Supports 'Rigid', 'affine', or 'non-linear' transformation
Usage
niftyreg_coreg(
ct_path,
mri_path,
coreg_path = NULL,
reg_type = c("rigid", "affine", "nonlinear"),
interp = c("trilinear", "cubic", "nearest"),
verbose = TRUE,
...
)
cmd_run_niftyreg_coreg(
subject,
ct_path,
mri_path,
reg_type = c("rigid", "affine", "nonlinear"),
interp = c("trilinear", "cubic", "nearest"),
verbose = TRUE,
dry_run = FALSE,
...
)Arguments
- ct_path, mri_path
absolute paths to 'CT' and 'MR' image files
- coreg_path
registration path, where to save results; default is the parent folder of
ct_path- reg_type
registration type, choices are
'rigid','affine', or'nonlinear'- interp
how to interpolate when sampling volumes, choices are
'trilinear','cubic', or'nearest'- verbose
whether to verbose command; default is true
- ...
other arguments passed to
register_volume- subject
'RAVE' subject
- dry_run
whether to dry-run the script and to print out the command instead of executing the code; default is false
Value
Nothing is returned from the function. However, several files will be generated at the 'CT' path:
'ct_in_t1.nii'aligned 'CT' image; the image is also re-sampled into 'MRI' space
'CT_IJK_to_MR_RAS.txt'transform matrix from volume 'IJK' space in the original 'CT' to the 'RAS' anatomical coordinate in 'MR' scanner
'CT_RAS_to_MR_RAS.txt'transform matrix from scanner 'RAS' space in the original 'CT' to 'RAS' in 'MR' scanner space