Connectome Worbench v2.1.0 Released

Version 2.1.0 of Connectome Workbench (WB) brain visualization and analysis software has been released. This version adds new features, including hippocampus visualization (montage, flat, and volume surface outline), CIFTI structure support for hippocampus and dentate surfaces, addition of Edit Sample mode to support dissection planning for transcriptomic analyses, and hierarchy support in CIFTI label files, GIFTI label files, and volume files.  Full list of changes below.  

The Workbench distribution, available for 64-bit Linux, Mac OSX, and Windows 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.  Please note that wb_command must be run from a terminal window (not double-clicked on Mac or Windows).

The Workbench v1.5 Tutorial and the Workbench Guide to Annotations are compatible with v2.1.0 and available at https://www.humanconnectome.org/software/get-connectome-workbench. The WB v1.5 tutorial data and the HCP 1200 Group Average Atlas data are available to download on the BALSA database. Access to both datasets requires a BALSA login and acceptance of the HCP Open Access Data Use Terms.  

Download the WB v2.1.0 source code from GitHub. Under v2.1.0, click the “Source code (zip)” or “Source code (tar.gz)” button.

Discussion of Connectome Workbench usage, bugs, and features can be posted to the https://groups.google.com/u/0/a/humanconnectome.org/g/hcp-users. 

Changes in Workbench v2.1.0

wb_view New Features

* In Focus mode, added a "Move" mode that allows dragging a focus to a new location

* For chart axes, add a mode that allows displaying map names instead of numeric subdivisions along an axis

* Added support for a label hierarchy in CIFTI label files, GIFTI label files, and volume files

* Added hippocampus and dentate surface montage and flat surface visualization

* Added volume surface outlines for hippocampus and dentate surfaces

* In Features Toolbox, added Find and Find Next controls for Annotations, Borders, Foci, Labels, and Samples

* Added ability to edit content of Annotation, Border, Foci, and Sample files including copying and moving items to another file

* Added “Flip” option to Histology Display

* Added ability to insert Unicode characters in text annotations (use Libertine font)

* Added Edit Samples mode

wb_view Improvements

* When creating foci by clicking on a surface, focus is no longer moved to the closest surface vertex but instead is placed at the location in the triangle where the mouse-click occurred

* Improved communication (reaffirm login status) when uploading files to BALSA database to prevent timeout (needed for very large uploads)

* Improved performance of label coloring

* Do not load dynamic connectivity data if the file is not enabled as a layer

* Added Open File Quickly (enter path to file for loading)

* Added axis orientation labels to Histology Slices

* Added new CIFTI Fiber Trajectory Map File.  Display fiber trajectories in Surface Display

wb_view Bug Fixes

* Corrections in volume surface outline drawing for open type surfaces such as a hippocampus and dentate

* Fixed blue background representing thresholded regions in the Histogram plot

* Fixed performance issues on Overlay and Map Settings dialog with finding files that were compatible for Thresholding

* Fixed cursor flashing bugs in Annotation editing mode

* Fixed saving and restoring of scenes where there are files with the same filename but in different paths for border, foci, and volume files

wb_view Changes to Existing Behavior

*  -cifti-create-dense-* copies palette settings from an input file

*  -volume-reorient and -volume-set-space now obey datatype global options

*  -cifti-math uses scalar output mapping in place of label input mappings, to better match other math commands, and to reduce display confusion

*  added warning for substantial voxel size mismatch between sform and qform

wb_command New Features

*  -background option in -volume-resample, to avoid adding zeros to images

*   hierarchy support in label-type files

*   -dilate-missing option in volume to surface ribbon mapping

*   -match-surface-area option in -surface-distortion

*    support for arbitrary surface structures in some cifti commands, add not-yet-standard hippocampus dentate structure support to cifti

*   -spec-file-modify for removing (and/or adding) multiple data files, deprecates -add-to-spec-file

*  added support for hippocampus and dentate surfaces in CIFTI structures

wb_command Bug Fixes

 *   -metadata-string-replace on dscalar, dlabel, surface

 *  -file-information -only-* options were reading unneccesary data

 *   -cifti-convert -from-text no longer warns when there are exact zeros

Notes on launching Workbench: (1) wb_command must be run from a terminal window (not double-clicked on Mac or Windows); (2) wb_view may crash if used with a remote desktop due to problems with Xcb and OpenGL in the remote desktops.  VirtualGL works for some users.  Even if wb_view runs in a remote desktop, performance may be poor as they often use software implementations of OpenGL.