make_predictors: Make CT Predictors

In neuroconductor-devel/ichseg: Intracerebral Hemorrhage Segmentation of X-Ray Computed Tomography (CT) Images

Description

Create a set of predictors for ICH segmentation for CT

Usage

make_predictors(img, mask, roi = NULL, nvoxels = 1, moments = 1:4,
  center = c(FALSE, TRUE, TRUE, TRUE), lthresh = 40, uthresh = 80,
  sigmas = c(5, 10, 20), save_imgs = TRUE, outdir = NULL,
  stub = NULL, overwrite = FALSE,
  template.file = system.file("scct_unsmooth_SS_0.01.nii.gz", package =
  "ichseg"), mean.img = system.file("Mean_Image.nii.gz", package =
  "ichseg"), sd.img = system.file("SD_Image.nii.gz", package = "ichseg"),
  zscore.typeofTransform = "SyN", zscore.interpolator = "Linear",
  flip.typeofTransform = "Affine",
  flip.interpolator = "LanczosWindowedSinc", low_thresh = 1e-13,
  verbose = TRUE, shiny = FALSE, erode_mask = TRUE, ...)

Arguments

img	Filename of image intensities
mask	Filename of brain mask
roi	Filename of ROI for Y
nvoxels	Voxel neighborhood
moments	Moments of neighborhood to take
center	Center the moments
lthresh	Lower threshold for neighborhood setting
uthresh	Upper threshold for neighborhood setting
sigmas	Sigma values for Gaussian smoothed images (in mm)
save_imgs	Logical to save all images that are created as predictors
outdir	Output directory of saved images, needs to be set if save_imgs = TRUE
stub	Basename to write image names if save_imgs = TRUE
overwrite	If save_imgs is TRUE, then should the files be overwritten? If not, then files will be read instead instead of code being re-run.
template.file	Template to register to (CT Template)
mean.img	Mean image in template space for z-scoring
sd.img	SD image in template space for z-scoring
zscore.typeofTransform	type of transform for z-scoring
zscore.interpolator	type of interpolator for z-scoring
flip.typeofTransform	type of transform for flipped difference
flip.interpolator	type of interpolator for flipped difference
low_thresh	Threshold for forcing values to zero
verbose	Logical indicator if output messages should be printed
shiny	Should shiny progress be called?
erode_mask	Should the brain mask be eroded?
...	options passed to get_neighbors

Value

List of a data.frame of Predictors and set of indices to keep in mask and an empty nifti object for plotting. Also the number of voxels of the roi that were not in the mask

neuroconductor-devel/ichseg documentation built on Sept. 5, 2019, 8:01 p.m.