxel resolution" has been specified correctly (or more conveniently if it was extracted from the file header during project creation). The kernel width is specified by the FWHM parameter. 
 
Parameters:
FWHM - number, Full width at half maximum of the smoothing kernel
UnitsFWHM
- String, should indicate 'mm' or 'pixel'

 




o SpatialGaussianSmoothingEx( number FWHM, string UnitsFWHM, number InSpaceDomain, number In3D, string NewFMRFile, string NewSTCPrefix)

Spatial Gaussian smoothing for FMR projects - extended version If you want to run gaussian smoothing only within the slices, specify the 2D or the 3D (default) parameter. Spatial smoothing is executed in the space domain (image space) as default, which is fast for small kernels. For large kernels (more than 15 mm), smoothing in the frequency domain is often faster. If you want to use frequency domain gaussian smoothing, specify the the frequency domain parameter. 
 
Parameters:
FWHM - number, Full width at half maximum of the smoothing kernel
UnitsFWHM
- String, should indicate 'mm' or 'pixel'
Specification
- whether to smooth in space domain or not (otherwise in frequency domain)
Smooth
- in 3D (default) (or 2D) (boolean)
Name
- of new FMR file
name
- of new *.stc prefix

 




o TemporalGaussianSmoothing( number FWHM, string UnitsFWHM)

Temporal Gaussian smoothing Since temporal gaussian smoothing blurs timing information across neighboring data points, it is not recommended as default. Temporal smoothing improves, however, the signal-to-noise ratio by removing high frequency fluctuations. The width of the kernel can now be specified in seconds. Note that the specification in seconds is only correct if the TR value has been specified correctly. The kernel width has a default value of "2.8" seconds. If you want to specify the width of the kernel in units of data points (TR's), set the data points parameter instead of the secs parameter. 
 
Parameters:
Width - of the smoothing kernel full width at half a maximum - default 2.8 secs
Smoothing
- units - "sec" or "TR"

 




o TemporalGaussianSmoothingEx( number FWHM, string UnitsFWHM, number InTimeDomain, string NewFMRFile, string NewSTCPrefix)

Temporal Gaussian smoothing - extended version Since temporal gaussian smoothing blurs timing information across neighboring data points, it is not recommended as default. Temporal smoothing improves, however, the signal-to-noise ratio by removing high frequency fluctuations. The width of the kernel can now be specified in seconds. Note that the specification in seconds is only correct if the TR value has been specified correctly. The kernel width has a default value of "2.8" seconds. If you want to specify the width of the kernel in units of data points (TR's), set the data points parameter instead of the secs parameter. 
 
Parameters:
Width - of the smoothing kernel full width at half a maximum - default 2.8 secs
Smoothing
- units - "sec" or "TR"
Domain
- where the smoothing takes place - time domain or frequency domain
Name
- of the new FMR file
Name
- of teh new STC prefix

 




o LinearTrendRemoval()

Remove linear drifts from the data 
 

 




o LinearTrendRemovalEx( string NewFMRFile, string NewSTCPrefix)

Remove linear drifts from the data - extended version 
 
Parameters:
Name - of new FMR file //@param Name of new STC prefix

 




o TemporalHighPassFilter( number HighPassValue, string UnitsHighPass)

Apply a HighPassFilter in the temporal domain; typically used with '2D' fmr files HighPassFiltered fmr file is saved under name <previous_name>_THP<nr>c. 'THP' means 'temporal high pass filter' and <nr>c saves the number of cycles. 
 
Parameters:
HighPassValue -
UnitsHighPass
-

 




o TemporalHighPassFilterEx( number HighPassValue, string UnitsHighPass, string NewFMRFile, string NewSTCPrefix)

Apply a HighPassFilter in the temporal domain; typically used with '2D' fmr files HighPassFiltered fmr file is saved under name <previous_name>_THP<nr>c. 'THP' means 'temporal high pass filter' and <nr>c saves the number of cycles. 
 
Parameters:
HighPassValue - in cycles
UnitsHighPass
- in cycles
NewFMRFile
- new name of the fmr file to be filtered
NewSTCPrefix
- new prefix of the stc files

 




o ClearStimulationProtocol()

Used to start a new stimulation protocol; 
 

 




o AddCondition(string ConditionName)

Adds a condition to a stimulation protocol 
 
Parameters:
conditionName -

 




o AddInterval( string ConditionName, number IntervalStart, number IntervalEnd)

Add an interval to a stimulation protocol. Example: 'doc.AddInterval "Images in RVF", 1, 2'. 
 
