Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] Add use of session entity as example of encoding multi-site studies in a single dataset #1803

Merged
merged 3 commits into from
May 22, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 14 additions & 4 deletions src/longitudinal-and-multi-site-studies.md
Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ for practical guidance when curating a new longitudinal dataset.

This version of the BIDS specification does not explicitly cover studies with
data coming from multiple sites or multiple centers (such extension is planned
in [BIDS `2.0`](https://github.com/bids-standard/bids-2-devel).
in [BIDS `2.0`](https://github.com/bids-standard/bids-2-devel/issues/11)).
There are however ways to model your data without any loss in terms of metadata.

### Option 1: Treat each site/center as a separate dataset
Expand All @@ -92,11 +92,21 @@ Apps and everything should just work.

### Option 2: Combining sites/centers into one dataset

Alternatively you can combine data from all sites into one dataset. To identify
which site each subjects comes from you can add a `site` column in the
Alternatively you can combine data from all sites into one dataset.
This can be done in two ways:


#### Option 2.a: Collate sites at subject level

To identify which site each subjects comes from you can add a `site` column in the
`participants.tsv` file indicating the source site. This solution allows you to
analyze all of the subjects together in one dataset. One caveat is that subjects
analyze all subjects together in one dataset. One caveat is that subjects
from all sites will have to have unique labels. To enforce that and improve
readability you can use a subject label prefix identifying the site. For example
`sub-NUY001`, `sub-MIT002`, `sub-MPG002` and so on. Remember that hyphens and
underscores are not allowed in subject labels.

#### Option 2.b: Use different sessions for different sites

In case of studies such as "Traveling Human Phantom" it is possible to incorporate site within session label.
For example `sub-human1/ses-NUY`, `sub-human1/ses-MIT`, `sub-phantom1/ses-NUY`, `sub-phantom1/ses-MIT` and so on.