Help Running TGV-QSM on Cluster

[FrancescaPentimalli]

Hi Neurodesk Team,

I’m trying to run TGV-QSM on my university's HPC cluster. I followed the instructions to use run_transparent_singularity.sh, but I ran into this error:

INFO: Converting SIF file to temporary sandbox...
FATAL: while extracting tgvqsm_1.0.0_20210629.simg: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled
It seems this might be due to user namespace or fakeroot permissions not being enabled on the cluster. I’ve contacted IT support to address this, but I want to confirm:
Am I following the correct steps to run TGV-QSM with Neurodesk on a cluster?
Is enabling these permissions the only solution, or is there something else I can try?
Thanks for your help! :)

[stebo85]

It could be a wrong configuration in your cluster for apptainer/singularity.

You could try our latest QSMxt container: https://qsmxt.github.io/QSMxT/

It's build with newer apptainer versions and might work for you. QSMxt includes TGV qsm and a lot of great wrappers to process the data quickly.