Announcing the release of version 1.5.0 of Connectome Workbench (WB) brain visualization and analysis software. This release fixes several bugs and adds significant features, notably palette previews, line charts, manual tile tabs layout, reopening closed tabs, annotation Z-ordering, and an improved volume resampling command that can combine multiple transforms (including a series of motion correction affines).
The Workbench distribution, available for 64-bit Mac OSX, Windows, and Linux, 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.
A new Workbench v1.5 Tutorial and dataset are available on BALSA. Access for downloading the data require a ConnectomeDB account (login with the same credentials at BALSA) and acceptance of the HCP Open Access Data Use Terms.
Download the WB v1.5.0 source code from GitHub: Under v1.5.0, click the “Source code (zip)” or “Source code (tar.gz)” button.
Discussion of Connectome Workbench usage, bugs, and features can be posted to the hcp-users discussion list at https://groups.google.com/a/humanconnectome.org/g/hcp-users.
Changes in Workbench v1.5.0
New Features in wb_view:
- New Display Type for Images: Like other data types, images are selected in the Overlay Toolbox using layers. Images are panned and zoomed using the same mouse actions as surface/volumes. Pre-existing functionality of image display using Features Toolbox remains but its use is not recommended and may be removed in a future release of Workbench.
- Manual Tile Tabs Layout System: Provides extensive flexibility of tile tabs layouts including ordering of overlapping tabs. A manual layout is edited using the annotation functionality.
- Charting Updates: New "Lines" chart type that displays the content from a file's data (e.g., timeseries data) as a line chart. Matrix charts support panning/zooming and have axes. Axes for all chart types have been improved including custom subdivisions. Line and matrix charts support axis yoking. Line charts support text display of a selected point with index/x/y and normalization of line chart data to match a given mean and/or standard deviation.
- Scale bar added: Allows display of a scale bar that is edited using the annotation functionality. Editable properties are line thickness/color/, font size/color; optional units; ticks/subdivisions.
- Foci symbols are sized in millimeters or percentage (percentage useful for cross-species analysis). Added option to show Foci at stereotaxic or projected coordinates.
- Splash screen replaced with a Recent Files dialog (also selectable from the file menu): This dialog lists recently opened Scene and Spec Files. Preferences allow for limiting number of recent items in dialog and supports exclusion of paths that may contain protected data.
- Reopen a closed tab added.
- Identification data formatting is improved with table format: Added filtering of types of data displayed and of individual files; option to show information in overlay toolbox or in separate window; option to show identification symbol in millimeters or percentage (percentage useful for cross-species analysis). Symbols may be unique sizes in each tab.
- Annotation Z Stacking: Overlapping annotations can be reordered front-to-back using options similar to those in PowerPoint.
- New Annotation Shape: Polylines are a series of connected line segments.
- Overlay and Map Settings Dialog: In palette selector, a color bar representing the palette's coloring is displayed next to the name of the palette.
- Reload all files option added to Spec File Management dialog.
- When identifying data in a CIFTI File, show "no data" Identification when there is no corresponding brainordinate in the CIFTI file.
- On MacOS, when starting wb_view by opening a file in Finder, allow user to open the file in a currently executing wb_view or to open the file in a new instance of wb_view.
- black-red, etc. palettes created for better single-color contrast
Bug Fixes in wb_view:
- Image Captures: Corrects saving to some image formats (png, bmp) when transparency is used.
- Fixed crash when loading a scene but volume files are missing.
- Long scene descriptions no longer cut off in scene dialog.
- Fixed rotation of flat surfaces.
- Fixed moving color bar between tab and window.
- Improved performance of voxels drawn as cubes.
- Fixed creation of foci to use the primary anatomical surface (has correct stereotaxic coordinates) instead of viewed surface.
- Updates have been made to Help documentation.
- Fixed identification for surfaces with flipped normals.
Changes to existing behavior in wb_command:
- Label key conflicts cause errors or warnings by default.
- -create-signed-distance-volume output changed to have fewer gaps, less likely for approximate distances to be wrong.
New Features in wb_command:
- Interpolated ribbon mapping, weighted roi ribbon mapping
- New -volume-resample command for chaining transforms and motion-correction affines
- Options for smoothing to be specified in fwhm
- wb_command global -cifti-read-memory option (to avoid ulimit issues)
- wb_command global option to control data type and scaling for both volume and cifti outputs
- -from-data-file option for -set-map-names
Bug fixes in wb_command:
- -scene-file-merge crash on older scene files fixed.
- Fixed some excessive seek/flush calls.
- Fixed column option handling in label-to-border commands.
- Fixed compression buffer sizing for small gifti files.
- Fixed math for edge values of spline-resampled volumes.
- Fixed writing of ants-format warpfields.
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.