participant information

[karl-koschutnig]

Hi Marcel,

I was wondering if it would be possible to add an option in the bidseditor for specifying participant-related values. It’s great that the tool automatically generates a participants.tsv and corresponding JSON file, but it would be really helpful to be able to define variables like sex (and potentially others) directly through the interface.

For instance, the current participants.json includes a "Level" entry for age, which doesn’t quite fit unless we’re categorizing participants into discrete groups like “young” or “old.” A format similar to what’s used in the neurobagel project might be a good reference.

What do you think?

Best,
Karl

[marcelzwiers]

So if I understood you properly, you'd like to be able to specify dynamic values for the participants.tsv file? Something like (each key is a column in the participants-table):

participants:
  participant_id: <<filepath:/raw/sub-(.*?)/>>
  session_id: <<filepath:/raw/sub-.*?/ses-(.*?)/>>
  group:
  age: <<PatientAge>>
  sex: <<PatientSex>>
  size: <<PatientSize>>
  weight: <<PatientWeight>>

Currently, this info is collected in the plugins and then written to the participants-file. But that's hard coded, I guess it may indeed be useful to be able to add to that using the GUI

[karl-koschutnig]

Thanks for the quick reply (as always!!)

Yeah, a GUI option would be nice. Indeed, it would be great to have a way to change the corresponding json file. So for example we get the sex from the DCM-Tag and also want to set the levels in the json file.
That ultimate renders to:

"sex": {
    "Description": "sex of the participant as reported by the participant",
    "Levels": {
        "M": "male",
        "F": "female"
    }
},

[marcelzwiers]

I will give it a try to see how it works out. Btw, do you have Presentation logfiles in your dataflow? Because in the upcoming version I added a new feature to convert that to BIDS too (i.e. to a sub*_events.tsv file) and I can always use feedback :-)

[karl-koschutnig]

Great - thanks a lot!

Yes, we do have some "old" studies that have used neurons. I am happy to help and try it out!
We invested much time in dealing with events files and made a little psychopy module (https://psychopy-bids.readthedocs.io/en/stable/).

[marcelzwiers]

I played around a bit with the interface and I can make something to customize the participants.tsv file. The json-sidecar is much harder though, because of its nested structure. Yet, I understood it's the sidecar that you are after, right? Or would you also like to tweak the table?

[karl-koschutnig]

I know this is not easy to implement. I really appreciate your effort.
Have you had the chance to look at the neurobagel approach (link in the first post). There, you "upload" a tsv and can annotate basic stuff. Something like that would be great.
In my world, it would be perfect to have some basic participants info in the exact same format after coining them. Later, I would tweak the table (but not in the conversion process).