NIH Blueprint: The Human Connectome Project

News and Updates

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


Project News | March 8, 2013

Workbench beta version 0.81 released

Screen shot 2013-03-14 at 3.59.44 PMHCP has released the newest beta version of its Connectome Workbench brain surface/volume visualization and analysis software to coincide with the HCP Quarter 1 data release. Workbench software is freely available to all on the HCP website.

Several features have been updated in v0.81 beta, including a redesigned interface to open files remotely (e.g. large connectivity files from ConnectomeDB), more complete scene file saving capabilities, improvements to map thresholding and border/foci drawing, and the addition of various Workbench command operations.

If you are not yet familiar with Workbench, here are a few basic questions and answers to get you up to speed:

Why use Connectome Workbench?

Workbench software is being specifically designed for interactive viewing of data associated with the HCP, especially multi-dimensional time series, scalar, and connectivity maps in the relatively new CIFTI format that incorporates surface vertices (both hemispheres) plus subcortical gray-matter voxels in a single file format. While you can view HCP files that are in standard NIFTI and GIFTI format using other brain-mapping software platforms, currently only Connectome Workbench is compatible with CIFTI formatted data.

If you give it a try, you will also see that we have put a considerable effort into making Workbench easy to use, even for beginners, while it still serves the purposes of more advanced users.

How do I learn to use Workbench?

Tutorials and associated datasets are available to help you quickly explore using Workbench, or take a deeper dive into its detailed functionality. The Q1 Workbench Tutorial is written for taking a short tour of the additionally processed group average data (myelin maps, task fMRI contrasts, and functional connectivity) for 20 Q1 participants. The Beta v0.7 Workbench Tutorial offers a more comprehensive guide, beginning with a chapter that shows you how to navigate through several types of brain mapping data, then providing more detail in subsequent chapters, including instructions on how to import your own data into Workbench.

Why the “beta”?

Although earlier versions of Workbench have been publicly available since last June, the software is still considered “beta” because a considerable amount of functionality for data being generated by HCP analysis pipelines (which are themselves under active development) has yet to be included in the software.

What can I look forward to in future versions of Workbench?

Some features on the horizon are: capabilities for interactive viewing of probabilistic tractography, viewing of parcellated functional connectivity, ability to create custom color palettes,  improved graphing of data series (eg. resting state timeseries or ICA components graphed by vertex), and more seamless interactivity with ConnectomeDB.

Related: Download Connectome Workbench.

Press Releases | March 5, 2013

Human Connectome Project releases major dataset on brain connectivity


A map of average “functional connectivity” in human cerebral cortex (including subcortical gray matter). Regions in yellow are functionally connected to a “seed” location in the parietal lobe of the right hemisphere, whereas regions in red and orange are weakly connected or not connected at all.

The Human Connectome Project, a five-year endeavor to link brain connectivity to human behavior, has released a set of high-quality imaging and behavioral data to the scientific community. The project has two major goals: to collect vast amounts of data using advanced brain imaging methods on a large population of healthy adults, and to make the data freely available so that scientists worldwide can make further discoveries about brain circuitry.

The initial data release includes brain imaging scans plus behavioral information — individual differences in personality, cognitive capabilities, emotional characteristics and perceptual function — obtained from 68 healthy adult volunteers. Over the next several years, the number of subjects studied will increase steadily to a final target of 1,200. The initial release is an important milestone because the new data have much higher resolution in space and time than data obtained by conventional brain scans.

The Human Connectome Project (HCP) consortium is led by David C. Van Essen, PhD, Alumni Endowed Professor at Washington University School of Medicine in St. Louis, and Kamil Ugurbil, PhD, Director of the Center for Magnetic Resonance Research and the McKnight Presidential Endowed Chair Professor at the University of Minnesota.

“By making this unique data set available now, and continuing with regular data releases every quarter, the Human Connectome Project is enabling the scientific community to immediately begin exploring relationships between brain circuits and individual behavior,”  says Van Essen. “The HCP will have a major impact on our understanding of the healthy adult human brain, and it will set the stage for future projects that examine changes in brain circuits underlying the wide variety of brain disorders afflicting humankind.”

The consortium includes more than 100 investigators and technical staff at 10 institutions in the United States and Europe ( It is funded by 16 components of the National Institutes of Health via the Blueprint for Neuroscience Research (

“The high quality of the data being made available in this release reflects an intensive, multiyear effort to improve the data acquisition and analysis methods by this dedicated international team of investigators,” says Ugurbil.

The data set includes information about brain connectivity in each individual, using two distinct magnetic resonance imaging (MRI) approaches. One, called resting-state functional connectivity, is based on spontaneous fluctuations in functional MRI signals that occur in a complex pattern in space and time throughout the gray matter of the brain. Another, called diffusion imaging, provides information about the long-distance “wiring” – the anatomical pathways traversing the brain’s white matter. Each method has its own limitations, and analyses of both functional connectivity and structural connectivity in each subject should allow deeper insight than by either method alone.

Each subject is also scanned while performing a variety of tasks within the scanner, thereby providing extensive information about “Task-fMRI” brain activation patterns. Behavioral data using a variety of tests performed outside the scanner are being released along with the scan data for each subject. The subjects are drawn from families that include siblings, some of whom are twins. This will enable studies of the heritability of brain circuits.

The imaging data set released by the HCP takes up about two terabytes (2 trillion bytes) of computer memory — the equivalent of more than 400 DVDs — and is stored in a customized database called “ConnectomeDB.”

“ConnectomeDB is the next-generation neuroinformatics software for data sharing and data mining. It’s a convenient and user-friendly way for scientists to explore the available HCP data and to download data of interest for their research,” says Daniel S. Marcus, PhD, assistant professor of radiology and director of the Neuroinformatics Research Group at Washington University School of Medicine. “The Human Connectome Project represents a major advance in sharing brain imaging data in ways that will accelerate the pace of discovery about the human brain in health and disease.”

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