NIH Blueprint: The Human Connectome Project

News and Updates

Project News,Recommended Reading,The Science of Connectome | August 26, 2016

Nature Neuroscience: “The Human Connectome Project’s neuroimaging approach”

Screen shot 2016-08-26 at 11.53.08 AMPublished today in Nature Neuroscience is a primer on the Human Connectome Project’s style of data collection, processing, analysis, and open-access distribution.

“The Human Connectome Project’s neuroimaging approach”

Nature Neuroscience 19, 1175–1187 doi:10.1038/nn.4361

The data for this study has been uploaded to the BALSA database as Connectome Workbench-compatible scene files for interactive viewing and comparison to other imaging data/analyses.

Authors: Matthew F Glasser, Stephen M Smith, Daniel S Marcus, Jesper L R Andersson, Edward J Auerbach, Timothy E J Behrens, Timothy S Coalson, Michael P Harms, Mark Jenkinson, Steen Moeller, Emma C Robinson, Stamatios N Sotiropoulos, Junqian Xu, Essa Yacoub, Kamil Ugurbil & David C Van Essen

Abstract: Noninvasive human neuroimaging has yielded many discoveries about the brain. Numerous methodological advances have also occurred, though inertia has slowed their adoption. This paper presents an integrated approach to data acquisition, analysis and sharing that builds upon recent advances, particularly from the Human Connectome Project (HCP). The ‘HCP-style’ paradigm has seven core tenets: (i) collect multimodal imaging data from many subjects; (ii) acquire data at high spatial and temporal resolution; (iii) preprocess data to minimize distortions, blurring and temporal artifacts; (iv) represent data using the natural geometry of cortical and subcortical structures; (v) accurately align corresponding brain areas across subjects and studies; (vi) analyze data using neurobiologically accurate brain parcellations; and (vii) share published data via user-friendly databases. We illustrate the HCP-style paradigm using existing HCP data sets and provide guidance for future research. Widespread adoption of this paradigm should accelerate progress in understanding the brain in health and disease.

Posted by Jenn Elam @ 9:34 am

Project News |

Connectome Workbench v1.2.3 Released

Screen shot 2016-08-26 at 11.38.35 AMWe are pleased to announce version 1.2.3 of Connectome Workbench (WB) brain visualization and analysis software is now available for 64-bit Mac OSX, Windows, and Linux at:

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 v1.2.3 include:

  • Zip scene file wb_command function is now available from within the wb_view GUI
  • wb_shortcuts script implemented to more easily do common tasks for interactive shells
  • New Preferences option for hiding dynamic connectivity *.dynconn layers by default

Changes to existing behavior:

  • warnings produced when creating files with an extension not matching what wb_view expects
  • interpolation of volume with a length-1 spatial dimension always uses enclosing voxel
  • wb_command accepts (but warns) about unicode non-ascii dashes, but also replaces them in filenames
  • nifti headers default pixdim[] to all 1s even when unused (cifti)


  •  -cifti-label-import -drop-unused-labels option fixed
  • files loaded by scene properly restore the “in spec” status
  • chart timecourse status properly restored from scenes

WB v1.2.3 is compatible with the WB v1.0 tutorial and the processed 900 Subjects Group Average Data available to download at and on the ConnectomeDB HCP project page. Access to both datasets require ConnectomeDB login and signature of the HCP Open Access Data Use Terms.

To download the WB v1.2.3 source code from GitHub: follow the link, click releases (near the top of the page), then under v1.2.0, click the “Source code (zip)” or “Source code (tar.gz)” button.

We encourage you to check out Connectome Workbench v1.2.3 for visualizing and performing analysis on imaging data from the HCP and elsewhere and for making scenes and figures. Discussion of Connectome Workbench usage, bugs, and features can be posted to the hcp-users discussion list. Sign up for hcp-users at


Posted by Jenn Elam @ 8:49 am

Press Releases,Project News,Recommended Reading,The Science of Connectome | July 20, 2016

Nature article: Cortical brain maps at the highest resolution to date

Screen Shot 2016-07-20 at 11.21.20 AM

Matthew Glasser, Ph.D. of the Van Essen lab at Washington University in St. Louis.

Major new work based on Human Connectome Project data and methods published in July 20 issue of Nature promises to be a boon to neuroanalysis research for years to come.

The study, A multi-modal parcellation of human cerebral cortex, led by Matthew Glasser and David Van Essen of Washington University, used information derived from structural and functional MRI data collected on 210 HCP subjects to create a new 180 region per hemisphere map of the cerebral cortex of the human brain. Further improvements to previous maps were achieved by using the multimodal surface matching algorithm pioneered by HCP investigators at Oxford U to precisely align the individual brains before analysis. Results were validated and the maps applied to individuals from an independent set of 210 HCP subjects.

Although the new map will be very important in raising the accuracy of work to delineate the connections between brain regions by the HCP and others, it will continue to improve as more, higher resolution data is added to the analyses.

As Glasser told the Washington University Record:

“We ended up with 180 areas in each hemisphere, but we don’t expect that to be the final number,” Glasser said. “In some cases, we identified a patch of cortex that probably could be subdivided, but we couldn’t confidently draw borders with our current data and techniques. In the future, researchers with better methods will subdivide that area. We focused on borders we are confident will stand the test of time.”

and added in Nature:

“We’re thinking of this as version 1.0,” says Glasser. “That doesn’t mean it’s the final version, but it’s a far better map than the ones we’ve had before.”

The parcellation and Connectome Workbench scenes for each of the main article and supplemental figures are being shared in the new Brain Analysis Library of Spatial maps and Atlases (BALSA) database being developed by the Van Essen lab at Washington University.

The parcellation for use as a reference is most easily accessed in the Glasser_et_al_2016_HCP_MMP1.0_5_StudyDataset.scene study dataset.

Nature produced a video highlighting the work in the context of previous brain mapping efforts:

In addition to the article itself, Nature is distributing a wealth of supplemental information, as David Van Essen told the Washington University Record:

“We were able to persuade Nature to put online almost 200 extra pages of detailed information on each of the 180 regions as well as all of the algorithms we used to align the brains and create the map,” Van Essen said. “We think it will serve the scientific community best if they can dive down and get these maps onto their computer screens and explore as they see fit.”

The seminal work has also garnered much press:

B.T. Thomas Yeo & Simon B. Eickhoff authored a Nature News and Views article.

Nature News: Human Brain Mapped in Unprecedented Detail

Washington University Record: Map provides detailed picture of how the brain is organized

NIH News: Connectome map more than doubles human cortex’s known regions

New York Times: Updated Brain Map Identifies Nearly 100 New Regions

Wall Street Journal: Brain Mappers Create a Detailed Atlas of the Human Cortex

The Scientist: Mapping the Human Connectome

Popular Science: This New, Ultra-Detailed Map Of The Brain Could Change Medicine

Wired: A New Map of the Brain Redraws the Boundaries of Neuroscience


Older Posts »