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

Changes in Workbench v1.3.0

wb_view:

Charting

  • Chart View fully revised to include a layer-like system and support for histograms and for charts from many more file types
  • Improved and expanded options for control of axes
  • Old version of charting remains for compatibility with older scenes

Annotations

  • Improved aspect locking with notifications
  • Warn if annotation text is too small
  • Added new coordinate space for adding annotations in the new version of charting
  • Line thickness maximum removed and line thickness scales with tab height

Compatibility with the Brain Atlas Library of Spatial Maps and Atlases (BALSA) database for sharing analyzed data as WB scenes

  • Improved dialog for uploading scene file to BALSA with ability to create and edit BALSA study names
  • Scene Identifiers are requested from BALSA and added to the scene file after successful upload of a scene file to BALSA
  • Added automatic detection of the base path (for recreating directory structure of shared datasets)

Scenes

  • Scenes window revised, including ability to save scene files directly without using Save/Manage Files
  • Added List Files... button to show all data files referenced by a scene file
  • Scenes reload a file if the version on disk has been modified since loaded into memory
  • Warn if there are modified files prior to loading a scene
  • Volume attributes (crosshairs, labels, etc.) are saved to scenes

Volumes

  • Volume surface outline scales with tab height
  • Improved sform support of non LPI oriented files
  • Warn if a NIFTI volume file contains invalid qform and sform
  • Added masking option for oblique slice drawing so that edge effects from cubic interpolation can be hidden

Miscellaneous

  • Reading of GIFTI RGBA files is now supported
  • Upgraded to Qt 5.7 and compilers that support C++11; using Qt 5.7 may help with some "XCB errors" encountered on Linux

Overlay Settings

  • Added thresholding of Overlay Layers using data from another data file and map
  • Added inversion of Palettes for brainordinate coloring

wb_command:

Changes to Existing Behavior

  • corrected qform calculation in oblique or unusual orientation volume files
  • built against QT5, on newer OSes for mac and linux
  • surface to volume mapping defaults have changed for less overshoot and sharper results (volume to surface defaults are unchanged, but has option available for sharper results)
  • Window->Identify... cifti index now uses 1-based indexing
  • volume to surface myelin mapping method has been fixed to use the cylindrical cutoff described in the paper, with a new option to restore the old unintended behavior
  • -*-stats commands now use multi-map roi files to output multiple columns of stats

New Notable Features

  • override map index for yoking group in -show-scene, give error message on command failure
  • tab completion for wb_command (extensive) and wb_shortcuts (basic) in bash
  • acceleration of correlation by use of SIMD instructions - thanks to Kristian Loewe
  • ability to write smaller low-precision cifti using integer datatypes and scaling
  • new -*-label-probability commands
  • new strain-based surface and volume distortion measures
  • generates warnings when writing files with incorrect extensions

Bugfixes

  • wb_shortcuts concatenate functions don't fail with "unbound variable"
  • -cifti-merge-dense fixed for volume label data
  • -cifti-parcel-mapping-to-label help corrected
  • -cifti-create-dense-from-template handling of -cifti with voxel data
  • GEO_GAUSS and GEO_GAUSS_EQUAL smoothing methods now use the corrected vertex areas in their distance computation (GEO_GAUSS_AREA, the default, recommended method, already used them)

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 v1.3.0 update has been released as of May 8, 2018 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: https://github.com/Washington-University/workbench.