Hippocampal/Enthorhinal segmentation using "Deep Flash"

Perform hippocampal/entorhinal segmentation in T1 and T1/T2 images using labels from Mike Yassa's lab---https://faculty.sites.uci.edu/myassa/

deepFlash(
  t1,
  t2 = NULL,
  doPreprocessing = TRUE,
  antsxnetCacheDirectory = NULL,
  useRankIntensity = TRUE,
  verbose = FALSE
)

Arguments

t1	raw or preprocessed 3-D T1-weighted brain image.
t2	optional raw or preprocessed 3-D T2-weighted brain image.
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 inst/extdata/ subfolder of the ANTsRNet package.
useRankIntensity	If false, use histogram matching with cropped template ROI. Otherwise, use a rank intensity transform on the cropped ROI.
verbose	print progress.

list consisting of the segmentation image and probability images for each label.

The labeling is as follows:

Preprocessing on the training data consisted of:

n4 bias correction,
affine registration to deep flash template. which is performed on the input images if doPreprocessing = TRUE.

Tustison NJ

if (FALSE) {
library( ANTsRNet )
library( keras )

image <- antsImageRead( "t1.nii.gz" )
results <- deepFlash( image )
}