Running BIDS App freesurder on HPC

Hi all,

I am trying to run freesurfer on the cloud.
I run singularity locally using this code

sudo docker run --privileged -ti --rm -v /var/run/docker.sock:/var/run/docker.sock -v /home/…/singularity_images:/output singularityware/docker2singularity bids/freesurfer

uploaded it to the HPC and ran

singularity run --cleanenv /home/project/DTI/bids_freesurfer.simg
-v /home/project/DTI:/bids_dataset:ro
-v /home/project/DTI/Freesurfer:/outputs
-v /home/project/DTI/license.txt:/license.txt
bids/freesurfer /bids_dataset /outputs participant
–license_file “/license.txt”

It ran for 10 s instead of 8 hours and the out put was bids example version …
With no errors.

I am new to HPC and BIDS App and would appreciate any help.

Cheers,
Nachshon

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