Hi Jenifer,
yes, you could do that for each label defined in the aseg.stats file (or the FreeSurferColorLUT.txt, but that will contain labels that don't exist in that volume).
what else are you trying to do that you need help with?
Bruce
On Mon, 14 May 2007, Juranek, Jenifer wrote:
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