Description Usage Arguments Value
View source: R/preprocess_mri_within.R
This function performs skull stripping of the first image, within-visit registration using a rigid-body transformation, inhomogeneity correction, and potentially re-correcting after skull stripping.
1 2 3 4 5 | preprocess_mri_within(files, outfiles = NULL, correct = TRUE,
correction = "N4", retimg = FALSE, reorient = FALSE,
typeofTransform = "Rigid", interpolator = "LanczosWindowedSinc",
skull_strip = FALSE, bet.opts = "-B -f 0.1 -v", betcmd = "bet",
maskfile = NULL, correct_after_mask = FALSE, verbose = TRUE, ...)
|
files |
filenames (or nifti objects) of images to be processed. Will register to the first scan |
outfiles |
(character) name of output files, with extension |
correct |
do Bias field correction |
correction |
(character) N3 or N4 correction? |
retimg |
(logical) return list of images of class nifti |
reorient |
(logical) If retimg, should file be reoriented
when read in?
Passed to |
typeofTransform |
type of transformed used, passed to
|
interpolator |
Interpolation to be performed, passed to
|
skull_strip |
do Skull stripping with FSL BET |
bet.opts |
Options to pass to |
betcmd |
Command to pass to |
maskfile |
Filename (or nifti object) of mask for image to be registered to |
correct_after_mask |
Should the inhomogeneity correction be run
after masking. If |
verbose |
Diagnostic messages |
... |
arguments to |
List of outfiles, maskfile, and output from registration
.
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