https://github.com/dipterix/threebrain - CRAN Release 1.2.0

First, this package is back on CRAN now.

Check https://github.com/dipterix/threeBrain/blob/master/NEWS.md for release notes.

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Published by dipterix over 1 year ago

https://github.com/dipterix/threebrain - CRAN Release 1.0.1

This version focuses on enhanced support on NIfTI format, allowing users to replace mgh/mgz with nii when preprocessing imaging data using pipelines other than FreeSurfer

• 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

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Published by dipterix almost 3 years ago

https://github.com/dipterix/threebrain - CRAN Release 1.0.0 (Egypt)

This version is a major update since the major functions in electrode localization have been implemented.

• 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

The version code is chosen in memory of Egypt, who just passed away earlier today.

The photo is licensed under Creative Commons Attribution-NonCommercial-NoDerivs (CC-BY-NC-ND).

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Published by dipterix almost 3 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.2.9

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)

Screenshot of the electrode localization.

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Published by dipterix about 3 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.2.7

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

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Published by dipterix over 3 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.2.5

Changes since 0.2.0:

Highlights:

• Added electrode localization with aligned re-sampled CT image. Can be accessible via brain$localize(ct_path). Rendering original CT is in the dev schedule
• Users can download electrode coordinates as csv directly from the control panel
• Added support to download other templates such as fsaverage, bert, cvs_avg35 etc.
• Allow to show volume data directly in the viewer (toggle with key l)
• Allow surface vertex color to be sampled from volume or electrodes (projected to the surface with Gaussian blur) via shortcut k.

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.
• 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.
• Supported video content to display auditory visual stimuli along the response
• Default to closing the default and volume side folders
• Renamed recording button to Chrome-specific
• Can download electrodes as csv

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
• Added 3 vignettes
• Added TextTexture in the internal code to display text Sprite easily

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
• Fixed electrode localization interpolation issue
• Proper dispose the localized electrodes
• Fixed screenshot and video recording functions

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Published by dipterix about 4 years ago

https://github.com/dipterix/threebrain - Pre-Release 0.2.0

This (draft) release includes core engine updates and performance improvements. It's in testing phase.

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Published by dipterix almost 5 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.1.8

Changes

• Screenshot now downloads pdf format

Bug Fixes

• Fixed freesurferformats face index starting from 1 instead of 0

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Published by dipterix almost 6 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.1.7

Bundled update from 0.1.5

threeBrain 0.1.6 ~ 0.1.7

Changes

• Now displays MNI305 coordinates instead of tkRAS coordinates

• Removed reticulate and related functions to support native R functions

• 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

• Fixed MNI305 calculation issues
• Internally calculates anterior commissure

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Published by dipterix about 6 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.1.5

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Published by dipterix over 6 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.1.4

Compatible with RAVE ver. 0.1.8-beta and ravebuiltins ver. v0.1-alpha

• CRAN Current Release
• CRAN Archive Here

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Published by dipterix over 6 years ago

https://github.com/dipterix/threebrain - CRAN Release 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

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Published by dipterix over 6 years ago

https://github.com/dipterix/threebrain - CRAN Release 0.1.2

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Published by dipterix almost 7 years ago