We are working on using heudiconv to convert our DICOM files to BIDS for all the scans our lab has ever acquired. For most participants, we scanned them multiple times over the years. We have 6 fMRI project cohorts over about 18 years of scanning with over 300 subjects and a lot of demographic, behavioral, and physiological data. We’re in the process of seeing if we can make it public.
We are confused about session numbering in this longitudinal context. We could use absolute session numbering, which would be pretty straightforward. That way each participant will have multiple subfolders, one for each session, with session numbers ordered by date of acquisition. However, that might make fMRI analysis a bit confusing, for example if participant MOB101 did the stroop-task on session 1, but MOB120 did the stroop-task scan on session 3 (stroop-task visit 1) and again on session 4 (stroop-task visit 2).
In other words, we have two session counts: absolute session, and fMRI task session. Both are useful information.
When running fMRIprep or other software, how would you specify which sessions to use?
We could specify this with a single BIDS session tag: ‘ses-02-stroop-02’. Or, we could specify it with two tags: ‘ses-02’ and ‘cohortses-stroop-02’. However, there is no ‘cohortses’ tag, so this seems like a bad idea.
So, the files could be of the form of one of the following two examples:
If we just used absolute session and didn’t tag fMRI task sessions, then I guess we could make a list of which absolute session the relevant fMRI task could be found in, but that sounds like a confusing mess. I think that is the approach suggested in this thread, with a sessions.tsv file and a sessions.json data dictionary:
The “type” column in the sessions.tsv could specify the fMRI task cohort (aka wave). During analysis, you could use that type column to filter, so it would be clear if MOB101 did stroop-task on ses-01 and MOB120 did stroop-task on ses-03 and again on ses-04.
Basically, my question is this: Should we just use “ses-01” in our filenames, or should we add information about the fMRI cohort (like “ses-01-stroop-01” or “ses-01_cohortses-01”)? (As an aside, are multiple hyphens allowed in a BIDS tag?)