get_schaefer_atlas: Load Schaefer Brain Parcellation Atlas

In bbuchsbaum/neuroatlas: useful atlases/parcellations for neuroimaging analysis

Load Schaefer Brain Parcellation Atlas

Description

Retrieves and loads the Schaefer brain parcellation atlas, which provides a data-driven parcellation of the cerebral cortex based on both local gradient and global similarity approaches.

Usage

get_schaefer_atlas(
  parcels = c("100", "200", "300", "400", "500", "600", "800", "1000"),
  networks = c("7", "17"),
  resolution = c("1", "2"),
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE
)

Arguments

parcels	Character string specifying number of parcels. Options: "100", "200", "300", "400", "500", "600", "800", "1000"
networks	Character string specifying network count. Options: "7", "17"
resolution	Character string specifying MNI space resolution in mm. Options: "1", "2"
outspace	Optional NeuroSpace object for resampling the atlas
smooth	Logical. Whether to smooth parcel boundaries after resampling. Default: FALSE
use_cache	Logical. Whether to cache downloaded files. Default: TRUE

Details

The Schaefer atlas offers multiple resolutions of cortical parcellation (100-1000 parcels) and two network versions (7 or 17 networks). The atlas is based on resting-state functional connectivity from 1489 subjects. Features include:

• Multiple granularity levels (100-1000 parcels)

• Network assignments (7 or 17 networks)

• Bilateral parcellation

• Available in different resolutions (1mm or 2mm)

Value

A list with classes c("schaefer", "volatlas", "atlas") containing:

name

Character string identifying atlas version

atlas

ClusteredNeuroVol object containing the parcellation

cmap

Data frame with RGB colors for visualization

ids

Integer vector of region IDs

labels

Character vector of region names

orig_labels

Original region labels from source data

network

Network assignment for each region

hemi

Hemisphere designation for each region

Source

https://github.com/ThomasYeoLab/CBIG/

References

Schaefer, A., et al. (2018). Local-Global Parcellation of the Human Cerebral Cortex from Intrinsic Functional Connectivity MRI. Cerebral Cortex, 28(9), 3095-3114.

See Also

get_schaefer_surfatlas for surface-based version

Examples

## Not run: 
# Load 300-parcel atlas with 7 networks
atlas <- get_schaefer_atlas(parcels = "300", networks = "7")

# Load high-resolution version
atlas_hires <- get_schaefer_atlas(parcels = "400",
                                 networks = "17",
                                 resolution = "1")

# Resample to a different space
new_space <- neuroim2::NeuroSpace(dim = c(91,109,91),
                                 spacing = c(2,2,2))
atlas_resampled <- get_schaefer_atlas(parcels = "300",
                                     outspace = new_space)

## End(Not run)

bbuchsbaum/neuroatlas documentation built on Dec. 24, 2024, 4:22 a.m.