You can also use mri_binarize (it takes any format as input). We don't
have anything that will automatically generate a separate volume for
each label.
Bruce Fischl wrote:
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
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MGH-NMR Center
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