table of contents
LIPSIA     Region of Interest Analysis (ROIs)
vmaskedit
In some cases, the resulting contrast images need to be subjected to further post hoc analyses. Specifically, one may want to test whether the activation strength in 'regions of interest' (ROIs) differs between hemispheres and/or conditions or is influenced by some other factors.

The following steps must be performed:

A ROI-mask is created using 'vmaskedit' or 'vledit'. 'vledit' is an interactive drawing program.

In 'vmaskedit', the ROIs are defined as spheres that are given in an ASCII file containing a list of points (sphere centers). The format of this file is the same as that for the program 'vshowpts'.

Each line specifies one point and has the following format:

x y z id radius

Example:

10 20 35 1 2
10 23 24 1 2
18 33 17 2 3

This line produces two spheres of a two voxel radius and id '1', and one of a three voxel radius with id '2'. Spheres with identical id's are treated as one entity in subsequent analyses steps. If the radius is set to '0' then a single voxel is set in the mask. The radius is given in voxels (not millimeters).

The dimension of the output image (its matrix size) can be specified using the parameters '-nslices', '-nrows', '-ncolumns'. If set to '0', a default value is used.

Example:

vmaskedit -in pts.txt -system talairach -resolution 3 -out roi.v

The output 'roi.v' is a file containing all ROIs specified in 'pts.txt'. The parameter '-resolution' defines the voxel-size in mm. In this example, voxels in the output-file are of size 3x3x3mm.

Hint: The resulting file 'roi.v' can be visualized as follows:

vconvert -in roi.v -repn float -map linear -out roi_1.v
vlview -in normbrain.v -zmap roi_1.v

For details of vconvert see via-help.

Parameters of 'vmaskedit':
-help
Prints usage information.
-in
ASCII file containing list of coordinates. Required.
-out
Output file. Default: (none)
-system [ mm | talairach | mni ]
Type of coordinate system. Default: talairach.
-resolution
voxel size in mm. Default: 1
-nslices
number of slices in output image. Default: 0
-nrows
number of rows in output image. Default: 0
-ncolumns
number of columns in output image. Default: 0
Literature:
Bosch, V. (2000). "Statistical Analysis of Multi-Subject fMRI Data: Assessment of Focal Activations." Journal of Magnetic Resonance Imaging, 11(1), 61-64.


Max Planck Institute for Human Cognitive and Brain Sciences. Further Information: lipsia@cbs.mpg.de
Copyright © 2007 Max Planck Institute for Human Cognitive and Brain Sciences. All rights reserved.