HCP Pipelines v4.8.0 released

[Elam, Jennifer]

We are pleased to announce the release of v4.8.0 of the HCP pipelines. This version of the pipelines is being used for processing of Adult Aging Brain Connectomes (AABC, HCP-Aging follow-on study including additional longitudinal timepoints) going forward in the QuNex container described below.

 

Notable changes and features of v4.8.0

Main new features:

• Add the spatial ICA reclean pipeline (#279) with compiled feature generation (#281)
• Better support non-HCP/non-Siemens T1w, T2w, and T2w-FLAIR images (match mean of BC reference with mean of the input T1w/T2w image) with a new abstracted myelin map BC module to generate MyelinMap_BC files (#249) and associated changes in MSMAll.sh (#251), DeDriftAndResample.sh (#252), and other scripts (#259)
• Added correction for Philips (#271) and fix support for GE Healthcare (#285) fieldmap preprocessing
• Refactor MSMSulc.sh into a module, replacing a section of a PreFreesurfer internal script in the pipelines and to allow different MSMSulc to be run after an initial pipeline run (#290)
• Add multi-echo support to fMRI preprocessing
• Add task fMRI level 3 processing script
• Major improvements to tICA pipline, including (#284)

Other additions/changes:

• Refactoring of all pipelines to simplify the I/O interface code (#254, #280)
• MR FIX scripts updates and comments to support additional configurations and fewtimepoints icaDim mode for use with legacy data (#241).
• Modification of aff2rigid and ACPCAlignment for adapting to Non-Human Primates or other brains (#245)
• Enable frame range selection for fMRI runs in SingleSubjectConcat.sh and allow MSMAll to be run on partial timeseries (#247)
• Add custom outlier detection functions for tICA feature generation to maintain compatibility with MATLAB runtime r2017b (#263)
• Update conf2hires to remove reinitialization by bbregister for high resolution data in the FreeSurfer pipeline (#265)
• Introduce tICA weighted mode in RSN regression (#278)
• Add a seconds option for diffusion echo spacing to allow for harmonized time units across pipelines (#291)
• Miscellaneous improvements and bugfixes.

Full list of changes from 4.7.0 -> 4.8.0 available here

The HCP Pipelines are a set of tools (primarily, but not exclusively, shell scripts) for processing MRI images, originally developed for the Human Connectome Project and related studies. For v4.8.0 of the HCP Pipelines, we recommend installation of FSL 6.0.7.13, FreeSurfer v6.0 (Not v7.X), and Connectome Workbench v2.0. See the Installation and Usage Instructions in the GitHub repository for updated and detailed information on prerequisite software versions, installation and processing instructions, example data, and processing resource requirements.  Answers to frequently asked questions can also be found on our Github Repository: HCP Pipeline FAQ. Questions about running the pipelines are also frequently answered on this HCP-Users list.

A new version of the QuNex container (0.100.0) has been released that includes HCP Pipelines 4.8.0. New users that want to download the container need to register at https://qunex.yale.edu/qunex-registration and then follow the emailed instructions. Once registered, go to https://gitlab.qunex.yale.edu/qunex/qunexcontainer, login, and follow the instructions there to download and install Docker or Singularity containers.

Best,

HCP Consortia and Connectome Coordination Facility

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org

 

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