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Hello FreeSurfer Developers,

Thank you for your work ! 

I successfully set up Freesurfer and ran a test on my computer, and I am now attempting to run recon-all on all subjects in a folder ("/home/users/s/saccaro/Groupe_0" in the example script below). I run the analysis on a HPC (SLURM system).

I found that, concerning the recon-all command, "If no name is given after --s, the code will be run on ALL subjects in $SUBJECTS_DIR." but I do not find information on how this could work also for the previous step, mri_convert: is there a way to submit a job to segment all subjects in the folder "Groupe_0", and not just S001 (in the example below)? All folders are structured as follows: /S@@@/scans/struct/@@@@@@.nii . 

I am new to Freesurfer and I apologize if my question is naive but I cannot find a solution in any of the online resources.

Thank you very much for your time!
Best,

Giorgio

- Script, without SBATCH settings (I join the full version):

module load FreeSurfer/6.0.0-centos6_x86_64

source /home/users/s/saccaro/SetUpFreeSurfer.sh

FSDIR="/home/users/s/saccaro/Groupe_0"

mksubjdris ${FSDIR}/S001;

mri_convert -i ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.nii -o ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.mgz

recon-all -all -s S001

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