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We are processing a large database of multishell acquisitions. Occasionally, the bvec/bval files did not transfer with the dataset. If QSIPrep runs on these files, it simply runs without termination. I recognize that this could addressed by due diligence checking, but it's more interesting despite a bids validator error and missing essential files, the processes don't terminate. My sys admin got a hold of me that these images ran for 24+ hours without terminating and also without getting beyond denoising the diffusion.
Additional details
QSIPrep version: 0.20.0
What were you trying to do? Preprocess a dataset that includes intermittent files that have missing bvec/bval files
What did you expect to happen? I would expect that if there are no bvec/bval files, either QSIPrep fails immediately or the anatomical pipeline runs and then terminates.
What actually happened? Anatomical runs but then PIDs stay active indefinitely.
I like this idea a lot. I always use this flag when I run qsiprep. Should the flag to use the former default behavior be something like --continue-despite-errors?
Summary
We are processing a large database of multishell acquisitions. Occasionally, the bvec/bval files did not transfer with the dataset. If QSIPrep runs on these files, it simply runs without termination. I recognize that this could addressed by due diligence checking, but it's more interesting despite a bids validator error and missing essential files, the processes don't terminate. My sys admin got a hold of me that these images ran for 24+ hours without terminating and also without getting beyond denoising the diffusion.
Additional details
What were you trying to do? Preprocess a dataset that includes intermittent files that have missing bvec/bval files
What did you expect to happen? I would expect that if there are no bvec/bval files, either QSIPrep fails immediately or the anatomical pipeline runs and then terminates.
What actually happened? Anatomical runs but then PIDs stay active indefinitely.
Log file attached
QSIprep_log.txt
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