Install Request: HCP Pipelines

[cdkharris]

Application: HCP Pipelines, most recent stable version

Link: https://github.com/Washington-University/HCPpipelines

Cluster: Myriad

Description: The HCP Pipelines product is a set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project.

License: Several, but I don't see any obstacles

Special versions or variants: The request was specifically for the Diffusion Preprocessing tool, but I see no reason not to install all of them centrally.

Ticket number: IN:06191840

Prerequisite software
Installation

[ikirker]

Prerequisites

The HCP Pipelines have the following software requirements:

• A 64-bit Linux Operating System

• The FMRIB Software Library (a.k.a. FSL) version 6.0.2 or greater installed and configuration file properly sourced. The latest version of FSL is recommended.

• FreeSurfer version 6.0 available at http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall/

• FreeSurfer 7.X is not currently supported due to poor quality surface reconstructions.

  NB: You must create and install a license file for FreeSurfer by visiting and submitting the FreeSurfer registration form.

  NB: For now, FreeSurfer 5.3.0-HCP (used for original processing of HCP data) is still supported, but if you use it you must use the FreeSurferPipeline-v5.3.0-HCP.sh pipeline script instead,(i.e. modify FreeSurferPipelineBatch.sh ${queuing_command} line to use ${HCPPIPEDIR}/FreeSurfer/FreeSurferPipeline-v5.3.0-HCP.sh)

• Connectome Workbench version 1.4.2 or later

  The HCP Pipelines scripts use wb_command which is part of the Connectome Workbench. They locate wb_command using an environment variable. Instructions for setting this environment variable are provided below in the Running the HCP Pipelines on example data section.

• The HCP version of gradunwarp version 1.1.0 (gradient_unwarp.py, if gradient nonlinearity correction is to be done).

• MSM_HOCR v3.0/(github v1.0): https://github.com/ecr05/MSM_HOCR/releases This is the multi-modal surface matching algorithm used in MSMSulc and MSMAll. The pre-compiled binaries are fine if they work on your operating system.

• FSL FIX v 1.0.6.14+: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX sICA+FIX is used for cleaning spatially specific structured noise from fMRI data. Please see this page for supplemental instructions for sICA+FIX: https://github.com/Washington-University/HCPpipelines/blob/master/ICAFIX/README.md

• FSL 6 is already installed.
• Freesurfer 6 is already installed.
• MSM_HOCR seems to be downloadable as a binary and only depend on OpenBLAS. There are some other dependencies noted for the repo, but I don't think the binary this needs needs those.
• Connectome Workbench looks like a simple download of binaries (albeit an annoying module since all the normal FHS directories are suffixed).
• FIX is supposedly bundled with FSL?

[ikirker]

Connectome Workbench is installed. MSM_HOCR appears to be already installed as a component of FSL. That seems to complete the dependencies.

That means that anyone can clone or download the repository of HCP Pipelines and use them, if they load the modules for the dependencies.