I'm interested in parsing aseg.mgz into separate binary mask files for each aseg label. Is this possible? The closest topic I found was located at the following URL:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu nctionalSpace
2.0 Creating binary masks
The segmentation for a particular structure can be extracted to create a binary mask (i.e., a volume where the voxel value is 1 if it is in the structure and 0 otherwise). To make a binary mask of the left putamen, which has been assigned label 12 (see ${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command:
avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \ -thr 12 -uthr 12 \ ./fbert.feat/reg/freesurfer/lh.putamen.nii.gz
I checked the following for additional help...but still need some help...
http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands
Many Thanks,
Jenifer