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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 grayvalue of 1332 nii files , and 5 nii files maximum grayvalue is 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