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/MapSegmentationsToFunctionalSpace

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