HCP Pipelines v6.0.0 Released - NHP and Longitudunal integration

We are pleased to announce the release of v6.0.0 of the HCP pipelines. This version adds support for non-human primate (NHP) processing, completes support for longitudinal processing, and is being used for processing of Adult Aging Brain Connectomes (AABC) going forward in the QuNex container described below and for the Human and Mammalian Brain Atlas (HMBA) project for making NHP comparisons.

Notable changes and features of v6.0.0

Main new features:

• NHP HCP Pipeline Integration (support for macaque, marmoset, and chimpanzee)
  •   PreFreeSurfer
  •   FreeSurferNHP
  •   PostFreeSurfer
  •   Diffusion
  •   fMRIVolume
  •   fMRISurface
  •   sICA+FIX
• Full longitudinal processing support (structural previously released)
  •  fMRIVolume
  •  fMRISurface
  •  Diffusion
  •  sICA+FIX
  •  MSMAll
  •  tICA 
  •  TransmitBias
• Folding compensated cortical thickness by default in PostFreeSurfer, or to be run on existing results (better sensitivity and power for detecting inter individual differences in cortical thickness: Demirci et al., 2026 Imaging Neuroscience)
• fMRIStats pipeline (basic quality statistics for fMRI data)
• FreeSurfer 7 and 8 support
• Support for on-scanner field map correction (e.g., Siemens Static Field Correction) for fMRI (or other fMRI datatypes without distortion)

Other changes:

• Support for spin echo fieldmaps with different echo spacing or phase direction than BOLD, and precomputed fieldmaps
• Support different fMRINames list per longitudinal session in TransmitBias
• Allow running longitudinal FreeSurfer with a single timepoint
• Reorganize longitudinal FreeSurfer output with less symlinking
• Use conf2hires in longitudinal FreeSurfer
• New VolumeToCIFTI.sh global script
• Modernize sICA+FIX hand classification template scene
• Miscellaneous improvements and bugfixes

Note that we have bumped the version from 5.x to 6.x based on the addition of major new functionality, but 6.0.0 should be backwards compatible with the 5.x tree. 

Full list of changes from 5.0.0-->6.0.0 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 v6.0.0 of the HCP Pipelines, we recommend installation of FSL 6.0.7.15 (current latest), FreeSurfer (v6.X, 7.X, or 8.X), and Connectome Workbench v2.2.1. See the Installation and Usage Instructions and HCP Pipelines 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.

QuNex is a software suite that provides a containerized extensible platform for data organization, preprocessing, quality assurance, and analyses across neuroimaging modalities. A new version of QuNex (1.5.1, see release notes) has been released that includes HCP Pipelines 6.0.0 with all the tools needed for execution. There are now 2 QuNex containers released, the one versioned as 1.5.1 uses FreeSurfer 6 like all previous versions, the one tagged as 1.5.1_fs8 uses FreeSurfer 8. New users that want to download the container need to register at https://qunex.yale.edu/registration/ and then follow the instructions on the page that follows to download and install Docker or Singularity/Apptainer containers.