External Email - Use Caution
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