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Preparing the imaging metadata as a table

To be able to query information about available neuroimaging data in your dataset, you must provide Neurobagel with a .tsv file containing your dataset's neuroimaging metadata. We refer to this as a BIDS metadata table.

If your dataset is already in BIDS, the Neurobagel CLI provides a bids2tsv command that will automatically generate this table for you.

The BIDS metadata table lists each subject's available imaging files and modality information, using BIDS naming conventions, in the format shown below.

Example BIDS metadata table

sub ses suffix path
sub-01 ses-01 T1w /data/bids-examples/synthetic/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii
sub-01 ses-01 bold /data/bids-examples/synthetic/sub-01/ses-01/func/sub-01_ses-01_task-rest_bold.nii
sub-02 ses-01 T1w /data/bids-examples/synthetic/sub-02/ses-01/anat/sub-02_ses-01_T1w.nii
sub-02 ses-01 bold /data/bids-examples/synthetic/sub-02/ses-01/func/sub-02_ses-01_task-rest_bold.nii
... ... ... ...

About the BIDS metadata table

The table must include at least four columns named exactly sub, ses, suffix, and path (adapted from BIDS entities). Additional columns are allowed but will be ignored by Neurobagel.

Each row of the table indexes a single image file with the following metadata:

  • sub (required)
    • Subject ID in the format sub-<label>
    • Example: sub-PD123
  • ses (optional)
    • Session ID in the format ses-<label>, if applicable
    • Example: ses-01
  • suffix (required)
  • path (required)
    • Path to the image file
    • Example: /data/pd/qpn/sub-PD123/ses-01/anat/sub-PD123_ses-01_T1w.nii.gz

Supported BIDS imaging modalities

Neurobagel currently supports a subset of MRI modalities included in the BIDS specification, but we plan to expand this list for closer alignment with BIDS in the future.

Supported modalities are listed below using their BIDS suffixes:

  • dwi
  • T1w
  • T2w
  • bold
  • asl
  • eeg
  • meg
  • pet

Info

For more information, see also the "Modality specific files" section of the BIDS specification or consult this master list of image suffixes supported by BIDS.