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).

wb_view

New Features

• New Display Type for Images
• Manual Tile Tabs Layout System
• Charting Updates: New "Lines" chart type for timeseries, etc. 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.
• Scale bar
• 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). Preferences allow for limiting number of recent items in dialog and excluding paths (for instance, sensitive info in filename/path, or a slow sshfs mount).
• Reopen a closed tab
• Identification data formatting is improved with table format
• 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-ordering
• New Polylines annotation type
• Palette selection now contains preview of color bar
• 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

• Image Captures: Corrects saving to some image formats (png, bmp) when opacity 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
• Fixed identification for surfaces with flipped normals

wb_command

Changes to existing behavior

• 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

• 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

• -scene-file-merge crash on older scene files fixed
• Avoid some excessive seek/flush calls
• Fix column option handling in label-to-border commands
• Fix compression buffer sizing for small gifti files
• Fixed math for edge values of spline-resampled volumes
• Fix writing of ants-format warpfields

This is a bugfix release, most notably, to correct a crash that occurs when a parcel file is loaded and an identification (click or annotation on grayordinate) in the GUI is made.

wb_view:

Bug Fixes

• Fixed crash occurring upon identification/applying annotations when parcel files are loaded

wb_command:

Changes to existing behavior

• -metric-dilate roi behavior changed to match that of -volume-dilate

Bug Fixes

• improved speed of volume resampling
• improved speed of volume and surface dilation

This is a bugfix release mainly to correct the documentation of two commands.

• fixed order of fields in -foci-create command documentation
• removed confusing text from -annotation-resample
• fixed some errors on stricter compilers

This release fixes several bugs and adds significant features, most notably, a new implementation of animations/movies, the addition of a tangential surface annotation option, and the ability to import foci from a text file.

wb_view:

Changes to existing behavior

• Made scroll wheel direction consistent (now "natural scrolling" setting controls zoom direction on all platforms)
• Image capture defaults to 300 DPI
• Tab yoking does not apply to Volume slice planes (displayed planes may be different in the yoked tabs)
• Gap added to crosshairs to avoid obscuring data under the crosshairs
• Default palette mode is now Absolute Percentile
• Allow for Border point sphere size setting prior to drawing any borders
• Upon Right click over a brainordinate, selections for connectivity files, but only those that contain the brainordinate, are displayed
• Improved window tab dragging performance (for changing a tab’s position in tile tabs)
• Default description for a new scene streamlined
• Percentile coloring of single-value ROIs uses max palette color rather than min

New Features

• New implementation of animation and movie recording
• "Tangential" surface annotation option (annotation rotates with and appears to be "painted" onto the surface)
• Orthogonal Volume Slice Scrolling by dragging the mouse in view window
• Data ToolTips (information displayed about brainordinate in top-most selected layer under mouse hover)
• Dynamic connectivity added for GIFTI and NIFTI volume files containing time-series data
• Preference for ALL slice layout; can now be single column, row, or grid
• Preference for window background color (for region not covered by a tab's content)
• Spacer rows/columns added to grid tile tabs layout for adding titles (via annotations)
• Display of files with the same file name, but different directory paths is supported and a partial path is displayed in the GUI for distinguishing files with the same file name

Bug Fixes

• Identification on asymmetric parcel connectivity files fixed
• Removed absolute paths in Scene file that were causing errors (now using relative paths)
• Selection of thin Annotation lines fixed
• Various BALSA interface bugs and error messages; including bug with special characters causing JSON error
• palette "apply to all" was unnecessarily slow

wb_command:

Changes to existing behavior

• dilation default exponent and cutoff calculation changed to reduce edges, volume dilate speed improved
• -cifti-parcellate now uses -include-empty behavior by default, old method is available via -legacy-mode
• remove files before opening for writing, so that overwriting a symlink doesn't try to modify the existing file

