FREESURFER MRICoreg — ni_freesurfer_mri

This program registers one volume to another

Usage

ni_freesurfer_mri_coreg(
  reference_file,
  source_file,
  subject_id,
  args = NULL,
  brute_force_limit = NULL,
  brute_force_samples = NULL,
  conform_reference = NULL,
  dof = NULL,
  ftol = NULL,
  initial_rotation = NULL,
  initial_scale = NULL,
  initial_shear = NULL,
  initial_translation = NULL,
  linmintol = NULL,
  max_iters = NULL,
  no_brute_force = NULL,
  no_coord_dithering = NULL,
  no_cras0 = NULL,
  no_intensity_dithering = NULL,
  no_smooth = NULL,
  num_threads = NULL,
  out_lta_file = TRUE,
  out_params_file = NULL,
  out_reg_file = NULL,
  ref_fwhm = NULL,
  reference_mask = NULL,
  saturation_threshold = NULL,
  sep = NULL,
  source_mask = NULL,
  source_oob = NULL,
  subjects_dir = NULL,
  .cwd = NULL,
  .env = NULL,
  .engine = NULL,
  .profile = NULL,
  dry_run = FALSE,
  echo = interactive()
)

Arguments

reference_file: Character; file path. reference (target) file Required.
source_file: Character; file path. source file to be registered Required.
subject_id: Character. freesurfer subject ID (implies reference_mask == aparc+aseg.mgz unless otherwise specified) Required.
args: Character. Additional parameters to the command
brute_force_limit: Numeric. constrain brute force search to +/- lim
brute_force_samples: Integer. number of samples in brute force search
conform_reference: Logical. conform reference without rescaling
dof: Character; one of: "6", "9", "12". number of transform degrees of freedom
ftol: Numeric. floating-point tolerance (default=1e-7)
initial_rotation: Character or numeric vector. initial rotation in degrees
initial_scale: Character or numeric vector. initial scale
initial_shear: Character or numeric vector. initial shear (Hxy, Hxz, Hyz)
initial_translation: Character or numeric vector. initial translation in mm (implies no_cras0)
linmintol: Numeric
max_iters: Character. maximum iterations (default: 4)
no_brute_force: Logical. do not brute force search
no_coord_dithering: Logical. turn off coordinate dithering
no_cras0: Logical. do not set translation parameters to align centers of source and reference files
no_intensity_dithering: Logical. turn off intensity dithering
no_smooth: Logical. do not apply smoothing to either reference or source file
num_threads: Integer. number of OpenMP threads
out_lta_file: Character or numeric vector. output registration file (LTA format)
out_params_file: Character or numeric vector. output parameters file
out_reg_file: Character or numeric vector. output registration file (REG format)
ref_fwhm: Numeric. apply smoothing to reference file
reference_mask: Character or numeric vector. mask reference volume with given mask, or None if False
saturation_threshold: Character. saturation threshold (default=9.999)
sep: Character or numeric vector. set spatial scales, in voxels (default [2, 4])
source_mask: Character. mask source file with given mask
source_oob: Logical. count source voxels that are out-of-bounds as 0
subjects_dir: Character; directory path. FreeSurfer SUBJECTS_DIR
.cwd: Working directory override.
.env: Named character vector of environment variables.
.engine: Execution engine override.
.profile: Runtime profile override.
dry_run: Logical; preview command without executing.
echo: Logical; echo stdout/stderr in real time.

Value

An ni_result object.