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@coalsont coalsont released this Nov 5, 2019 · 9 commits to master since this release

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
Assets 2

@jese11 jese11 released this Nov 1, 2019 · 15 commits to master since this release

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
Assets 2

@coalsont coalsont released this Aug 28, 2018 · 448 commits to master since this release

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
Assets 2

@coalsont coalsont released this Jun 5, 2018

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
Assets 2

@coalsont coalsont released this May 9, 2018 · 583 commits to master since this release

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)
Assets 2
Dec 15, 2016
First version of charting implementation.

@coalsont coalsont released this Aug 26, 2016

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
Assets 2

@coalsont coalsont released this Jul 21, 2016

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
Assets 2
Pre-release

@coalsont coalsont released this Jul 21, 2016 · 1439 commits to master since this release

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

Please use the v1.2.2 release instead.

Assets 2

@coalsont coalsont released this May 20, 2016 · 1538 commits to master since this release

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
Assets 2
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