DTI Metrics + FRF Error

21

Hi Arnaud,

The command is below:

nextflow run /path/to/tractoflow/main.nf -profile use_gpu --bids_config /path/to/sub-0122/code/tractoflow_bids_struct.json -with-singularity /path/to/scilus_1.6.0.sif -resume -with-report report.html --run_pft_tracking false --run_local_tracking true --local_seeding_mask_type fa --local_fa_seeding_mask_threshold 0.1 --local_tracking_mask_type fa --local_fa_tracking_mask_threshold 0.1 --max_dti_shell_value 3000

Best,
Ameen

22

Ok, I may have an idea.

A couple of months ago singularity/apptainer had an issue with some NVIDIA libraries. Here is the PR already merged. It has been part of apptainer since version 1.2.5.

Can you make sure you using apptainer/singularity >= 1.2.5 ?

Hope it will solve your issue.
Arnaud

23

Hi Arnaud,

I am using the singularity version 1.6.0 (scilus_1.6.0.sif). Is this what you are referring to?

Best,
Ameen

24

Hi @ameenq05 ,

I am a collegue of Arnaud. I will try to help you out while he’s out of office.

What Arnaud’s referring to is not the version of the scilus singularity (1.6.0), but the version of the singularity/apptainer software you are using. If you are using a software version prior to 1.2.5, the local tractography step will fail.

You need to upgrade the version you are using to at least 1.2.5, to have OpenCL work on Nvidia graphics cards, which in turns makes the tractography step work.

Best,

Alex

25

Hi Alex,

Thanks for clarifying. I am using singularity version 3.6.4.

Best,
Ameen

26

Hi @ameenq05,

I realized the version 1.2.5 I gave you is for apptainer only, it aligns to about version 3.8.5 of Singularity. Thus, your version of Singularity is outdated. You need to upgrade it to at least 3.8.0 to get full GPU capabilities.

Best,

Alex

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