Version 2.2.1 of Connectome Workbench (WB) brain visualization and analysis software has been released. This version adds new features and commands, including adding Setup Volume Montage, support for Dark / Light mode, and a scene file restructure operation to aid in flattening directory structure for sharing datasets on BALSA. Plus improvements, including to thresholding and histogram display, identification, and border editing. Notably, this version includes a notarized MacOS distribution which will resolve security issues that affected some users. 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 v2.2.1 and available here. The WB v1.5 tutorial data and the HCP 1200 Group Average Atlas data are available to download in the BALSA repository. Access to both datasets requires BALSA login and acceptance of the HCP Open Access Data Use Terms.
Download the WB v2.2.1 source code from GitHub. Under v2.2.1, click the “Source code (zip)” or “Source code (tar.gz)” button.
Discussion of Connectome Workbench usage, bugs, and features can be posted to the hcp-users discussion list.
* MacOS version now notarized eliminating security problems preventing use for some users
* Compact layout for hippocampus surface montage
* Light / Dark mode support on macOS and Linux
* Added hierarchical directory search option on Recent Files Dialog
* Volume Menu -> Setup Volume Montage dialog assists with setting volume montage within a range of slices/coordinates
* New annotation types: Arrow and Marker
* Import "Graphics" from a CZI file as annotations
* Add scene file restructure operation that copies scene and data files into a flat hierarchy
* Add "Open File Quickly"-- Enter path to open the file
* Thresholding min/max initialized to data min/max
* In histogram dialog: Large, red "X" indicates data not displayed due to thresholding
* Added label outlines to Volume MPR Viewing
* Volume slice plane selection: now any combination of the Axial, Coronal, or Parasagittal slices are selectable for viewing
* Improved quality of volume data drawn over histology slices
* When viewing a volume montage in MPR mode, the step between slices may be a non-integer value
* Identification now includes distance (linear and geodesic) between two most recently identified items
* Border Editing now supports moving of a border point
* Volume montage step size can now be non-integer in MPR mode. The unit step is still equal to the smallest dimension of the voxel size.
* Allow color bar display without numerical text above it
* MPR Intensity view allows display of more than one volume
* Eliminate blending (opacity) artifacts in Histology and MPR Volume Viewing with opacity
* Bug fixes for some layouts in Features ToolBox
* Fixed order of identified items restored from a scene (now most-recent first)
* -probtrackx-dot-convert and -convert-matrix4-to-matrix2 have an added mandatory parameter to choose between generic wbsparse (new) or cifti output format
* change -volume-erode "all face neighbors" logic to match -volume-dilate (volumes with non-isotropic voxels had been able to bypass this behavior)
* label-type files now default the unlabeled color to "fully-transparent black" instead of "fully-transparent white", which may improve aesthetics in scene captures of histology view for some OSMesa versions
* -convert-fiber-orientations now replaces nan/inf values with 0
* metric interpolate gaps command
* volume label resample command
* volume transform sequence support in -cifti-resample, "LABEL" volume resampling method
* geodesic distance to roi command
* match maps option for bad vertex roi in -metric-dilate
* cifti seeds option in -convert-matrix4-to-workbench-sparse
* fix writing of closed borders to legacy border file format