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BIDS scripts

These are scripts that we use to convert our behavioral and imaging data to BIDS format.

The function to arrange imaging data into BIDS format relies mostly upon a database with the following information:

  • The name of the series that is being converted to BIDS (which can correspond to one of several types of scans- anatomical, functional, DTI, field map).
  • The DICOM path to that series (for extracting meta information stored in the sidecar JSONs).
  • The NifTI path for that series.

Parts of it will need to be adapted for non-Rockland datasets. The functions to convert behavioral data will differ substantially from other studies.
Some elements of it we would certainly like to improve.

It chiefly depends upon:

  • nibabel
  • pydicom
  • numpy
  • sqlite3 (for the database portion; the scripts might also be adapted to use other inputs, such as csvs containing the necessary info)

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Scripts used to process Rockland sample scans into BIDS format.

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