Skip to contents

Coregister an atlas volume to a FreeSurfer subject

Source: R/coregister_volume.R
coregister_volume.Rd

Computes a rigid-plus-scale registration from a volumetric atlas onto a FreeSurfer subject's T1 grid (e.g. cvs_avg35_inMNI152) using mri_coreg. The resulting LTA can be reused by mri_vol2vol to resample the atlas (or any volume in the same source space) onto the target's grid, which is the first step toward producing subcortical atlases that show realistic brain-outline anatomical context in their 2D slices.

Usage

coregister_volume(
  input_volume,
  target_subject = "cvs_avg35_inMNI152",
  target_volume = "brain",
  output_lta = NULL,
  dof = 12,
  binarise = TRUE,
  subjects_dir = freesurfer::fs_subj_dir(),
  skip_existing = FALSE,
  verbose = get_verbose()
)

Arguments

input_volume

Path to the atlas volume to coregister, or an RNifti object.

target_subject

FreeSurfer subject name to register to. Defaults to "cvs_avg35_inMNI152", which is in MNI152 1mm space.

target_volume

Name of the volume in the subject's mri/ directory used as the registration target. Defaults to "brain" (i.e. brain.mgz).

output_lta

Path to write the resulting LTA file. Defaults to a temporary file.

dof

Degrees of freedom for mri_coreg (6, 9, or 12). Defaults to 12 (rigid + per-axis scale + shear).

binarise

Logical. If TRUE (default), binarise both volumes before coregistration. Set to FALSE to register on raw intensities.

subjects_dir

FreeSurfer SUBJECTS_DIR. Defaults to freesurfer::fs_subj_dir().

skip_existing

Skip generating output files that already exist, allowing interrupted atlas creation to resume. If not specified, uses options("ggseg.extra.skip_existing") or the GGSEG_EXTRA_SKIP_EXISTING environment variable. Default is TRUE.

verbose

Verbosity level: 0 (silent), 1 (standard progress, default), or 2 (debug, includes FreeSurfer output). Logical values are accepted (TRUE = 1, FALSE = 0). If not specified, uses the value from options("ggseg.extra.verbose") or the GGSEG_EXTRA_VERBOSE environment variable.

Value

Path to the LTA file (invisibly).

Details

Both volumes are binarised (any non-zero voxel becomes brain) before coregistration so that the alignment is driven by tissue extent rather than label values. To skip the binarisation and align using raw intensities, set binarise = FALSE.

See also

project_volume_anatomical(), prepare_subcortical_anatomical()

Examples

if (FALSE) { # \dontrun{
lta <- coregister_volume(
  input_volume = "shen_2mm_268_parcellation.nii.gz",
  target_subject = "cvs_avg35_inMNI152"
)
} # }