Lunching the pipeline on Compute-canada

[mahdimplus]

Hi,

I have a question regarding the execution environment. Can the pipeline be run using Compute Canada’s terminal/bash?

Thank you!

[mahdimplus]

actually on the Narval server, we created the micapipe container by using the singularity build command to pull the image directly from DockerHub (docker://micalab/micapipe:v0.2.3) and convert it into a Singularity Image Format (.sif) file, as follows: singularity build micapipe_v0.2.3.sif docker://micalab/micapipe:v0.2.3.
Also,
For the proc_structural part of the pipeline, the process does not complete successfully, encountering errors such as “command not found” for tools like mrinfo and fslreorient2std, as well as warnings about oblique datasets, despite the input dataset being processed without issues on a local machine.