Preprocess data for ICH Segmentation

Source: R/ich_preprocess.R

Will do skull stripping and registration to the CT template

ich_preprocess(
  img,
  skull_strip = TRUE,
  robust = TRUE,
  mask = NULL,
  n4_correct = FALSE,
  template.file = system.file("scct_unsmooth_SS_0.01.nii.gz", package = "ichseg"),
  outprefix = NULL,
  typeofTransform = c("Rigid", "Affine"),
  interpolator = "Linear",
  outfile = NULL,
  verbose = TRUE,
  shiny = FALSE,
  roi = NULL,
  ...
)

ich_cnn_preprocess(
  ...,
  template.file = system.file("scct_unsmooth_SS_0.01_128x128x128.nii.gz", package =
    "ichseg")
)

Arguments

img

CT image, object of class nifti or character filename
skull_strip

Should the image be skull stripped? If not, a mask must be specified. If mask specified, will override this option
robust

If skull stripping, should CT_Skull_Strip_robust be used vs. CT_Skull_Strip
mask

binary brain mask, object of class nifti or character filename
n4_correct

Should N4 bias-field correction be done after skull-stripping
template.file

Template to register to (Skull stripped template)
outprefix

Passed to registration for the output transformations
typeofTransform

Transformation to the template
interpolator

Interpolation to be done after transformation
outfile

Output filename for transformed registered image
verbose

Print diagnostic output
shiny

Should shiny progress be called?
roi

Filename of ROI, which will be transformed
...

Additional options passsed to CT_Skull_Strip_robust or CT_Skull_Strip

Value

List of output images and transformations