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.

[rcruces]

Hi,

Thank you for your message!

Regarding your question about running the pipeline on Compute Canada’s terminal/bash, I am aware that someone has successfully run it on Compute Canada, so it should work in theory. Could you please include the log files from the run? This will help in identifying any issues more clearly.

For the proc_structural part of the pipeline, you mentioned encountering errors such as “command not found” for tools like mrinfo and fslreorient2std, as well as warnings about oblique datasets. This could indicate that certain dependencies or environment variables are not properly set up in the Singularity container.

Could you also send the Singularity script you are using? One thing to try is adding the --writable-tmpfs --containall options, which isolates the environment and may help resolve some issues related to missing dependencies.

Let me know if you have other questions or need further assistance!