Package: brainloc 0.1.0

brainloc: Find Region Names and Coordinates for a Point on the Human Brain

Given a point on the human brain, identify the closest brain regions according to a brain atlas.

Authors:Tim Schäfer [aut, cre]

brainloc_0.1.0.tar.gz
brainloc_0.1.0.zip(r-4.7-any)brainloc_0.1.0.zip(r-4.6-any)brainloc_0.1.0.zip(r-4.5-any)
brainloc_0.1.0.tgz(r-4.6-any)brainloc_0.1.0.tgz(r-4.5-any)
brainloc_0.1.0.tar.gz(r-4.7-any)brainloc_0.1.0.tar.gz(r-4.6-any)
brainloc_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
brainloc/json (API)

# Install 'brainloc' in R:

install.packages('brainloc', repos = c('https://dfsp-spirit.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dfsp-spirit/brainloc/issues

On CRAN:

atlas brain coordinate-systems distances freesurfer fsaverage mri neuroimaging

2.70 score 1 stars 1 scripts 27 exports 12 dependencies

Last updated from:9770ef0763 (on v0.1.0). Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	141
source / vignettes	OK	263
linux-release	OK	177
macos-release	OK	120
macos-oldrel	OK	112
windows-devel	OK	86
windows-release	OK	91
windows-oldrel	OK	94
wasm-release	OK	126

Exports:brainparc brainparc_fs brainparc_neighbors cluster_location_details cluster_peaks cluster_region_overlap clusterinfo clusterinfo_from_thresholded_overlay coord_closest_regions coord_closest_vertex coord_MNI152_to_talairach coord_MNI305_info coord_MNI305_to_MNI152 fs_home get_clusters get_subjects_dir get_surface get_surface_coords get_talairach_label has_fs hemilist is.brainparc is.clusterinfo name_regions segmentation_centers vertex_closest_regions vertex_regions

Dependencies:cli collections curl freesurferformats pkgfilecache rappdirs Rcpp RcppArmadillo RcppEigen rlang Rvcg xml2

brainloc

About brainloc | Preparation: Getting the data required to run the examples | Using the template subjects from a local FreeSurfer installation | Have the brainloc package download them for you from the internet | Usage Examples Part I: Location information for a vertex or coordinate | Creating a brainparc object | Finding the vertex closest to a query coordinate | Finding the MNI152 and Talairach coordinates for a point or vertex in MNI305 space | Finding the brain atlas region a vertex belongs to, and the distance to all other brain atlas regions from the vertex | Usage Examples Part II: Location information for a cluster

Rendered frombrainloc.Rmdusingknitr::rmarkdown

Last update: 2021-12-14
Started: 2021-12-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create a brain parcellation from custom data.	brainparc
Create a brain parcellation from a subject in a FreeSurfer recon-all output directory	brainparc_fs
Compute adjacency of surface parcellation (annot) regions.	brainparc_neighbors
Get details on cluster locations.	cluster_location_details
Compute cluster peaks.	cluster_peaks
Compute overlapping atlas regions for clusters.	cluster_region_overlap
Create clusterinfo data structure from files or pre-loaded data.	clusterinfo
Create clusterinfo instance from thresholded per-vertex data overlays.	clusterinfo_from_thresholded_overlay
Find closest regions to coordinate using Euclidean or geodesic distance.	coord_closest_regions
Find closest surface vertex to a point, using Euclidean distance.	coord_closest_vertex
Transform MNI152 coords to approximate Talairach space using Matthew Brett's approach.	coord_MNI152_to_talairach
Get info on MNI305 surface coordinate in various coordinate systems.	coord_MNI305_info
Transform MNI305 coords (FreeSurfer fsaverage surface) to MNI152 coordinates.	coord_MNI305_to_MNI152
Return FreeSurfer path.	fs_home
Get the clusters from a clusterinfo instance.	get_clusters
Find subjects_dir or stop.	get_subjects_dir
Extract the surface hemilist from a brainparc.	get_surface
Extract the vertex coordinates from the brainparc surface.	get_surface_coords
Retrieve Talairach labels for Talairach coordinates from 'talairach.org' files.	get_talairach_label
Check whether a FreeSurfer installation can be found on the system.	has_fs
Create hemilist.	hemilist
Check whether object is a brainparc instance.	is.brainparc
Check whether x is a clusterinfo instance.	is.clusterinfo
Get names of regions in labeled volume from color lookup table (colorLUT).	name_regions
Print description of a brainparc instance (S3).	print.brainparc
Find center of mass of regions in a brain volume segmentation.	segmentation_centers
Find closest regions to vertex using Euclidean or geodesic distance.	vertex_closest_regions
Find regions for vertices in all brainparc atlases.	vertex_regions