Package index • threeBrain

All functions

AbstractGeom: R6 Class - Abstract Class of Geometries

BlankGeom: A geometry that renders nothing

DataCubeGeom: R6 Class - Generate Data Cube Geometry

DataCubeGeom2: R6 Class - Generate Data Cube Geometry via 3D Volume Texture

FreeGeom: R6 Class - Generate Geometry from Vertices and Face Indices

GeomGroup: R6 Class - Generate Group of Geometries

LineSegmentsGeom: R6 Class - Generate Line Segments

SphereGeom: R6 Class - Generate Sphere Geometry

SpriteGeom: R6 Class - Generate Sphere Geometry

TubeGeom: R6 Class - Generate Tube Geometry

brain_proxy(): Shiny Proxy for Viewer

brain_setup(): Setup Package, Install Environment

calculate_rotation(): Calculate rotation matrix from non-zero vectors

check_freesurfer_path(): Function to check whether `FreeSurfer` folder has everything we need

conform_volume(): Conform imaging data in 'FreeSurfer' way

create_group(): Create a geometry group containing multiple geometries

cross_prod(): Calculate cross-product of two vectors in '3D'

default_template_directory(): Default Directory to Store Template Brain

freesurfer_brain() freesurfer_brain2(): Read `FreeSurfer` surface and volume files

freesurfer_lut: Query the 'FreeSurfer' labels

generate_cortical_parcellation(): Generate cortical annotations from template using surface mapping

generate_smooth_envelope(): Generate smooth envelope around surface

generate_subcortical_surface(): Approximate 'sub-cortical' surfaces from 'parcellation'

geom_freemesh(): Creates any mesh geometry given vertices and face indices

geom_sphere(): Create sphere geometry

get_digest_header(): Function to read digest header

get_ijk2ras(): Get 'voxel' to world matrix

import_fs() import_suma(): Import 'FreeSurfer' or 'SUMA' files into the viewer structure

import_from_freesurfer(): Import from `FreeSurfer` and create `JSON` cache for 3D viewer

list_electrode_prototypes() load_prototype(): List or load all electrode prototypes

localization_module(): Launch a 'shiny' application to localize electrodes

merge_brain(): Create Multi-subject Template

new_electrode_prototype(): Create or load new electrode prototype from existing configurations

plot_slices(): Plot slices of volume

read_fs_asc(): Read `FreeSurfer` ascii file

read_fs_labels(): Read FreeSurfer Annotations

read_fs_m3z(): Read `FreeSurfer` m3z file

read_fs_mgh_mgz(): Read `FreeSurfer` `mgz/mgh` file

read_gii2(): Function to load surface data from `Gifti` files

read_mgz(): Function to load `FreeSurfer` `mgz/mgh` file

read_volume(): Read volume file in 'MGH' or 'Nifti' formats

renderBrain: Shiny Renderer for threeBrain Widgets

reorient_volume(): Function to reshape data to `RAS` order

save_brain(): Save threeBrain widgets to local file system

seeg_prototype(): Create 'sEEG' shaft geometry prototype

download_template_subject() download_N27() set_default_template() threebrain_finalize_installation() available_templates(): Download and Manage Template Subjects

threeBrain(): Create a brain object

threejsBrainOutput: Shiny Output for threeBrain Widgets

threejs_brain(): Create a Threejs Brain and View it in Browsers

video_content(): Add video content to the viewer

volume_to_surf(): Generate surface file from 'nii' or 'mgz' volume files

create_colormap() save_colormap() freeserfer_colormap() load_colormap(): Color maps for volume or surface data

add_voxel_cube() add_nifti() create_voxel_cube(): Generate volume data from 'MNI' coordinates