SpatialSmoothingFD3D Method


Description

Spatially filters each 3D volume of a VTC file in the frequency domain.

Syntax

objDocument.SpatialSmoothingFD3D(intHighPass, intLowPass)

Remarks

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. The high- and low pass values are interpreted in cycles per spatial dimension measured in voxels. 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 everyghing 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 substring 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 substring "_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 substrings 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.

Example

' VBScript
Set doc = BrainVoyager.
OpenDocument("subject.vmr")
doc.
LinkVTC "cg_objects_SC.vtc"
doc.
TemporalSmoothingFD3D 3, 200 ' produces "cg_objects_SC_FTS-3-200.vtc"
doc.
SpatialSmoothingFD3D 1, 14 ' produces "cg_objects_SC_FTS-3-200_FSS-1-14.vtc"

// JScript
doc = BrainVoyager.
OpenDocument("subject.vmr");
doc.
LinkVTC("cg_objects_SC.vtc");
doc.
TemporalSmoothingFD3D(3, 200);
doc.
SpatialSmoothingFD3D (1, 14);

# PerlScript
$doc = $BrainVoyager->
OpenDocument("subject.vmr");
$doc->
LinkVTC("cg_objects_SC.vtc");
$doc->
TemporalSmoothingFD3D(3, 200);
$doc->
SpatialSmoothingFD3D (1, 14);