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Register a T1w image to a T1w template with a pinned preset

Source: R/ni_ants_template.R
ni_ants_register_to_template.Rd

Runs antsRegistration (Rigid, Affine, then SyN) with a schedule from ni_ants_template_preset(), writing the moving image resampled into the template and the ITK composite transforms (<prefix>Composite.h5 and <prefix>InverseComposite.h5), the form fMRIPrep writes.

Usage

ni_ants_register_to_template(
  fixed_image,
  moving_image,
  output_prefix,
  preset = c("precise", "testing"),
  ...,
  .cwd = NULL,
  .env = NULL,
  .engine = NULL,
  .profile = NULL,
  timeout = Inf,
  dry_run = FALSE,
  echo = interactive()
)

Arguments

fixed_image

The template (reference) image, usually brain-extracted.

moving_image

The T1w image to register, brain-extracted like the template.

output_prefix

Path prefix for the transforms and the warped image (<prefix>Warped.nii.gz).

preset

Preset name; see ni_ants_template_preset().

...

Named ants.registration inputs that replace preset values whole, e.g. random_seed = 1 or fixed_image_mask = "mask.nii.gz". NULL removes a preset value. Related values are not adjusted: replacing metric keeps the preset's radius_or_number_of_bins. Giving initial_moving_transform drops the preset's initial_moving_transform_com, since only one initialisation applies.

.cwd

Working directory override.

.env

Named character vector of environment variables.

.engine

Execution engine override.

.profile

Runtime profile override.

timeout

Seconds before the registration is stopped.

dry_run

Logical; preview command without executing.

echo

Logical; echo stdout/stderr in real time.

Value

An ni_result (or an execution plan when dry_run = TRUE).

Details

This is a named preset, not the default of ni_ants_registration(): the "precise" schedule is tuned for about 1 mm T1w-to-template registration and is the wrong schedule for other modalities or resolutions. A registration can run, write a transform, and not fold while still stopping at a poor optimum, so check it with ni_ants_registration_qa().

See also

ni_ants_registration_qa()

Examples

if (FALSE) { # \dontrun{
reg <- ni_ants_register_to_template(
  fixed_image = "/data/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz",
  moving_image = "/data/sub-01_desc-brain_T1w.nii.gz",
  output_prefix = "/data/out/sub-01_from-T1w_to-MNI_"
)
ni_ants_registration_qa(reg,
  fixed_mask = "/data/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz",
  moving_mask = "/data/sub-01_desc-brain_mask.nii.gz"
)
} # }