[ERR] REPETITION_TIME_MISMATCH

[giulia-berto]

With bl2bids, I came across this error using the Cam-Can dataset: [ERR] Repetition time did not match between the scan's header and the associated JSON metadata file. (code: 12 - REPETITION_TIME_MISMATCH).

This is a known error to which a solution was already proposed: https://neurostars.org/t/bids-validator-error-tr-mismatch-between-nifti-header-and-json-file-and-bids-validator-is-somehow-finding-tr-0-best-solution/1799/2.

What do you think if we do something similar? I already drafted the code, which modifies the header of the images though. Let me know. @soichih

[soichih]

I see. So according to the thread you found, it seems that RepetitionTime mistach issue was reported to Cam-Can as early as 2018 but they still haven't corrected it. I am not sure why they aren't interested in fixing it.

I feel that, copying the entire input nifti files just to override the nifti header for the sole purpose of passing the bids-validator to be somewhat wasteful, and also could make the data processing a bit less transparent. On app-fmriprep, I've added an option to skip bids-validator if user choose to do so. I think we could make sure that any BIDS App will have capability to skip the bids-validation, like app-fmriprep so that user can first try with the bids-validation turned on (usually by default on most BIDS Apps I believe), then try without validation later if they so choose.

But if you feel strongly that we should go ahead and modify the header, we could do that. When you do, you will need to store a copy of original input nifti file instead of modifying the original input file as you will not able to modify the input data.

[giulia-berto]

Ok, I would also be cautious in modifying input files. Let's leave it like that, keeping in mind that one would need to enable the skip bids-validation option if using the Cam-Can dataset.