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

Description

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,
  ...
)

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

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