v1.2.2

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

v1.2.1

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

Please use the v1.2.2 release instead.

v1.2.0

Major wb_view changes:

• Annotations are a powerful new feature for placing text and symbols within wb_view tabs and windows. They enable generation of publication-ready figures without the need for further annotation in a separate application (e.g., Photoshop). * Annotation features are extensively documented in “Guide to WB Annotations”.
• New options for locking the aspect ratio for tabs and windows when converting between Tile Tabs and single tile views and when adjusting the wb_view viewport (aka viewing area).
• Improved control over gaps and margins between tabs.
• More flexible control over color bars and associated labels.
• Refinements to scene files, including the option to override the user’s default background/foreground color settings.
• Separate panning and zooming enabled between left and right hemisphere flatmaps.

Other changes:

• changes to existing behavior:
  • JET256 colors changed very slightly
  • fsl_* palettes corrected
  • -volume-dilate on label volumes with weighted method uses popularity logic, no longer gives warning
  • -cifti-create-dense-timeseries and -scalar warn about empty volume structure definitions instead of erroring
  • -cifti-create-dense-scalar now preferentially takes map names from input metric files
  • surface-type resampling commands now use the structure of the input file as the output file's structure, rather than a sphere's structure
  • cubic volume resampling no longer has ringing effects when the edge of the volume is nonzero (includes oblique volume display)
  • -cifti-resample now uses weighted dilation by default
  • -cifti-dilate now uses weighted popularity dilation on volume label data
• new notable features:
  • -surface-average now takes per-surface weights, uses much less memory
  • -(spec|scene)-file-relocate, for changing the location of spec/scene files relative to their data files
  • new -label-to-volume-mapping command, with ribbon mapping method
  • add ribbon mapping to -volume-label-to-surface-mapping
  • -cifti-resample has more dilate options
  • -volume-dilate uses popularity logic for label data
  • -cifti-parcellate weighting and reduction type options
  • -cifti-create-parcellated-from-template
  • -cifti-merge-parcels
  • -surface-curvature
  • -border-length
  • -*-erode commands
• bugfixes:
  • -cifti-create-dense-from-template -volume option fixed
  • -*-reduce commands with INDEXMAX/INDEXMIN and -exclude-outliers now behave as expected
  • -add-to-spec-file now works as expected for spec files outside current directory, and symlinks no longer get changed
  • -border-merge now copies colors into merged file
  • -volume-label-to-surface-mapping handling of differing label tables with 3 or more maps
  • pconn (and possibly other cifti files) now save palettes from GUI
  • cifti volume labels no longer add "Invalid Label Index" text to label name in identify operations

Prerelease: v1.2.0-pre1

NOTE: This is a prerelease. It has features in progress that may not fully work, and may not be compatible with the eventual release that contains them. You are advised not to use this version other than for testing.

The main purpose of this prerelease is to track a version of wb_command that was used to overcome a memory use problem when averaging surfaces of large numbers of subjects.

v1.1.1

Bugfixes:

• Saving a map from ConnectomeDB cifti files was giving an error related to filename generation.
• Scenes now identify files including path name so that files that are named the same, but have a different paths, can be correctly restored in layers.

Other changes:

• Addition of the -metric-to-volume-mapping command to map a metric file to volume space.
• For border files in which names have been modified or created after a scene was made using the file, only border names with a status set to On are displayed when the scene is loaded.
• Averaging connectivity across voxels in a Volume label/ROI now works properly.

v1.1

New Features:

• Improved Help Searching
• Layer Yoking now includes a layer’s display status
• Border Mode Improvements:
• Continuous border drawing and voxel editing added
• Border optimize added that provides semi-automatic optimization of parcel borders based on single or multi-modal gradients
• Volume ROI drawing/editing added using “Volume” mode functions
• All data in a parcel file is now used to set the coloring of parcel files on a surface or in a matrix chart
• Label file properties settings added in Overlay Toolbox>Layers>Settings
• Loading and viewing of image files enabled (displayed as underlay in selected Viewing Tab)
• Improvements to parcellated file behavior and display (more infor in Info Box)
• Palette Settings Improvements:
• High/low threshold value linking function added
• Threshold setting via right click on histogram added
• Thresholding and Palette ranges and step sizes respect range of data
• Normalize palette function added
• Absolute Percentile Palette range added
• Full File names/paths in Layers can be display via tooltips
• Copy path/filename and map name functions added to Layer construction menu
• Charting Improvements:
• Series chart History display options added
• Toggle display of selection of rows in matrix chart added
• More Information saved when Scenes are created/modified
• Identify Brainordinate function (head Icon in Toolbar) added for selecting or highlighting a brainordinate, parcel, or CIFTI row
• Volume ID symbol can be displayed upon clicking voxels (option in Preferences)
• ID Symbol default size reduced

Changes to existing command behavior:

• -cifti-extrema now writes dscalar
• more error checking in -probtrackx-dot-convert
• -cifti-replace-structure on label files doesn't drop unused keys unless asked
• -metric-fill-holes, -metric-remove-islands use surface area
• -set-map-names will error if no options to change map names are present

New commands and features:

• -cifti-create-dense-from-template for easier creation of cifti files with matching brainordinates
• command help format shortened by moving parameters with descriptions to the top, replacing the bare list of parameters
• --stats and --weighted-stats
• equality/boolean operators added in -*-math
• -cifti-separate can now output label volume for subcortical structures
• -cifti-convert -*-text for transferring data to/from other tools
• -cifti-copy-mapping
• better formatting of command help, logging info, wb_command errors
• deprecated commands (those that have been replaced with other commands) are available with via: -list-deprecated-commands

Notable bugfixes:

• -map wasn't working in -gifti-label-to-roi or -cifti-label-to-roi
• -cifti-extrema -sum-maps didn't work
• symlinking to bin scripts didn't work
• reading compressed nifti from URL didn't work

v1.0

First non-beta release!

Changes to existing behavior to take note of:

• the "workbench" executable is now "wb_view"
• "-nifti-convert" and "-cifti-convert -version-convert" have been moved to "-file-convert", nifti convert arguments changed
• new format for border files, one structure per file (left cortex, right cortex), contains the surface number of vertices
  • old-format single-structure files can be converted by loading them in the gui with a surface and saving them
  • multi-structure files must be split before editing or saving, using option in Data menu
  • the "-file-convert -border-version-convert" command can also convert them (either case)
• "-*-resample" commands now require area options when using ADAP_BARY_AREA method, rather than reusing the spheres
• "-border-to-rois" now fills the parts of a multipart border in a single map

Other behavior changes:

• parcellated CIFTI files are now colored according to the file's full range of data, not just the map range
• "-metric-gradient" and related commands now take vertex area into account, and unroll neighbors rather than unfolding (minor changes to output)
• volume files are now written using "MNI152" as the sform/qform codes

Also, many new features, but we don't have a full list of them. Here are a few:

• integrated help dialog in wb_view
• outline visualization setting for surface label data
• montage for volume oblique view mode

Beta 0.85

This release adds CIFTI-2 support, and switches to writing CIFTI files as CIFTI-2.

If needed, any CIFTI file can be rewritten with a specific version using:

wb_command -cifti-convert -version-convert <current file> <desired version> <output file>