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Hi I ran the following command not the subject on HPC

module load matlab/r2013a

module load freesurfer/6.0.0

source $FREESURFER_HOME/SetUpFreeSurfer.sh

fixup_mni_paths

recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid ADHD-${PBS_ARRAYID} -hippocampal-subfields-T1 -sd /hpf/projects/glongoni/ADHD-200/ -openmp 8

in the output directory I get only following files for both left and right hemisphere

lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

lh.hippoSfLabels-T1.v10.mgz

lh.hippoSfVolumes-T1.v10.txt

How can I get following files?

lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.CA.mgz lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz

I try to find this command but it is not available in my installation

segmentHA_T1.sh

Regards,

Naveed