Two things to check
1. Look at the image and make sure it has all the segs you expect, if, so
2. You may need to give mri_segstats a color table like
$FREESURFER/FreeSurferColorLUT.txt. Does the Choi atlas come with one?
You can pass it with --ctab colortab.txt
On 5/14/2025 11:56 AM, Payam Sadeghi Shabestari wrote:
External Email - Use Caution
Thanks Douglas, looks like it only returns the whole cerebellum volume
(see attached).
*From: *freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Date: *Wednesday, 14 May 2025 at 16:38
*To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Striatum and cerebellum parcellation stats
from Choi2012 and Buckner 2011
Have you tried using mri_segstats, eg,
mri_segstats --seg cerebellum_17_network_${mask_option}_mask.nii.gz
--sum cerebellum_17_network_${mask_option}_mask.stats
On 5/8/2025 4:15 AM, Payam Sadeghi Shabestari wrote:
* External Email - Use Caution *
Hi FS team,
I'm trying to obtain anatomical statistics for the regions defined
in the Choi 2012 and Buckner 2011 parcellations, but I couldn't
figure out how to get stats on them. I already did:
for mask_option in "${mask_options[@]}"; do
mri_vol2vol --mov $SUBJECTS_DIR/$subject_id/mri/norm.mgz \
--s $subject_id \
--targ
$SUBJECTS_DIR/MNI152/buckner_atlas/17_network_${mask_option}_mask.nii.gz
\
--m3z $SUBJECTS_DIR/MNI152/mri/transforms/talairach.m3z \
--noDefM3zPath \
--o
$SUBJECTS_DIR/$subject_id/mri/cerebellum_17_network_${mask_option}_mask.nii.gz
\
--inv-morph \
--interp nearest
Thank you and best regards,
Payam
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