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Documentation for package ‘threeBrain’ version 1.2.0

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AbstractGeom R6 Class - Abstract Class of Geometries
add_nifti Generate volume data from 'MNI' coordinates
add_voxel_cube Generate volume data from 'MNI' coordinates
available_templates Download and Manage Template Subjects
BlankGeom A geometry that renders nothing
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_colormap Color maps for volume or surface data
create_group Create a geometry group containing multiple geometries
create_voxel_cube Generate volume data from 'MNI' coordinates
cross_prod Calculate cross-product of two vectors in '3D'
DataCubeGeom R6 Class - Generate Data Cube Geometry
DataCubeGeom2 R6 Class - Generate Data Cube Geometry via 3D Volume Texture
default_template_directory Default Directory to Store Template Brain
download_N27 Download and Manage Template Subjects
download_template_subject Download and Manage Template Subjects
FreeGeom R6 Class - Generate Geometry from Vertices and Face Indices
freeserfer_colormap Color maps for volume or surface data
freesurfer_brain Read 'FreeSurfer' surface and volume files
freesurfer_brain2 Read 'FreeSurfer' surface and volume files
freesurfer_lut Query the 'FreeSurfer' labels
generate_smooth_envelope Generate smooth envelope around surface
generate_subcortical_surface Approximate 'sub-cortical' surfaces from 'parcellation'
GeomGroup R6 Class - Generate Group of Geometries
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-suma Import 'FreeSurfer' or 'SUMA' files into the viewer structure
import_from_freesurfer Import from 'FreeSurfer' and create 'JSON' cache for 3D viewer
import_fs Import 'FreeSurfer' or 'SUMA' files into the viewer structure
import_suma Import 'FreeSurfer' or 'SUMA' files into the viewer structure
LineSegmentsGeom R6 Class - Generate Line Segments
list_electrode_prototypes List or load all electrode prototypes
load_colormap Color maps for volume or surface data
load_prototype List or load all electrode prototypes
localization_module Launch a 'shiny' application to localize electrodes
merge_brain Create Multi-subject Template
N27 Download and Manage Template Subjects
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
save_colormap Color maps for volume or surface data
seeg_prototype Create "sEEG" shaft geometry prototype
set_default_template Download and Manage Template Subjects
SphereGeom R6 Class - Generate Sphere Geometry
SpriteGeom R6 Class - Generate Sphere Geometry
template_subject Download and Manage Template Subjects
threeBrain Create a brain object
threebrain_finalize_installation Download and Manage Template Subjects
threejsBrainOutput Shiny Output for threeBrain Widgets
threejs_brain Create a Threejs Brain and View it in Browsers
TubeGeom R6 Class - Generate Tube Geometry
video_content Add video content to the viewer
volume_to_surf Generate surface file from "nii" or "mgz" volume files
voxel_colormap Color maps for volume or surface data
voxel_cube Generate volume data from 'MNI' coordinates