Description Usage Arguments Value
View source: R/T1_Registration_function.R
This function performs registration to a template using ANTsR and SyN transformation, carry out the transformation on other images, and can back-transform atlases in template space to the native space of the iimage
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ants_regwrite(
filename,
skull_strip = FALSE,
correct = FALSE,
correction = "N3",
retimg = TRUE,
outfile = NULL,
template.file = file.path(fsldir(), "data", "standard", "MNI152_T1_1mm_brain.nii.gz"),
interpolator = "Linear",
other.files = NULL,
other.outfiles = NULL,
native.cereb = FALSE,
native.fname = NULL,
atlas.file = NULL,
typeofTransform = "SyN",
remove.warp = TRUE,
outprefix = NULL,
bet.opts = "-B -f 0.1 -v",
betcmd = "bet",
verbose = TRUE,
reproducible = TRUE,
seed = 1,
...
)
|
filename |
filename of T1 image |
skull_strip |
do skull stripping with FSL BET |
correct |
do Bias correction |
correction |
N3 or N4 correction, see |
retimg |
return a nifti object from function |
outfile |
output filename should have .nii or .nii.gz extension |
template.file |
Filename of template to warp to |
interpolator |
interpolation done for
|
other.files |
Filenames of other iamges to be transformed with the T1 |
other.outfiles |
Output filenames of |
native.cereb |
Logical indicating if native cerebellum should be
created to |
native.fname |
filename of native cerebellum file |
atlas.file |
Filename of atlas used for warping labels |
typeofTransform |
type of transformed used, passed to
|
remove.warp |
(logical) Should warping images be deleted? |
outprefix |
Character path of where the warp files should be stored.
Required if |
bet.opts |
Options passed to |
betcmd |
BET command used, passed to |
verbose |
Print diagnostic messages |
reproducible |
Sets the seed and
|
seed |
will execute
|
... |
arguments to |
NULL or object of class nifti for transformed T1 image
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