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-Y9WZa9anAVybKAgr13rFXfcD8Bmu... ." 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
That does not apply to the recon-all command, only to mri_segment_hypothalamus_subunits
On 7/1/2021 12:23 PM, g.toniol@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
g.toniol＠libero.it