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Longitudinal and multi-site studies

Multiple sessions (visits) are encoded by adding an extra layer of directories and filenames in the form of a session (for example ses-<label>) and with a *_sessions.tsv file.

├─ sub-control01/
│  ├─ ses-predrug/
│  │  ├─ anat/
│  │  │  ├─ sub-control01_ses-predrug_T1w.nii.gz 
│  │  │  ├─ sub-control01_ses-predrug_T1w.json 
│  │  │  ├─ sub-control01_ses-predrug_T2w.nii.gz 
│  │  │  └─ sub-control01_ses-predrug_T2w.json 
│  │  ├─ func/
│  │  │  ├─ sub-control01_ses-predrug_task-nback_bold.nii.gz 
│  │  │  ├─ sub-control01_ses-predrug_task-nback_bold.json 
│  │  │  ├─ sub-control01_ses-predrug_task-nback_events.tsv 
│  │  │  ├─ sub-control01_ses-predrug_task-nback_physio.tsv.gz 
│  │  │  ├─ sub-control01_ses-predrug_task-nback_physio.json 
│  │  │  └─ sub-control01_ses-predrug_task-nback_sbref.nii.gz 
│  │  ├─ dwi/
│  │  │  ├─ sub-control01_ses-predrug_dwi.nii.gz 
│  │  │  ├─ sub-control01_ses-predrug_dwi.bval 
│  │  │  └─ sub-control01_ses-predrug_dwi.bvec 
│  │  ├─ fmap/
│  │  │  ├─ sub-control01_ses-predrug_phasediff.nii.gz 
│  │  │  ├─ sub-control01_ses-predrug_phasediff.json 
│  │  │  └─ sub-control01_ses-predrug_magnitude1.nii.gz 
│  │  └─ sub-control01_ses-predrug_scans.tsv 
│  ├─ ses-postdrug/
│  │  ├─ func/
│  │  │  ├─ sub-control01_ses-postdrug_task-nback_bold.nii.gz 
│  │  │  ├─ sub-control01_ses-postdrug_task-nback_bold.json 
│  │  │  ├─ sub-control01_ses-postdrug_task-nback_events.tsv 
│  │  │  ├─ sub-control01_ses-postdrug_task-nback_physio.tsv.gz 
│  │  │  ├─ sub-control01_ses-postdrug_task-nback_physio.json 
│  │  │  └─ sub-control01_ses-postdrug_task-nback_sbref.nii.gz 
│  │  └─ fmap/
│  │     ├─ sub-control01_ses-postdrug_phasediff.nii.gz 
│  │     ├─ sub-control01_ses-postdrug_phasediff.json 
│  │     └─ sub-control01_ses-postdrug_magnitude1.nii.gz 
│  └─ sub-control01_sessions.tsv 
├─ participants.tsv 
├─ dataset_description.json 
├─ README 
└─ CHANGES

sub-control01_sessions.tsv content:

session_id  acq_time    systolic_blood_pressure
ses-predrug 2009-06-15T13:45:30 120
ses-postdrug    2009-06-16T13:45:30 100

See this example dataset that has been formatted using this specification and can be used for practical guidance when curating a new longitudinal dataset.

Multi-site or multi-center studies

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). 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

The simplest way of dealing with multiple sites is to treat data from each site as a separate and independent BIDS dataset with a separate participants.tsv and other metadata files. This way you can feed each dataset individually to BIDS 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. 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 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.