Dear Naveed,

You need the development version; these files are not given by FreeSurfer 6.0.

Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Muhammad Naveed Iqbal Qureshi <mniqureshi@hotmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 6 December 2019 at 13:44
To: Freesurfer maillist <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampus subfields outputs missing

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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