Extract brain and strip skull — brain

Function brain_mask and brain_extraction use the ants base package. Function antspynet_brain_extraction uses antspynet to extract the brain using deep neural network. This requires additional configuration. Print antspynet$brain_extraction to see the original documentation.

Usage

antspynet_brain_extraction(
  x,
  modality = c("t1", "t1nobrainer", "t1combined", "flair", "t2", "t2star", "bold", "fa",
    "t1t2infant", "t1infant", "t2infant"),
  verbose = FALSE
)

brain_mask(
  x,
  work_path = tempfile(pattern = "rpyant_brain_extraction_"),
  verbose = TRUE,
  auto_clean = TRUE
)

brain_extraction(
  x,
  skull_alpha = 0,
  threshold_quantile = 0.85,
  ...,
  verbose = TRUE
)

Arguments

x: input image or image path
modality: modality type, used by antspynet_brain_extraction only
verbose: whether to print out process to the screen
work_path: working directory; default is temporary path
auto_clean: whether to automatically clean the working path if the path is temporary; default is true
skull_alpha: used by brain_extraction, the opacity of the skull in the final image; default is 0 (completely strip the skull); set to values between 0 to 1 to add skulls (in such case, the background noises will be set to 0)
threshold_quantile: used only when skull_alpha is positive to remove the noises
...: see work_path and auto_clean

Value

brain_mask: Brain mask image
brain_extraction: extracted brain
antspynet_brain_extraction: Brain mask image