ich_preprocess: Preprocess data for ICH Segmentation

Description Usage Arguments Value

View source: R/ich_preprocess.R

Description

Will do skull stripping and registration to the CT template

Usage

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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


neuroconductor-releases/ichseg documentation built on Dec. 16, 2019, 12:37 a.m.