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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_${mask_option}_mask.nii.gz \ --inv-morph \ --interp nearest Thank you and best regards, Payam
Have you tried using mri_segstats, eg, mri_segstats --seg cerebellum_17_network_${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_${mask_option}_mask.nii.gz \
--inv-morph \
--interp nearest
Thank you and best regards, Payam
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Thanks Douglas, looks like it only returns the whole cerebellum volume (see attached).
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU Date: Wednesday, 14 May 2025 at 16:38 To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011 Have you tried using mri_segstats, eg, mri_segstats --seg cerebellum_17_network_${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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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 $FREESURFER/FreeSurferColorLUT.txt. Does the Choi atlas come with one? You can pass it with --ctab colortab.txt
On 5/14/2025 11:56 AM, Payam Sadeghi Shabestari wrote:
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Thanks Douglas, looks like it only returns the whole cerebellum volume (see attached).
*From: *freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@MGH.HARVARD.EDU *Date: *Wednesday, 14 May 2025 at 16:38 *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Striatum and cerebellum parcellation stats from Choi2012 and Buckner 2011
Have you tried using mri_segstats, eg, mri_segstats --seg cerebellum_17_network_${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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1f_hEA-30hIYbnujEQKRSrU0kIoyvSLf9gSMJA5luQdDbLAfCsbhdrsi7V06AW73Fh3jjnm5wr8aHUcj0GCAtTV3DeMUdzyvd1bFb50UxrnNxVHsw6lorft4UCUNJxbSKaAAGD0mLXIg3_v6Zl4mar5vjRq2cxndt14gVUvCTYcL6cNFTLqgfFFaoYgnuRU2O80rx-rOPX4Xn0ReKQT-ey9ejcrUVAoh0diD84FhgFSRx3WNM0GCdixqfkCDeag6NuY2B9slmlw9Q-gnN1-uCRsSVk-mdN6_HRqR_rKQKIC4Yw7vtv9aQxfegY2eSx9ZSxkZBtaffplH3_JBS27c1zw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Douglas N. Greve -
Payam Sadeghi Shabestari