I’m working on getting our data into a BIDS-compatible format and have begun testing some of the Docker container images like MRIQC. For some of our participants, we have multiple runs (e.g., 3 T1w due to movement/poor quality at scan time). After running MRIQC, the need for the multiple runs is confirmed. From a BIDS-compatability perspective, where should low-quality, unused images go? Obviously, full-on deleting them seems like a poor idea. Should there be a top level folder like “unused”?
I didn’t see anything in the 1.0.2 specification but maybe I just missed it.
The problem with this issue is subjectivity - your criteria for exclusion may be only relevant to your intended use and current state of the data processing tools. This can change in the future, the data can be used for other types of analyses and tools will improve helping to deal with noisy data.
So what I would recommend is the following:
- Add _scans.tsv file for each sub/ses and include a new column in it called qc_exclude (or something similar). See section 8.10
- Add a data dictionary (scans.json) explaining the nature of the new column and the exclusion criteria. See section 4.2
- Explaining the exclusion cryteria once again in the README.
I hope this helps!
This has been discussed in the BIDS group. Maybe worth reading - https://groups.google.com/forum/m/#!topic/bids-discussion/21NOkxDSUqE
In practice, you’ll want to stick with Chris’ recommendations.
Thanks @ChrisGorgolewski and @oesteban. I’ll follow Chris’s recommendations for this as I’m building out our folders.