v4.1.3 HCP Pipelines released
Elam, Jennifer
We are pleased to announce the release of v4.1.3 of the HCP pipelines scripts. This version of the pipelines is being used for functional preprocessing of HCP Lifespan Aging and Development data to be released later this spring and adds support for processing of non-HCP style legacy MRI data (see below).
Notable changes and features of v4.1.3
- New debugging library, with error trapping turned on in all scripts as a default
- Increase dilation in fMRI subcortical segmentation to avoid invalid CIFTI files being produced, plus add checking for mismatching atlas subcortical segmentation and subject's brain mask
- Improve/fix masking of dMRI data for voxels outside of the FOV
- Add assessment of spatial coverage completeness within both fMRIVolume and fMRISurface
- Add capability to use FLAIR style acquisitions within FreeSurferPipeline.sh
- Improvements to dimensionality estimation of multi-run FIX (MR-FIX)
- Extend single-run FIX to support the MotionRegression=FALSE condition
- Compiled matlab now uses R2017b (same version as used for the current FSL FIX compiled matlab)
- dMRI QC report generated using FSL's eddy “QUAD” QC tool
- Added option to use custom brain image or mask in PreFreeSurfer pipeline
Added a --processing-mode parameter option to process legacy (non-HCP style) data, specifically to:
- Allow structural processing without a high resolution T2w image
- Allow functional processing without susceptibility distortion correction
- Enable use of slice timing correction
- Enable use of expanded fMRI masks
- Enable use of a reference fMRI run with linear or additional nonlinear registration to the reference fMRI run
The HCP Pipelines are set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project. v4.1.3 of the HCP Pipelines require installation of FSL 6.0.2, FreeSurfer v6.0, and Connectome Workbench v1.4.2. See the Installation and Usage Instructions in the GitHub repository for 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.
Best,
HCP Consortium and Connectome Coordination Facility