Register a computerized tomography (CT) image to MRI via 'NiftyReg'

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