rescale_img: Image Rescaler

In neuroconductor-devel-releases/neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

Description

Rescales an image to be in certain value range. This was created as sometimes DICOM scale and slope parameters may be inconsistent across sites and the data need to be value restricted

Usage

rescale_img(
  filename,
  pngname = NULL,
  write.nii = FALSE,
  outfile = NULL,
  min.val = -1024,
  max.val = 3071,
  ROIformat = FALSE,
  drop_dim = TRUE,
  writer = "dcm2nii",
  ...
)

Arguments

filename	filename of image to be read into R or nifti object
pngname	filename of png of histogram of values of image to be made. For no png - set to NULL (default)
write.nii	logical - should the image be written.
outfile	if write.nii = TRUE, filename of output file
min.val	minimum value of image (default -1024 (for CT)). If no thresholding set to -Inf
max.val	maximum value of image (default 3071 (for CT)). If no thresholding set to Inf
ROIformat	if TRUE, any values $< 0$ will be set to 0
drop_dim	Should drop_img_dim be applied?
writer	character value to add to description slot of NIfTI header
...	extra methods to be passed to writenii

Value

Object of class nifti

Examples

img = nifti(array(rnorm(10^3, sd = 1000), dim = rep(10, 3)))
outfile = tempfile(fileext = ".nii.gz")
pngname = tempfile(fileext = ".png")
rescale_img(img, write.nii = TRUE, outfile = outfile,
pngname = pngname)

neuroconductor-devel-releases/neurobase documentation built on May 6, 2020, 4:25 p.m.