# Your Advanced 3D Brain Visualization

## Documentation for package ‘threeBrain’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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