Fixes additional flags in srun_fastsurfer and T2 processing #656
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dkuegler
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Basic testing complete, now testing on a bigger dataset. |
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looks generally ok. As long as the tests work and normal processing is not breaking, we can merge it. |
Additional flags (including --t2) did not work properly from the subject_list file in srun_fastsurfer.sh The Bug is actually in stools.sh:translate_cases, where the lines are not correct parsed. This Commit fixes this issue and properly parses the file. Also, the check to find non-existent files in stools.sh:check_subject_images. This Commit also adds a check if files are symlinks, which may cause problems with folders mounted in singularity (this needed a small change in srun_fastsurfer.sh - an additional argument to check_subject_images).
…s passed for seg_only module in srun_fastsurfer.sh as well as add a license check if a T2 image is passed to run_fastsurfer.sh
Pass SLURM_ARRAY environment variables through to the segmentation process (not doing so causes the segmentation process to not detect which "batch" to process) Fix number of jobs in brun_fastsurfer.sh Fix device detection in brun_fastsurfer.sh
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Additional flags (including --t2) did not work properly from the subject_list file in srun_fastsurfer.sh
The Bug is actually in stools.sh:translate_cases, where the lines are not correct parsed.
This PR fixes this issue and properly parses the file. Also, the check to find non-existent files in stools.sh:check_subject_images.
This PR also adds a check if files are symlinks, which may cause problems with folders mounted in singularity (this needed a small change in srun_fastsurfer.sh - an additional argument to check_subject_images).
This PR fixes #654