cerebellumMorphology: Cerebellum tissue segmentation, Schmahmann parcellation, and...

In ANTsX/ANTsRNet: Neural Networks for Medical Image Processing

Cerebellum tissue segmentation, Schmahmann parcellation, and thickness.

Description

Perform cerebellum segmentation using a modification of the set of MaGET cerebellum atlases — https://www.cobralab.ca/cerebellum-lobules.

Usage

cerebellumMorphology(
  t1,
  cerebellumMask = NULL,
  computeThicknessImage = FALSE,
  doPreprocessing = TRUE,
  antsxnetCacheDirectory = NULL,
  verbose = FALSE
)

Arguments

t1	raw or preprocessed 3-D T1-weighted whole head image.
cerebellumMask	Option for initialization. If not specified, the cerebellum ROI is determined using ANTsXNet brain_extraction followed by registration to a template.
computeThicknessImage	Compute KellyKapowski thickness image of the gray matter.
doPreprocessing	Perform N4 bias correction and spatiall normalize to template space.
antsxnetCacheDirectory	destination directory for storing the downloaded template and model weights. Since these can be ressed, if is.null(antsxnetCacheDirectory), these data will be downloaded to the inst/extdata/ subfolder of the ANTsRNet package.
verbose	print progress.

Details

Current citation: https://www.medrxiv.org/content/10.1101/2023.01.17.23284693v4

The tissue labeling is as follows:

• Label 1 :CSF

• Label 2 :Gray matter

• Label 3 :White matter

The parcellation labeling is as follows:

• Label 1 :L_I_II

• Label 2 :L_III

• Label 3 :L_IV

• Label 4 :L_V

• Label 5 :L_VI

• Label 6 :L_Crus_I

• Label 7 :L_Crus_II

• Label 8 :L_VIIB

• Label 9 :L_VIIIA

• Label 10 :L_VIIIB

• Label 11 :L_IX

• Label 12 :L_X

• Label 101:R_I_II

• Label 102:R_III

• Label 103:R_IV

• Label 104:R_V

• Label 105:R_VI

• Label 106:R_Crus_I

• Label 107:R_Crus_II

• Label 108:R_VIIB

• Label 109:R_VIIIA

• Label 110:R_VIIIB

• Label 111:R_IX

• Label 112:R_X

Value

List consisting of the multiple segmentation images and probability images for each label and foreground. Optional thickness image.

Author(s)

Tustison NJ, Tustison MG

Examples

## Not run: 
library( ANTsRNet )
library( keras )

image <- antsImageRead( "t1.nii.gz" )
cereb <- cerebellumMorphology( image )

## End(Not run)

ANTsX/ANTsRNet documentation built on April 23, 2024, 1:24 p.m.