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norment / tsd_issues

Repo to track issues with TSD as tickets
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FSL pipeline doesn't run on TSD #4

Closed ofrei closed 4 years ago

ofrei commented 4 years ago

I don't know details but it seem to be a big issue..

tobias-kaufmann commented 4 years ago

Description: FSL pipeline for analyzing fMRI data from raw data to fully processed networks used to run on the old system but fails on colossus 3. We are seeing errors in the beginning of the pipeline (feat) but it will likely be more errors later on in the pipeline. Priority level: Getting FSL to run is quite central for several ongoing projects in the imaging group and as soon as the software is working again, we will feed thousands of images through the pipeline. Status: TSD support is already working on a solution!

tobias-kaufmann commented 4 years ago

Update: FSL 6.0.3 has now been deployed by TSD support and can be loaded using source /cluster/software/fsl/6.0.3/setup.source A first test of feat succeeded. We will now test the rest of the FSL pipeline.

ofrei commented 4 years ago

@tobias-kaufmann was this resolved?

tobias-kaufmann commented 4 years ago

Not yet. FSL Feat runs smoothly I think but some libraries are missing for FSL Fix/Aroma.

ofrei commented 4 years ago

As we discussed today this is fixed by Sabry and FSL works well.