Parameters:
conditionName -
intervalStart
-
intervalEnd
-

 




o SetConditionColor( string ConditionName, number ColorR, number ColorG, number ColorB)

Sets the condition color in stimulation protocol. Example: 'doc.SetConditionColor "Images in LVF", 0, 255, 0'. 
 
Parameters:
ColorR - Red intensity in a scale from 0 to 255
ColorG
- Green intensity in a scale from 0 to 255
ColorB
- Blue intensity in a scale from 0 to 255

 




o SaveStimulationProtocol(string StimulationProtocolFileName)

Save the created protocol. Example: 'doc.SaveStimulationProtocol "CG_OBJECTS_FROMSCRIPT.prt"' 
 
Parameters:
stimulationProtocolFileName -

 




o ClearDesignMatrix()

Create a design matrix. Example: 'doc.ClearDesignMatrix' 
 

 




o AddPredictor(string PredictorName)

Adds a predictor to a design matrix Example: 'docAddPredictor "RVF"' 
 
Parameters:
predictorName -

 




o SetPredictorValuesFromCondition( string PredictorName, string ConditionName, number ValueForConditionIntervals)

Set predictor value for a condition in a design matrix. Example: 'doc.SetPredictorValuesFromCondition "RVF", "Images in RVF", 1.0'. 
 
Parameters:
predictorName -
conditionName
-
valueForConditionIntervals
-

 




o SetPredictorValues( string PredictorName, number IntervalStart, number IntervalEnd, number ValueForInterval)

Set any predictor value at any time point (interval) in a design matrix. Example: 'doc.AddPredictor "Linear Trend" For i = 1 To doc.NrOfVolumes value = i*0.1 doc.SetPredictorValues "Linear Trend", i, i, value Next' 
 
Parameters:
predictorName -
intervalStart
-
intervalEnd
-
valueForInterval
-

 




o ApplyHemodynamicResponseFunctionToPredictor(string PredictorName)

Apply the hemodynamic response function to a predictor in a design matrix Example: 'docApplyHemodynamicResponseFunctionToPredictor "RVF"' 
 
Parameters:
predictorName -

 




o LoadSingleStudyGLMDesignMatrix(string DesignMatrixFileName)

Loads an existing design matrix. Example: 'doc.LoadSingleStudyGLMDesignMatrix "CG_OBJECTS_FROMSCRIPT.rtc"' 
 
Parameters:
designMatrixFileName -

 




o SaveSingleStudyGLMDesignMatrix(string DesignMatrixFileName)

Save the single study design matrix (reference time course, *rtc) 
 
Parameters:
RTCFileName - Name and filepath of design matrix

 




o ComputeSingleStudyGLM()

Run the single study GLM 
 

 




o ClearContrast()

Clear contrast in design matrix 
 

 




o SetContrastValue( string PredictorName, int ValueForContrastElement)

Define whether a predictor is included in the model Example: 'docSetContrastValue "RVF", -1' 
 
Parameters:
valueForContrastElement -

 




o ClearMultiStudyGLMDefinition()

Clear/create multi study, multi subject GLM to specify study x predictor interaction effects 
 
Since:
4.6.0

 




o AddStudyAndDesignMatrix( string StudyFileName, string DesignMatrixFileName)

Add subject study and design matrix to multi study, multi subject GLM 
 
Parameters:
studyFileName - Should be a .fmr or .vtc file
designMatrixFileName
- Should be a .rtc file

 




o ComputeMultiStudyGLM(string GLMFileName)

Run the multi study, multi subject GLM 
 
Parameters:
GLMFileName - Multi study, multi subject GLM file (*.mdm)

 




o LoadMultiStudyGLMDefinitionFile(string MultiStudyGLMDefinitionFileName)

Loads an existing multi study, multi subject design matrix 
 
Parameters:
multiStudyGLMDefinitionFileName - Should be a *.mdm file

 




o SaveMultiStudyGLMDefinitionFile(string MultiStudyGLMDefinitionFileName)

Saves a mulit study, multi subject design matrix 
 
Parameters:
multiStudyGLMDefinitionFileName - Name with *.mdm extension

 


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