New Features

• -cifti-correlation-gradient has new -double-correlation option to avoid needing to write a dconn to disk
• -foci-import (import foci from a text file)
• -annotation-resample (move annotations to new mesh)
• log2 option for new distortion measures and math commands
• L2norm reduction method
• -cifti-merge uses considerably less memory
• option in -zip-scene-file and -zip-spec-file to continue despite missing files

Bug Fixes

• cifti separate ROW with longer rows than columns was crashing

This release fixes a few bugs and adds some features, most notably Annotation substitutions, which allows one to efficiently make a series of annotations (text labels) with content loaded from a CSV file (*.wb_annsub.csv).

wb_view:

New Features

• Yoked annotation substitutions (and updates in Workbench Help and Guide to Annotations)
• Updates to BALSA Upload dialog including notification of updated extraction directory prefix
• Tab number always included in the name of the tab since some GUI controls (volume surface outline) use the tab number Bug Fixes
• Fixes for sizing of color bars

wb_command:

New Features

• new -surface-geodesic-all-to-all command
• fwhm estimation now has "whole file" and "demean" options

This is a bugfix release, mainly to correct a crash when attempting to view label volumes.

wb_view:

New Features

• Scene numbers using a file added next to files in scene "list files" window
• Scenes "replace all" no longer shows tab highlight outline in captured previews
• Builds with older QT5 no longer have very large overlay toolbox by default

Bug Fixes

• fixed wb_view crash when loading label volumes
• Settings synchronized across overlay settings windows that refer to the same file

wb_command:

New Features

• -*-roi-from-extrema commands give warnings when output has no maps
• -volume-set-space now has a -file option to take space information from another volume
• -volume-math copies timestep from input files

Bug Fixes

• bash completion for wb_shortcuts should now work reliably
• wb_shortcuts -cifti-demean should not give warnings about extensions for temporary files

wb_view:

The major changes since the previous release include a full revision of charting, substantial changes to annotations, and an improved process for uploading files to BALSA. Otherwise, there are many minor updates and bug fixes.

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

BALSA compatibility (BALSA = Brain Analysis Library of Spatial Maps and Atlases 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

• Window->Identify... cifti index now uses 1-based indexing
• 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 (workbench prefers sform, and pipelines use standard orientations, so this rarely affects users)
• 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)
• 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)

Major new features:

• zip scene file from within wb_view
• wb_shortcuts script to more easily do common tasks for interactive shells
• new preference for hiding dynconn layers by default

Other changes:

• changes to existing behavior:
  • produces warnings when creating files with an extension not matching what wb_view expects
  • interpolation of volume with a length=1 spatial dimension always uses enclosing voxel
  • wb_command accepts (but warns about) non-ascii unicode dashes, but also replaces them in filenames
  • nifti headers default pixdim[] to all 1s even when unused (cifti)
• bugfixes:
  • -cifti-label-import -drop-unused-labels option fixed
  • files loaded by scene properly restore the "in spec" status
  • chart timecourse status properly restored from scenes

Known bug: -cifti-erode, -metric-erode, and -label-erode crash on multi-column file input

Please use the v1.2.2 release instead.

Major wb_view changes:

• "dynconn" computation of correlation from dtseries files on the fly
• initial integration with BALSA website (balsa.wustl.edu)

Other changes:

• changes to existing behavior:
  • loading a timeseries now computes correlation on any identification, use "connectivity" tab in overlay toolbox to turn off
  • -file-information lists data files in each scene unless -no-map-info is specified
• new notable features:
  • -cifti-help and -gifti-help commands to explain file formats
  • -cifti-change-mapping command deprecates -cifti-copy-mapping, -cifti-change-timestep, and -cifti-convert-to-scalar
  • -file-information has an added -only-metadata option
  • -scene-file-merge
• bugfixes:
  • fixed gifti external binary reading on windows
  • non-XYZ-oriented volumes now display properly in Volume view mode
  • fix reading of uncompressed volume files with frames larger than 2GiB
  • some crashes when interacting with layers after opening wb_view without data files
  • -spec- and -scene-file-relocate were putting absolute paths in output files
  • -*-erode commands no longer crash on multi-column files