NEWS.md

In threeBrain: 3D Brain Visualization

threeBrain 1.0.1

• Updated controller library to have reasonable input focus
• Allow MRI slices to be NIfTI format
• Set slices to be visible by default when the surface is not available
• Fixed transform for datacube2
• Fixed qform when reading NIfTI files
• Fixed auto-refine functions in electrode localization
• Removed clipboard auto-copy and auto-paste functions since they conflict with other viewers; instead users can use controllers to copy and paste state

threeBrain 1.0.0 - Egypt

This version is a major update.

• Created threeBrain::threeBrain as the formal way to create brain objects
• Updated JavaScript engine to v150
• Allow getting HTML tags from saved widget so the widget can be used from Jupyter notebook
• Added $render method to remember viewer states
• Allowing set title via proxy driver
• Added citation information
• Fixed hemisphere issue in localization when electrodes are closer to opposite hemispheres
• Added electrode registration from anatomical slice cross-hair

threeBrain 0.2.9

This version plans for a major update. Here are some highlights:

• Electrode localization can be done from original CT instead of re-sampled ones
• Completely isolate JavaScript engine from R code. The JavaScript code is available as npm package and is used via sub-module
• Implemented file readers directly from JavaScript, this allows reading files directly in viewer, and no cache is needed
• No home-brew version of threejs is required: standard npm distribution is used
• New controller GUI is implemented
• The viewer can be driven via JavaScript directly via event dispatchers
• Anatomical segmentation map is visible from the side panels; the voxel values are displayed when setting crosshair

Detailed Changes

• Added step size in datacube2 material uniforms
• Upgraded threejs to r148, and use npm distribution "three"
• Massive code re-factory (variable names, trackball controls, legacy classes...)
• Removed data-GUI and use lil-GUI
• Fixed compass (finally...)
• Added title to the viewer
• Reworked the whole message signal system, added ThrottledEventDispatcher.js
• Added MouseKeyboard class to track mouse and keyboard events, greatly reduced canvas burden
• Added animParameter object to canvas to keep track of the animation parameters
• reworked shiny drivers
• fixed one-voxel shift issues
• Added format support for nii, mgh/mgz, FreeSurfer surface, FreeSurfer node value binary formats
• Added function threeBrain to allow 3D viewer to run without cache (with fs only)
• Fixed memory leak issues in JavaScript code
• Geometry groups can now change its storage path
• JS is completely independent now (available on npm now)
• Peel event dispatcher from the canvas class so the events can be managed separately
• Hide time-stamps when there is no data/animation available
• Added experimental support to show labels on regular electrodes; currently no depth-test is turned on
• Added GUI support to change electrode label visibility and size
• Electrode label size adjusts along with electrode radius
• handle_resize now put off resizing function when detecting widget size is too small

Bug fixes

• Fixing xfm not parsed correctly when the line starts with blank spaces
• Stopped rendering canvas when canvas is too small (less than 10 pixels)

threeBrain 0.2.7

Changes

• Rewired events, allowing to drive the viewer via JavaScript events
• Allowed to set animation playback status
• Remove modal by default if raveio or ravedash is loaded
• Edited launch script to always use Python3

Bug fixes

• Fixed installation issues (template brain) on Windows, avoid backslashes

threeBrain 0.2.6

Changes

• Allowed users to pan the camera when localizing electrodes
• Added line segment geometry type that can either display static line segments (such as DTI), or connect two electrodes dynamically
• Printing brain now uses more accurate terms
• Allowed CT to be either path or the actual data when calling localizing function

Bug fixes

• Fixed NifTi orientation issues and use sform
• Fixed localization issue when NifTi transform matrix has determinant not equally to 1
• Fixed volume shader, resolved shift issues when panning the camera

threeBrain 0.2.5

Changes

• Surface sync from voxels now clamp the surface nodes
• Added Voxel Display controller to toggle volume display modes
• Changed shortcut l from Voxel Type to Voxel Display
• Volume fragmentShader uses non-linear function to calculate fragment colors combined with face normal; this will create smoother results
• DataCube2 geometry uses ConvexHull instead of box/sphere to improve the performance
• DataCube2 are no longer hidden when sync from voxels is on: users can use shortcuts l and k to easily control the visibility.
• download_template_subject can download other templates such as fsaverage, cvs_avg35, bert.

Bug fixes

• Fixed a volume rendering issue where ray-marching directions are not calculated correctly
• Fixed color not set correctly when changing Voxel Labels while surface colors are sync from voxels

threeBrain 0.2.4

This version mainly works on the electrode localization. Most changes occur in the JavaScript engine.

Changes

• Allows electrodes to be reset
• Displays electrode labels along with the electrodes
• Allows resizing electrode size on the fly
• Allows resizing the electrode labels
• Localization module has been integrated into RAVE
• Added line mesh to mark the distance of the electrode deviating from its original position. The line color changes with the distance value.

