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!