NIH Blueprint: The Human Connectome Project

News and Updates

Press Releases,Project News | September 10, 2014

HCP Processing Pipelines Released

PipelinesGithubThe WU-Minn HCP Consortium is pleased to announce the open source release of HCP data processing pipelines at https://github.com/Washington-University/Pipelines.

To download, click releases (near the top of the page), then under v3.4.0, click the “Source code (zip)” or “Source code (tar.gz)” button.

These v3 pipelines were used to process HCP image data from the HCP 500 Subjects Release (June 2014).

The HCP Pipelines are set of tools (primarily, but not exclusively, shell scripts) for processing MRI images for the Human Connectome Project. Among other things, these tools implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013.

We are releasing the HCP Pipelines now for use to the community, but we are still in the process of making the scripts more robust, well-documented, and usable in other environments (other versions of operating systems, other queueing systems, other versions of prerequisite tools, etc.). We cannot guarantee that you will not have to make modifications to the scripts for them to be used successfully in your environment.

The HCP Pipelines require installation of FSL 5.0.6, FreeSurfer v5.3.0-HCP, and Connectome Workbench v1.0. See the README.md 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.

We encourage user feedback and improvement suggestions on the HCP Pipeline tools and the documentation. Discussion of HCP Pipeline usage and improvements can be posted to the hcp-users discussion list. Sign up for hcp-users at http://humanconnectome.org/contact/#subscribe

Best,

The WU-Minn HCP Consortium

Press Releases,Project News |

Connectome Workbench v1.0 Released

The WU-Minn HCP Consortium is pleased to announce Connectome Workbench (WB) version 1.0 brain visualization and analysis software has been released at  http://humanconnectome.org/connectome/get-connectome-workbench.html

WB v1.0 is available for 64-bit Mac OSX, Windows, and Linux (32-bit Windows is no longer supported).

The Workbench distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

New features in WB v1.0 include:

  • The “workbench” GUI executable has been renamed “wb_view”
  • Integrated Help information in wb_view accessible through the “?” button
  • Additions to capabilities for displaying matrix charts for parcellated connectivity CIFTI files
  • New border file format that carries structure and vertex count (see -file-convert or tutorial instructions for conversion of old format border files)
  • wb_commands “-nifti-convert” and “-cifti-convert -version-convert” have been moved to “-file-convert“, nifti convert arguments changed
  • New viewing capabilities for asymmetric dense connectome CIFTI file, multi-slice oblique volume, and label data outlines

With the release we have created a streamlined, updated WB v1.0 tutorial and dataset featuring processed HCP 500 Subjects data that are available to download at http://humanconnectome.org/connectome/get-connectome-workbench.html and on the ConnectomeDB HCP project page. Access to the tutorial data requires ConnectomeDB login and signature of the HCP Open Access Data Use Terms.

To download the WB v1.0 source code from GitHub: follow the link, click releases (near the top of the page), then under v1.0, click the “Source code (zip)” or “Source code (tar.gz)” button .

We encourage you to check out Connectome Workbench for visualizing and performing analysis on imaging data from the HCP and elsewhere. Discussion of Connectome Workbench usage, bugs, and features can be posted to the hcp-users discussion list. Sign up for hcp-users at http://humanconnectome.org/contact/#subscribe

Press Releases,Project News | September 2, 2014

Beta Release of Group-ICA maps, Node timeseries, and Network matrices

The Human Connectome Project (HCP) WU-Minn consortium is pleased to announce a beta-release of Resting-state fMRI (rfMRI) analyses on the HCP 500 Subjects data released in June 2014. This rfMRI data was processed, using data from all 468 subjects having four rfMRI runs, yielding the following outputs:Netmat_Fig

  • A group-average “parcellation”, obtained by means of group-ICA (independent component analysis).
  • Subject-specific sets of “node timeseries” – for each subject, a representative time series per ICA component (“parcel” node).
  • A subject-specific “parcellated connectome”or “netmat” – for each subject, a nodes x nodes matrix – the functional connectivity between node timeseries.

As a shorthand, we are calling this rfMRI analysis dataset the HCP 500 Subjects Parcellation, Timeseries, Netmats Release, or “HCP 500 Subjects PTN Release”, for short.

These rfMRI analyses are being “beta” released because the analysis methods used are still works-in-progress and may be improved in the future. We encourage the community to look at the released data and discuss the methods and results.

What’s in the HCP 500 Subjects PTN Release? The data is available as a single package release containing:

  • Group-ICA “parcellations” at five different dimensionalities (levels of detail), including spatial-ICA maps for each distinct ICA decomposition dimensionality and volumetric MNI152 3D-space projected versions of the spatial-ICA maps, primarily for display purposes.
  • Node-timeseries (individual subjects), estimated by 2 distinct timeseries estimation approaches for each group-ICA dimensionality.
  • Netmats (parcellated connectomes). Full and partial correlation netmats for each subject and at the group-level (all subjects) for each choice of group-ICA dimensionality and node timeseries estimation approach.

A summary document for the HCP 500 Subjects PTN Release is included in the released package. It contains details about methods used in these analyses, descriptions of released files, example MATLAB/FSLNets code, and references.

Access the HCP 500 Subjects PTN Release data on the HCP website. Download the dataset on the WU-Minn HCP 500 Subjects project page on ConnectomeDB under the HCP500 Parcellation + Timeseries + Netmats (PTN) heading.

Have more questions?  We encourage you send your questions to hcp-users@humanconnectome.org and join the hcp-users discussion group (http://www.humanconnectome.org/contact/#subscribe), so that you can tune in to technical discussions on issues that may be of interest.

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