BIDS format for between subject design


I am analysing a between subjects fMRI study (treatment vs. control).

What is the best way to implement this in the BIDS format in terms of subject names/folder structure?

At the moment, I am using:

controlsubjects = [01_0, 02_0, 03_0, etc.]
treatmentsubjects = [01_1, 02_1, 03_1, etc.]

So the last number (1 or 0) indicates the group (treatment or control).

The BIDS validator isn’t a fan of this so I get errors. I can’t find any online examples of between subjects designs in the BIDS format.

Any help would be much appreciated.

Many thanks,


Hi @PaulF,

In BIDS, labels need to be alphanumeric, so you’re not constrained to designators like _0 and _1 to indicate group. Also, underscores (_) are not valid alphanumeric characters, and have a semantic significance in BIDS filenames. You have a couple options.

  1. Put the group name right in the participant label, e.g., sub-control01, sub-treatment01, … In general, though, you shouldn’t count on software that you use to distinguish groups by patterns in the labels; those are there for human readability. You should specify the group in participants.tsv, as well.
  2. Simply assign labels and then use participants.tsv to distinguish the groups.

Hope this helps,

Hi Chris,

Thank you so much your quick response :slight_smile:

This is really helpful. I think I will go for the sub-control01 , sub-treatment01 option.

Many thanks,