Description Usage Arguments Value
View source: R/ich_preprocess.R
Will do skull stripping and registration to the CT template
1 2 3 4 5 6 7 8 9 10 | 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"))
|
img |
CT image, object of class |
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
|
mask |
binary brain mask, object of class |
n4_correct |
Should N4 bias-field correction be done after skull-stripping |
template.file |
Template to register to (Skull stripped template) |
outprefix |
Passed to |
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 |
List of output images and transformations
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