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.
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
, andFLAIR
- Most images have an
acq
tag:- Non-neuromelanin images:
acq-<plane><type>
, where<plane>
is one of:sag
,ax
, orcor
(for sagittal, axial, or coronal scans respectively)<type>
is one of:2D
, or3D
- Neuromelanin images:
acq-NM
- Non-neuromelanin images:
- 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 anacq
tag.
- The available suffixes are:
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
, orPA
- 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, wherevalue
is the b-value for that sequence.
- All imaging files have the
Currently, only structural (anat
) and diffusion (dwi
) MRI data are supported. Functional (func
) data has not been converted to the BIDS format yet.