One way to do it is with mri_binarize:
mri_binarize --i aseg.mgz --min 1.5 --max 2.5 --o wm-lh.mask.nii
This will find all the voxels whose value is between 1.5 and 2.5 and set
them to 1 in the output. In this case, it will make a binary mask of the
left cerebral white matter as that has a code of 2 (from
FreeSurferColorLUT.txt).
The output can be saved in any mri_convert output format (ie, mgh, mgz,
analyze, nifti, etc).
doug
Sasha Wolosin wrote:
Dear all,
Does aseg save out masks of the various subcortical regions measured?
If so, is it possible to visualize and/or edit these in tkmedit/scuba,
or export them to an external format?
Thanks,
Sasha
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