Try adding --labelwm to mri_aparc2aseg
On 3/12/2025 12:17 PM, Jin Liu wrote:
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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
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