HCP Pipeline Tools

The HCP Pipeline Tools product is a set tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project. Among other things, these tools implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013

Prerequisites

The HCP Pipelines Tools have the following software requirements:

  1. A 64-bit Linux Operating System
  2. The FMRIB Software Library (a.k.a. FSL) version 5.0.6 or greater installed and config properly sourced
  3. FreeSurfer version 5.3.0-HCP installed and config properly sourced
  4. ${HCPPIPEDIR}/src/gradient_unwarping installed with dependancies (source code located in this folder) if using gradient distortion correction

Notes

  1. You will need to define an environment variable named HCPPIPEDIR which should hold the path to the root folder in which the HCP Pipelines Tools reside.

    For example, you might set HCPPIPEDIR in a manner similar to one of the following.

    
   export HCPPIPEDIR=/home/NRG/tbrown01/projects/Pipelines
   export HCPPIPEDIR=/media/2TBB/Connectome_Project/Pipelines
   export HCPPIPEDIR=/nrgpackages/tools/hcp-pipeline-tools

  2. An example setup script is provided in ${HCPPIPEDIR}/Examples/Scripts/SetUpHCPPipeline.sh.

    That setup script will need to be edited to set the absolute path to the HCP Pipelines Tools root installation folder on your system. Your modified setup script will need to be sourced before running an HCP pipeline.

  3. To test that the pipelines work, there is example data located in: ${HCPPIPEDIR}/Examples/792564

  4. There are example batch scripts to call the pipelines on this data located in: ${HCPPIPEDIR}/Examples/Scripts

  5. In all example batch scripts, the following variables will need to be modified or checked prior to use:

    
   Subjlist="792564" #Space delimited list of subject IDs
   StudyFolder="/media/myelin/brainmappers/Connectome_Project/TestStudyFolder" #Path to subject's data folder
   EnvironmentScript="/media/2TBB/Connectome_Project/Pipelines/Examples/Scripts/SetUpHCPPipeline.sh" #Pipeline environment script