Skip to contents

Register 'CT' or 'MR' images via 'ANTs'

Source: R/cmd-ants-registration.R
ants_coreg.Rd

ants_coreg aligns 'CT' to 'MR' images; ants_mri_to_template aligns native 'MR' images to group templates

Usage

ants_coreg(
  ct_path,
  mri_path,
  coreg_path = NULL,
  reg_type = c("DenseRigid", "Rigid", "SyN", "Affine", "TRSAA", "SyNCC", "SyNOnly"),
  aff_metric = c("mattes", "meansquares", "GC"),
  syn_metric = c("mattes", "meansquares", "demons", "CC"),
  verbose = TRUE,
  ...
)

cmd_run_ants_coreg(
  subject,
  ct_path,
  mri_path,
  reg_type = c("DenseRigid", "Rigid", "SyN", "Affine", "TRSAA", "SyNCC", "SyNOnly"),
  aff_metric = c("mattes", "meansquares", "GC"),
  syn_metric = c("mattes", "meansquares", "demons", "CC"),
  verbose = TRUE,
  dry_run = FALSE
)

ants_mri_to_template(
  subject,
  template_subject = getOption("threeBrain.template_subject", "N27"),
  preview = FALSE,
  verbose = TRUE,
  ...
)

cmd_run_ants_mri_to_template(
  subject,
  template_subject = getOption("threeBrain.template_subject", "N27"),
  verbose = TRUE,
  dry_run = FALSE
)

ants_morph_electrode(subject, preview = FALSE, 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 'DenseRigid', 'Rigid', 'Affine', 'SyN', 'TRSAA', 'SyNCC', 'SyNOnly', or other types; see ants_registration

aff_metric

cost function to use for linear or 'affine' transform

syn_metric

cost function to use for 'SyN' transform

verbose

whether to verbose command; default is true

...

other arguments passed to ants_registration

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

template_subject

template to map 'MR' images

preview

whether to preview results; default is false

Value

Aligned 'CT' will be generated at the coreg_path path:

'ct_in_t1.nii.gz'

aligned 'CT' image; the image is also re-sampled into 'MRI' space

'transform.yaml'

transform settings and outputs

'CT_IJK_to_MR_RAS.txt'

transform matrix from volume 'IJK' space in the original 'CT' to the 'RAS' anatomical coordinate in 'MR' scanner; 'affine' transforms only

'CT_RAS_to_MR_RAS.txt'

transform matrix from scanner 'RAS' space in the original 'CT' to 'RAS' in 'MR' scanner space; 'affine' transforms only