Load Schaefer Brain Parcellation Atlas

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", "700", "800", "900", "1000"),
  networks = c("7", "17"),
  resolution = c("1", "2"),
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE
)

sy_100_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_100_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_200_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_200_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_300_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_300_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_400_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_400_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_500_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_500_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_600_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_600_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_700_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_700_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_800_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_800_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_900_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_900_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_1000_7(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

sy_1000_17(
  resolution = "2",
  outspace = NULL,
  smooth = FALSE,
  use_cache = TRUE,
  ...
)

Source

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

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
...: Additional arguments (currently unused, included for consistency with convenience functions)

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

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)

Convenience Functions

Shorthand functions are provided for common Schaefer atlas configurations. These functions call get_schaefer_atlas with the parcels and networks arguments pre-set. They all accept resolution (default "2"), outspace, smooth, use_cache, and ... arguments.

sy_100_7(): 100 parcels, 7 networks.
sy_100_17(): 100 parcels, 17 networks.
sy_200_7(): 200 parcels, 7 networks.
sy_200_17(): 200 parcels, 17 networks.
sy_300_7(): 300 parcels, 7 networks.
sy_300_17(): 300 parcels, 17 networks.
sy_400_7(): 400 parcels, 7 networks.
sy_400_17(): 400 parcels, 17 networks.
sy_500_7(): 500 parcels, 7 networks.
sy_500_17(): 500 parcels, 17 networks.
sy_600_7(): 600 parcels, 7 networks.
sy_600_17(): 600 parcels, 17 networks.
sy_800_7(): 800 parcels, 7 networks.
sy_800_17(): 800 parcels, 17 networks.
sy_1000_7(): 1000 parcels, 7 networks.
sy_1000_17(): 1000 parcels, 17 networks.

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.

Examples

if (FALSE) { # \dontrun{
# 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)
} # }