hippMapp3rSegmentation: hippMapp3rSegmentation

In ANTsX/ANTsRNet: Neural Networks for Medical Image Processing

hippMapp3rSegmentation

Description

Perform HippMapp3r (hippocampal) segmentation described in

Usage

hippMapp3rSegmentation(
  t1,
  doPreprocessing = TRUE,
  antsxnetCacheDirectory = NULL,
  verbose = FALSE
)

Arguments

doPreprocessing	perform preprocessing. See description above.
antsxnetCacheDirectory	destination directory for storing the downloaded template and model weights. Since these can be resused, if is.null(antsxnetCacheDirectory), these data will be downloaded to the subdirectory ~/.keras/ANTsXNet/.
verbose	print progress.
image	input 3-D T1-weighted brain image.

Details

https://www.ncbi.nlm.nih.gov/pubmed/31609046

with models and architecture ported from

https://github.com/AICONSlab/HippMapp3r

Additional documentation and attribution resources found at

https://hippmapp3r.readthedocs.io/en/latest/

Preprocessing consists of:

• n4 bias correction and

• brain extraction. The input T1 should undergo the same steps. If the input T1 is the raw T1, these steps can be performed by the internal preprocessing, i.e. set doPreprocessing = TRUE

Value

labeled hippocampal mask (ANTsR image)

Author(s)

Tustison NJ

Examples

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

url <- "https://github.com/mgoubran/HippMapp3r/blob/master/data/test_case/mprage.nii.gz?raw=true"
imageFile <- "head.nii.gz"
download.file( url, imageFile )
image <- antsImageRead( imageFile )
imageN4 <- n4BiasFieldCorrection( image, verbose = TRUE )
segmentation <- hippMapp3rSegmentation( imageN4, verbose = TRUE )

## End(Not run)

ANTsX/ANTsRNet documentation built on April 28, 2024, 12:16 p.m.