NIH Blueprint: The Human Connectome Project

Using Connectome Workbench

Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualiation platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data. wb_command is necessary for running HCP data processing pipelines.

Workbench version 1.1.1 is available for download for 64-bit Mac OSX, Windows, and Linux: Get Connectome Workbench now.

New features of Workbench v1.1.1

  • Improved Help Searching
  • Border mode improvements including Border optimize to provide semi-automatic optimization of parcel borders based on single or multi-modal gradients
  • Volume ROI drawing/editing added using “Volume” mode functions
  • Loading and viewing of image files enabled (displayed as underlay in selected Viewing Tab)
  • Improvements to parcellated file behavior and display
  • Palette Settings Improvements:
    • High/low threshold value linking and threshold setting via right click on histogram functions added
    • Thresholding and Palette ranges and step sizes respect range of data
    • Absolute Percentile Palette range and Normalize palette function added
  • Full File names/paths in Layers are displayed via tooltips and copy functions added to Layer construction menu
  • Charting Improvements:
    • Series chart History display options added
    • Toggle display of selection of rows in matrix chart added
  • Identify Brainordinate function (head Icon in Toolbar) added for selecting or highlighting a brainordinate, parcel, or CIFTI row
  • Volume ID symbol may be displayed upon clicking voxels (option in Preferences)
  • Changes to existing command behavior:
    • -cifti-extrema now writes dscalar
    • more error checking in -probtrackx-dot-convert
    • -cifti-replace-structure on label files doesn't drop unused keys unless asked
    • -metric-fill-holes, -metric-remove-islands use surface area
    • -set-map-names will error if no options to change map names are present
  • New commands and features:
    • -cifti-create-dense-from-template for easier creation of cifti files with matching brainordinates
    • command help format shortened by moving parameters with descriptions to the top, replacing the bare list of parameters
    • -*-stats and -*-weighted-stats
    • equality/boolean operators added in -*-math
    • -cifti-separate can now output label volume for subcortical structures
    • -cifti-convert -*-text for transferring data to/from other tools
    • -cifti-copy-mapping
    • better formatting of command help, logging info, wb_command errors
    • deprecated commands (those that have been replaced with other commands) are available with via: -list-deprecated-commands

Workbench allows you to explore data and activity on the surface, as well as in the volume of the brain. Connectome Workbench works seamlessly with ConnectomeDB to import averaged data from a group of subjects and view that data on a group averaged brain atlas in Workbench. In future versions of the software, users will be able to use Workbench to display and analyze functional task and connectivity, diffusion, and behavioral data from single subjects or groups of subjects defined by a user-initiated search of ConnectomeDB.

Screenshots (click to expand)

Software Plaftorm

The Workbench visualization platform and wb_command utilities are open-source and written in C++ by software developers in the Van Essen Laboratory at Washington University. (License)

Release Dates

Connectome Workbench v1.1.1 update has been released as of July 22, 2015 and is available for MacOSX, Linux, Windows platforms. Also available to use with Workbench are:

  • WB tutorial & user guide and HCP sample data available from ConnectomeDB
  • WB-compatible Group average functional connectivity dataset and dense connectome files available from ConnectomeDB

Source Code

Download the source code for Connectome Workbench from our GitHub repository: