Hello FreeSurfer team,

I’m trying to create a lobe segmentation for white matter. I first created the annotation files using mri_annotation2label with --lobesStrict for each hemisphere, and then tried to map the lobe parcellation onto segmentation volume by using mri_aparc2aseg. But somehow the resulting image was not segmented by lobes. It contains cortical parcellation by lobe, detailed subcortical segmentation by structure, and white matter is marked as a whole (cerebral white matter). I then checked the annotation files created by lobesStrict and they look fine, without any subcortical labels.

I wonder where I made a mistake, or if there is an easier way to do lobe segmentation. The code I used is as follows:

mri_annotation2label --subject 1300 --hemi lh --labelbase ./1300/label/aparc-lh --lobesStrict ./1300/label/lh.aparc.lobesStrict

mri_annotation2label --subject 1300 --hemi rh --labelbase ./1300/label/aparc-rh --lobesStrict ./1300/label/rh.aparc.lobesStrict

mri_aparc2aseg --s 1300 --annot aparc.lobesStrict --o ./1300/mri/lobesStrict.mgz

Best,

Jin