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 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


 


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