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
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!