normalizeRAVEL: RAVEL intensity normalization

In Jfortin1/RAVEL: Removal of Artificial Voxel Effect by Linear Regression

RAVEL intensity normalization

Description

RAVEL intensity normalization.

Usage

normalizeRAVEL(
  input.files,
  output.files = NULL,
  brain.mask = NULL,
  control.mask = NULL,
  mod = NULL,
  WhiteStripe = TRUE,
  WhiteStripe_Type = c("T1", "T2", "FLAIR"),
  stripped = TRUE,
  k = 1,
  returnMatrix = TRUE,
  writeToDisk = FALSE,
  verbose = TRUE,
  ...
)

Arguments

input.files	Vector of filenames for the input images. Must be NIfTI files.
output.files	Optional vector of filenames for the output images. By default, will be the input.files with suffix "RAVEL".
brain.mask	Filename for the brain binary mask specifying the template space brain. Must be a NIfTI file.
control.mask	Filename for the control region binary mask to be used in RAVEL. Must be a NIfTI file.
mod	Model matrix for outcome of interest and other covariates
WhiteStripe	Should White Stripe intensity normalization be performed prior to RAVEL?.
WhiteStripe_Type	What modality is used for WhiteStripe? Should be one of T1, T2 or FLAIR.
stripped	Is the image skull stripped? TRUE by default.
k	Number of unwanted factors to be included in the RAVEL model.
returnMatrix	Should the matrix of intensities be returned? TRUE by default.
writeToDisk	Should the scans be saved to the disk? FALSE by default.
verbose	Should messages be printed?
...	additional arguments to pass to whitestripe

Value

if returnMatrix is FALSE, no value returned, but RAVEL-corrected images are saved. If returnMatrix is TRUE, RAVEL-corrected images are saved and a matrix of normalized intensities is returned.

Author(s)

Jean-Philippe Fortin

Jfortin1/RAVEL documentation built on Sept. 14, 2023, 10:33 a.m.