Check fmriprep outputs

Software Support
1

Hello!

I’m running fmriprep on server preprocessing large datasets (Abide, ADHD200). And I wonder if there is a way to check all that thousands of outputs without seeing visual reports. Specifically, i want to know if there were some troubles or warnings when running fmriprep, even though it said “fmriprep finished successfully”.

Looking forward to your suggestions,

Tania

2

Hi @nomoreofanime,

You can always make a python or bash script to make sure (1) each output has the same kind of outputs (2) parse the output logs (i.e. your Slurm .out/.err files) for phrases such as “Error” (3) use something like Nilearn make quick visual summaries of easy to visualize outputs (like the brain mask).

Best,

Steven

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