Description Usage Arguments Value
View source: R/make_predictors.R
Create a set of predictors for ICH segmentation for CT
1 2 3 4 5 6 7 8 9 10 11 | 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, ...)
|
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 |
stub |
Basename to write image names if |
overwrite |
If |
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 |
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
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