walkthrough

walkthrough

The Markdown documents contained in this directory document the various steps that you can follow to (hopefully) re-produce our analyses and results. You can use the table of contents below to jump around, or click here to just start at the beginning.

Table of Contents

• Step 1: Set-up and installation
  • Required software
  • Getting the repository with git
  • Python dependencies
    • Using conda (recommended)
    • Using pip
    • Internal libraries
  • Docker and Singularity
• Step 2: Downloading data from the PPMI
  • Getting access to the data
  • Downloading the neuroimaging data
  • Downloading the rest of the data
• Step 3: BIDSifying the PPMI
  • PPMI to BIDS
  • The convert_ppmi() function
• Step 4: Processing the PPMI neuroimaging data
  • Re-running the ANTs pipeline
  • The modified ANTs BIDS App
  • Quality control
  • Parcellating the data
• Step 5: Reproducing the analyses
  • Preparing for SNF
  • The SNF procedure
  • Data concatenation versus SNF
  • PD patient biotypes
  • MRI contributions
  • Diffusion embedding
  • Supplementary analyses

If you have any questions, simply open an issue on this repository and someone will get back to you as soon as possible!