I have a general question about how fmriprep selects images from a BIDS repository. Specifically, with bids validation turned off, if there are image files that have BIDS non-compliant naming, will it ignore those images ? For example, if I have images such as *BADT1w.nii.gz, *BADbold.nii.gz, *BADphasediff.nii.gz, I think they will be ignored, but just wanted to make sure.
Yes they should be ignored, you can see the default bids filter file here: FAQ - Frequently Asked Questions — fmriprep version documentation.
That being said, what you are doing with naming is not recommended. The safer thing to do would to be something like having an
acq-bad label in your images and defining a bids filter file that will only process the
acq-good files. Or, if there is no use for the bad images, just don’t put them in the folders (maybe keep them in
sourcedata or something if you are afraid of losing them).
Thanks @Steven . One thing I noticed in the default bids filter is that it doesn’t specify a suffix for the fmap entity.
Thanks for suggestion on using
acq . We actually used a different git branch to handle the
BAD images, but didn’t remember to switch to the “good” branch before running fmriprep, hence making sure.
Well, as long as your bad fmaps aren’t associated with any good images, then it won’t matter anyways. A fieldmap may be made from your bad fmaps, but they won’t be applied anywhere. You can always just add a line to the filter file to exclude them if you want to be doubly sure though.
I supposed you mean
IntendedFor ? I checked to make sure that they don’t point to any, so we should be good. Thanks again!