Remi-Gau
commented
1 year ago it appears there is no simple way to ignore certain runs. Nothing standardize
The problem atm is it creates a robust template with all the runs available for a participant and won't tell unless you skim the logs.
Checking what will become the new spec for the BIDS app: it also makes no suggestions.
https://bids-standard.github.io/execution-spec/inputs.html#reserved-arguments
I would recommend the bids-filter-file approach the same way fmriprep does it. There is a suggestion to apply it to MRIQC and I have used it in BIDSPM.
Note that bids filter file just mentions scans to include though, not to exclude.
Your idea
I have a couple of subjects with several runs of T1w or FLAIR and I naively thought that
.bidsignorewas an (okay) place to indicate which runs to ignore. Little did I know,.bidsignoreis meant for the validator only and doesn't do anything (#131). Unless I missed something in the BIDS-App documentation, it appears there is no simple way to ignore certain runs. The problem atm is it creates a robust template with all the runs available for a participant and won't tell unless you skim the logs.The rogue way is to simply delete the undesired scans but I hope there could be way to deal with this problem without deleting files.
Would a
--bids-filter-fileà la smriprep #104 solve this problem? I never used such in the past so I don't know.. Maybe a simple hack to ignore specific runs for some subjects only already exists ?Am I right in thinking that the most straightforward approach to address this would likely involve passing a file that contains a list of scans to be ignored/removed when listing the T1w, T2, flair, etc.? Cheers!