hippMapp3rSegmentation: hippMapp3rSegmentation

In ANTsX/ANTsRNet: Neural Networks for Medical Image Processing

hippMapp3rSegmentation

Description

Perform HippMapp3r (hippocampal) segmentation described in

Usage

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

Arguments

doPreprocessing	perform preprocessing. See description above.
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 Nov. 21, 2024, 4:07 a.m.