Improvements

• Improved localization precision
• Auto-adjusting electrodes now respects the topology
• Electrodes in the localization mode now have LocElectrode class
• Volume rendering and ray-casters now respects the transform matrices

threeBrain 0.2.3

Changes

• Electrode localization now has a shiny application

Improvements

• Added 3 vignettes

threeBrain 0.2.2

Changes

• Supported video content to display auditory visual stimuli along the response
• Default to closing the default and volume side folders

Improvements

• Fixed electrode localization interpolation issue
• Proper dispose the localized electrodes
• Fixed screenshot and video recording functions
• Renamed recording button to Chrome-specific

threeBrain 0.2.1

Changes

• Finally, electrode localization is added!
• Added TextTexture in the internal code to display text Sprite easily
• Can download electrodes as csv

threeBrain 0.2.0

Changes

• More efficient volume rendering with transparency
• Added shader functions to surface instances, allowing color rendering from volume, electrodes, or vertices (major change)
• Added color-map generator for surface and volume data
• Added method to generate data cube (volume) from MNI305 coordinates
• Optimized loading procedure
• Removed crayon, base64enc, htmltools, pryr from dependence

Improvements

• Bumped threejs version to v131dev
• Fixed surface transparency losing fragments issue
• Added loaders to shiny applications to avoid performance issues on old computers
• Fixed electrodes not selected on mouse click-down (on Firefox)

threeBrain 0.1.9

Changes

• Added backend engine for volume rendering to show atlas files
• Standalone viewers now use native system tools for Mac and Linux (On Windows, it still needs R to be installed)

Improvements

• Allows super slow play speed to show animations in millisecond level
• Bumped threejs to a newer version and fixed compatibility issues
• Animation time range is more reasonable

threeBrain 0.1.8

Changes

• Screenshot now downloads pdf format

Improvements

• Fixed freesurferformats face index starting from 1 instead of 0

threeBrain 0.1.7

Changes

• Now displays MNI305 coordinates instead of tkRAS coordinates
• Removed reticulate and related functions to support native R functions

Improvements

• Fixed MNI305 calculation issues
• Internally calculates anterior commissure

threeBrain 0.1.6

Changes

• Implemented view_ct_t1 to view CT aligned to T1 images
• Updated document on how to generate FreeSurfer brain
• Removed dependency to nibabel and use native R packages
• Re-designed legends, added options to show, hide display information
• Added screenshot to download as image

Improvements

• Added hints for keyboard shortcuts

threeBrain 0.1.5

Changes

• Import FreeSurfer and SUMA files sulc
• Control element update
• Added brain_proxy to control in shiny element
• Separated display and threshold data
• FreeMesh material can be switched between MeshPhongMaterial and MeshLambertMaterial

Improvements

• UI will blur focus when clicking on canvas
• Allow customizing widgets background, cex (font magnification), timestamp (display time)
• Allow controllers (list) to override control UI
• Added preset syncviewers (threejs_brain(control_presets = ...)) to synchronize multiple viewers in shiny environment

threeBrain 0.1.4

Changes

• Implemented a new mesh type - volume rendering using ray marching
• Added alternative methods to read .nii files, nibabel is now optional
• Customized color palettes and value range for better visualizations with outliers
• Only requires T1.mgz or brainmask of brain.finalsurf is not found. This allows users only run FreeSurfer to the first stage, which only takes around 8 to 10 minutes instead of 6 hours.
• Fully compatible with htmlwidgets in shiny mode. When calling threejsBrainOutput under shiny::renderUI, the DOM element might get reset by shiny, causing a new 3D viewer created. This might consume more resource, causing memory leaks and even conflict context renderings. Also event listeners couldn't reset correctly. A cache is created and now is reusing the canvas.

Improvements

• More flexible directory requirement
• Added dispose function to canvas so that memory gets cleared correctly
• Renderer optimization and memory optimization

Bug Fixes

• Fixed keyboard listeners locking the keys
• Fixed huge memory leaks due to threejs not garbage collecting geometries and textures

threeBrain 0.1.3

Changes

• File structure change: now directly read in from FreeSurfer folder
• Added readers for .mgz, .m3z files
• Added coordinate system to align volume with surface data
• Implemented side-viewers, added three side cameras at XYZ axis
• Can now read, export electrodes as csv file
• Re-write brain generating function
• Can display/switch multiple value types
• Added transparency to surfaces
• Implemented experimental electrode localization
• Automatically determine color type (continuous or discrete) and value range

Improvements

• Shortcuts available at here
• Optimized electrode value settings

threeBrain 0.1.2

Changes

• Re-draw canvas on a 2D context to make customized overlay directly on canvas.
• Implemented continuous and discrete legends to replace D3.
• Added support to set main camera position and initial zoom level.
• Added 3D scatter plot and examples.
• Use hybrid render mode when animation not required to save battery usage.
• Improved color palette calculation.
• Support customized title.

Improvements

• Support customized datapath when saving widgets.
• Added instructions on how to embed widgets into websites without R.

threeBrain 0.1.1

• Implemented three types of geometries: plane, sphere and free. A free geometry takes arbitrary geometry vertices and faces to form a 3D mesh object.
• Added animation to sphere object.
• Replaced old JavaScript with npx driven modules.
• Implemented D3 side-widget

threeBrain 0.1.0

• Initial private beta release!

threeBrain documentation built on July 9, 2023, 6:32 p.m.