brain_extraction: Extract brain and strip skull
In rpyANTs: An Alternative Advanced Normalization Tools ('ANTs')

brain_extraction

R Documentation

Extract brain and strip skull

Description

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`