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README_PPMI.md

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Nipoppy: Parkinson's Progression Markers Initiative dataset

This repository contains code to process tabular and imaging data from the Parkinson's Progression Markers Initiative (PPMI) dataset. It is a fork of the main Nipoppy repository. Nipoppy is a lightweight workflow management and harmonization tools for MRI and clinical data. This fork adds scripts, configuration files, and downstream analyses that are specific to PPMI.

BIDS data file naming

The tabular/ppmi_imaging_descriptions.json file is used to determine the BIDS datatype and suffix (contrast) associated with an image's MRI series description. It will be updated as new data is processed.

Here is a description of the available BIDS data and the tags that can appear in their filenames:

  • anat
    • The available suffixes are: T1w, T2w, T2starw, and FLAIR
    • Most images have an acq tag:
      • Non-neuromelanin images: acq-<plane><type>, where
        • <plane> is one of: sag, ax, or cor (for sagittal, axial, or coronal scans respectively)
        • <type> is one of: 2D, or 3D
      • Neuromelanin images: acq-NM
    • For some images, the acquisition plane (sag/ax/cor) or type (2D/3D) cannot be easily obtained. In those cases, the filename will not contain an acq tag.
  • dwi
    • All imaging files have the dwi suffix.
    • Most images have a dir tag corresponding to the phase-encoding direction. This is one of: LR, RL, AP, or PA
    • Images where the phase-encoding direction cannot be easily inferred from the series description string do not have a dir tag.
    • Some participants have multi-shell sequences for their diffusion data. These files will have an additional acq-B<value> tag, where value is the b-value for that sequence.

Currently, only structural (anat) and diffusion (dwi) MRI data are supported. Functional (func) data has not been converted to the BIDS format yet.