Have you looked at the segmentations on top of the anatomy? It might be that they are so small that they sometimes don't get labeled.

On 3/19/2021 8:00 AM, 况况 wrote:

External Email - Use Caution

TO: freesurfer@nmr.mgh.harvard.edu SUBJECT: mri_segstats error: mri_extract_label mgz to nii Hello FreeSurfer Developers, I'm want to study the volume and function of amygdala subnucleis, so i need to acquire the mask of amygdala subnucleis in MNI space. mri_extract_label subject_001/mri/lh.hippoAmygLabels-T1.v21.mgz 7001 lateral_nucleus_001.nii i total 77 subjects,including left and right amygdala subnucleis , totally acquired 77*18=1332 nii files. Reading the maximum grayvalueof 1332 nii files , and 5 nii files maximum grayvalueis zero. 'lh.Anterior-amygdaloid-area-126.nii' 'lh.Medial-nucleus-111.nii' 'lh.Medial-nucleus-319.nii' 'rh.Anterior-amygdaloid-area-417.nii' 'rh.Anterior-amygdaloid-area-428.nii'

I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 2) Platform: CentOS release 6

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer