View source: R/preprocess_mri_within.R
preprocess_mri_within | R Documentation |
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.
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
.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.