yes, that looks correct
On 12/9/2025 1:48 PM, Carly McIntyre-Wood wrote:
External Email - Use Caution
Hi there,
Resending this as there seemed to be an issue with my previous email. We want to implement the Glasser atlas for cortical parcellation on a sample of participants that have been run through FreeSurfer 8.0. I found this example in the listserv and have adapted it.
Is someone able to confirm if this script would give me a reliable output? I also hope to do the same with the HCPex atlas. Am I also able to use the same script with the HCPex atlas file instead?
Thanks so much!
Carly
mri_surf2surf \
--hemi lh \
--srcsubject fsaverage \
--trgsubject $subj \
--sval-annot $datadir/fsaverage/label/lh.HCPMMP1.annot \
--tval ${SUBJECTS_DIR}/$subj/label/lh.HCPMMP1.annot
mri_surf2surf \
--hemi rh \
--srcsubject fsaverage \
--trgsubject $subj \
--sval-annot $datadir/fsaverage/label/rh.HCPMMP1.annot \
--tval $SUBJECTS_DIR/$subj/label/rh.HCPMMP1.annot
# Extract Thickness and Volume stats
mris_anatomical_stats \
-a $SUBJECTS_DIR/$subj/label/lh.HCPMMP1.annot \
-f ${SUBJECTS_DIR}/$subj/stats/lh.HCPMMP1.stats \
-b $subj lh
# Extract Thickness and Volume stats
mris_anatomical_stats \
-a $SUBJECTS_DIR/$subj/label/rh.HCPMMP1.annot \
-f ${SUBJECTS_DIR}/$subj/stats/rh.HCPMMP1.stats \
-b $subj rh
FREESURFER VERSION: 8.0.0
OS: macOS Monterey
Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.e...