Rigidly register a computerized tomography (CT) image to MRI with the built-in YAEL-reg3d engine

Aligns the 'CT' to the 'MRI' with register_volume3d, which is built into 'RAVE' and needs no external program. The registration always runs on the full-resolution images. Images with any side of max_side voxels or more are additionally saved as down-sampled copies (same field of view) so that viewers can load them; the original images are kept. Please use cmd_run_reg3d_rigid from pipelines: it saves a script that runs reg3d_rigid and records the results for the electrode localization.

Usage

reg3d_rigid(
  ct_path,
  mri_path,
  coreg_path,
  reg_type = c("Rigid", "DenseRigid", "FastRigid"),
  cost = c("mattes", "cc"),
  interp = c("trilinear", "bspline", "nearest"),
  max_side = 384,
  verbose = TRUE,
  ...
)

cmd_run_reg3d_rigid(
  subject,
  ct_path,
  mri_path,
  reg_type = c("Rigid", "DenseRigid", "FastRigid"),
  cost = c("mattes", "cc"),
  interp = c("trilinear", "bspline", "nearest"),
  verbose = TRUE,
  dry_run = FALSE
)

Arguments

ct_path, mri_path

absolute paths to 'CT' and 'MR' image files

coreg_path

directory where the results are saved; required. An existing directory is backed up (renamed) once the new results are complete, so a failed registration leaves it untouched

reg_type

registration preset; choices are 'Rigid' (three resolution levels, 20 percent of the voxels sampled), 'DenseRigid' (same levels, every voxel sampled; slower), or 'FastRigid' (coarser levels, fewer iterations, 5 percent of the voxels sampled; fast)

cost

cost function; choices are 'mattes' (mutual information, suitable for 'CT' to 'MRI') or 'cc' (normalized cross-correlation, for images of the same modality)

interp

interpolation used to re-sample the saved images; choices are 'trilinear', 'bspline', or 'nearest'; the alignment itself does not depend on it

max_side

images with any side of at least this many voxels are also saved as copies whose sides are at most max_side voxels; default is 384

verbose

whether to print the registration progress

...

passed to register_volume3d; overrides the preset, for example iterations or sampling_rate

subject

'RAVE' subject

dry_run

whether to only build the script without running it; default is false

Value

reg3d_rigid invisibly returns a list with the result directory (coreg_path) and the names of the files in it:

'CT_RAW.nii.gz', 'MRI_reference.nii.gz'

the 'CT' and 'MR' images; an image with any side of max_side voxels or more is saved as a down-sampled copy with the same field of view

'CT_ORIG.nii.gz', 'MRI_ORIG.nii.gz'

the original images; only saved when the images above are down-sampled copies

'ct_in_t1.nii.gz'

the 'CT' re-sampled onto the grid of 'MRI_reference.nii.gz'

'CT_RAS_to_MR_RAS.txt'

transform from the 'CT' scanner 'RAS' to the 'MR' scanner 'RAS' coordinates

'CT_IJK_to_MR_RAS.txt'

transform from the voxel indices of 'CT_RAW.nii.gz' (starting from 0) to the 'MR' scanner 'RAS' coordinates

'reg3d/reg3d.dcf'

registration record written by save_registration, with the 'ANTs'-style affine transform 'reg3d/reg3d0GenericAffine.mat'; it refers to the full-resolution images

cmd_run_reg3d_rigid returns a list with the script, its path, the log file, the image paths, and a function execute that runs the script.