Hello,

I am attempting to run two FS commands to provide data on the hippocampal subfields and the amygdala nuclei. I have run this on ~700 cases, but a few seem to have an error with the segmentation (see attached images for examples). Here is the script that I’ve run that shows where the data is and is run on the specific subject whose images are attached. This was written as a csh script.

#Hippocampal subfields

setenv SUBJECTS_DIR /autofs/space/rincewind_003/users/Amygdala/subjects

source /usr/local/freesurfer/nmr-stable6-env

recon-all -s HAB_133_FOK_2.1 -hippocampal-subfields-T1 -no-isrunning

#Amygdala nuclei

cd /autofs/space/rincewind_003/users/Amygdala/hippoAmyg

./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR left

./segmentSubject.sh HAB_133_FOK_2.1 $SUBJECTS_DIR right

If you have any insight on what might be going wrong with the segmentation, that would be most helpful. The recon-all.log is included.

Thanks!

Nick