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b/man/ich_preprocess.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/ich_preprocess.R |
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\name{ich_preprocess} |
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\alias{ich_preprocess} |
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\alias{ich_cnn_preprocess} |
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\title{Preprocess data for ICH Segmentation} |
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\usage{ |
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ich_preprocess( |
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img, |
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skull_strip = TRUE, |
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robust = TRUE, |
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mask = NULL, |
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n4_correct = FALSE, |
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template.file = system.file("scct_unsmooth_SS_0.01.nii.gz", package = "ichseg"), |
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outprefix = NULL, |
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typeofTransform = c("Rigid", "Affine"), |
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interpolator = "Linear", |
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outfile = NULL, |
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verbose = TRUE, |
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shiny = FALSE, |
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roi = NULL, |
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ss.template.file = system.file("scct_unsmooth_SS_0.01.nii.gz", package = "ichseg"), |
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ss.template.mask = system.file("scct_unsmooth_SS_0.01_Mask.nii.gz", package = "ichseg"), |
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... |
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) |
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ich_cnn_preprocess( |
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..., |
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template.file = system.file("scct_unsmooth_SS_0.01_128x128x128.nii.gz", package = |
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"ichseg") |
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) |
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} |
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\arguments{ |
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\item{img}{CT image, object of class \code{nifti} or |
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character filename} |
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\item{skull_strip}{Should the image be skull stripped? If not, |
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a mask must be specified. If mask specified, will override this |
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option} |
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\item{robust}{If skull stripping, should |
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\code{\link{CT_Skull_Strip_robust}} |
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be used vs. \code{\link{CT_Skull_Strip}}} |
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\item{mask}{binary brain mask, object of class \code{nifti} or |
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character filename} |
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\item{n4_correct}{Should N4 bias-field correction be done after |
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skull-stripping} |
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\item{template.file}{Template to register to (Skull stripped template)} |
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\item{outprefix}{Passed to \code{\link[extrantsr]{registration}} for |
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the output transformations} |
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\item{typeofTransform}{Transformation to the template} |
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\item{interpolator}{Interpolation to be done after transformation} |
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\item{outfile}{Output filename for transformed registered image} |
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\item{verbose}{Print diagnostic output} |
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\item{shiny}{Should shiny progress be called?} |
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\item{roi}{Filename of ROI, which will be transformed} |
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\item{ss.template.file}{Template file to pass to |
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\code{\link{CT_Skull_Strip_robust}} robust registration/neck removal} |
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\item{ss.template.mask}{Template mask to pass to |
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\code{\link{CT_Skull_Strip_robust}} robust registration/neck removal} |
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\item{...}{Additional options passsed to \code{\link{CT_Skull_Strip_robust}} |
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or \code{\link{CT_Skull_Strip}}} |
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} |
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\value{ |
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List of output images and transformations |
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} |
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\description{ |
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Will do skull stripping and registration to the CT template |
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} |