That does not apply to the recon-all command, only to
mri_segment_hypothalamus_subunits
On 7/1/2021 12:23 PM, g.ton...@libero.it wrote:
External Email - Use Caution
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
<https://secure-web.cisco.com/1cAYZmFGVfas4DCf91-Y9WZa9anAVybKAgr13rFXfcD8BmuTPUSvDFohmKg6XCOHsIyMh3GxdvII3R4KsnUNvVgmkFYaXaLUrV6D4KS_FHQoG-jh3udJfVenKYjfGnQ52GhpYoVVrX0tBf7dYQrUolGWmFw6e6_WhYzueJZGR4-f7wZgN7ElCR8p-E0JP_iMzorzjxp4ZS3pmsDJZJvZJBPtOe4ViP3yDrkR8Q0-xSgssKu5gO4tvQffgOtxO6IJ39HSHMy99mPGWxaH3WxM5sg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHypothalamicSubunits>."
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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