HCP-proc

Preprocessing of Human Connectome Project data for use in whole-brain modeling.

Goals

• Build the structural connectome
• Extract the parcellated resting state time series

Parcellation used is Desikan-Killiany (aparc+aseg from FreeSurfer), and both the connectome and the resting state time series are built for all cortical and subcortical regions (res_all/ directory in the generated data) and for cortical regions only (res_ctx/ directory in the generated data).

Prerequisities

1. HCP data (available from [db.humanconnectome.org])

   • "Structural Preprocessed" in data/Structural directory
   • "Resting State fMRI FIX-Denoised (Compact)" in data/rfMRI directory
   • "Diffusion Preprocessed" in data/Diffusion directory

2. Software

   • Connectome workbench
   • MRtrix3
   • Python 3.7 with standard (neuro-)scientific packages

Usage

1. Get the data and the software
2. From the working directory call snakemake sc fmri. Test it with a dry-run first (-n switch), and make sure you have sufficient computational resources for the tractography.