Release of HCP Pipelines v5.0.0

[Elam, Jennifer]

We are pleased to announce the release of v5.0.0 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 v5.0.0

Main new features:

• Addition of transmit field bias pipeline for correction of T1w/T2w myelin maps (#298)
• Addition of option to the ICAFIX pipeline to use python-based FIX (‘pyfix’), which is now the default for new set-ups. The legacy Matlab/R-based FIX will continue to be used by default for existing set-ups (see `--enable-legacy-fix` parameter for details). (#312)
• Addition of Longitudinal Structural pipelines (FreeSurfer and PostFreeSurfer) for processing of multiple timepoints for the same subject (#295).  Additional longitudinal pipelines are under development (e.g., for applying to the fMRI data).
• Addition of option to the ICAFIX pipeline to find the melodic ICA consensus decomposition using the ‘icasso’ algorithm and use it in a final ‘melodic’ run (#312)
• Addition of Gaussian mixture modeling to ‘RSNRegression’ to compute more valid z-stats (#310)
• Added Optional Wishart Filtering Capability after last temporal regression to all ‘RSNRegression’ modes to improve reproducibility of effect size maps

Other changes:

• Updated FSL binary location for FSL 6.0.6 and later to PATH (#299)
• Recompiled all MATLAB to MCR2022b
• Miscellaneous improvements and bugfixes.

Note that we have bumped the version from 4.x to 5.x based on the addition of major new functionality, but 5.0.0 should be backwards compatible with the 4.x tree.

 

Full list of changes from 4.8.0-->5.0.0 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 v5.0.0 of the HCP Pipelines, we recommend installation of FSL 6.0.7.15, FreeSurfer v6.0 (Not v7.X), and Connectome Workbench v2.0.1. See the Installation and Usage Instructions and HCP Pipeline FAQ in the GitHub repository for updated and detailed information on prerequisite software versions, installation and processing instructions, example data, and processing resource requirements. Questions about running the pipelines are also frequently answered on this HCP-Users list.

A new version of the QuNex container (1.0.0, see release notes) has been released that includes HCP Pipelines 5.0.0 with all the tools needed for execution. 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

 

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