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threeBrain (version 1.0.1)

3D Brain Visualization

Description

A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 'Safari'), and can be inserted into any websites. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. This feature has been fully adopted by 'RAVE' , an interactive toolbox to analyze 'iEEG' data. Documentation about 'threeBrain' is provided by and several vignettes included in this package. To cite the package, please check our 'NeuroImage' paper by Magnotti, Wang, and Beauchamp (2020, ), or see 'citation("threeBrain")' for details.

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Version

Install

install.packages('threeBrain')

Monthly Downloads

669

Version

1.0.1

License

GPL-3 | file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/dipterix/threeBrain

Homepage

https://dipterix.org/threeBrain/

Maintainer

Zhengjia Wang

Last Published

July 3rd, 2023

Functions in threeBrain (1.0.1)

Setup Package, Install Environment

Create a geometry group containing multiple geometries

check_freesurfer_path

Function to check whether `FreeSurfer` folder has everything we need

Import 'FreeSurfer' or 'SUMA' files into the viewer structure

Create Multi-subject Template

localization_module

Launch a 'shiny' application to localize electrodes

import_from_freesurfer

Import from `FreeSurfer` and create `JSON` cache for 3D viewer

Read `FreeSurfer` m3z file

Query the 'FreeSurfer' labels

read_fs_mgh_mgz

Read `FreeSurfer` `mgz/mgh` file

freesurfer_brain

Read `FreeSurfer` surface and volume files

default_template_directory

Default Directory to Store Template Brain

Add video content to the viewer

Function to load surface data from `Gifti` files

Function to load `FreeSurfer` `mgz/mgh` file

reorient_volume

Function to reshape data to `RAS` order

threejsBrainOutput

Shiny Output for threeBrain Widgets

Read `FreeSurfer` ascii file

Color maps for volume or surface data

Read FreeSurfer Annotations

Shiny Renderer for threeBrain Widgets

Objects exported from other packages

Create a brain object

template_subject

Download and Manage Template Subjects

Generate volume data from 'MNI' coordinates

Create a Threejs Brain and View it in Browsers

Save threeBrain widgets to local file system

LineSegmentsGeom

R6 Class - Generate Line Segments

R6 Class - Generate Data Cube Geometry

R6 Class - Abstract Class of Geometries

R6 Class - Generate Data Cube Geometry via 3D Volume Texture

R6 Class - Generate Tube Geometry

Shiny Proxy for Viewer

A geometry that renders nothing

R6 Class - Generate Geometry from Vertices and Face Indices

Create sphere geometry

R6 Class - Generate Sphere Geometry

generate_smooth_envelope

Generate smooth envelope around surface

R6 Class - Generate Group of Geometries

Creates any mesh geometry given vertices and face indices

get_digest_header

Function to read digest header