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