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yes, that looks correct

On 12/9/2025 1:48 PM, Carly McIntyre-Wood wrote:

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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
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