spm12_coregister: Batch SPM12 Coregister (Estimate and Reslice)

In muschellij2/spm12r: Wrapper Functions for 'SPM' (Statistical Parametric Mapping) Version 12 from the 'Wellcome' Trust Centre for 'Neuroimaging'

Batch SPM12 Coregister (Estimate and Reslice)

Description

Performs SPM12 coregistration estimation and reslicing on an Image

Usage

build_spm12_coregister(
  fixed,
  moving,
  other.files = NULL,
  cost_fun = c("nmi", "ecc", "ncc"),
  separation = c(4, 2),
  tol = c(0.02, 0.02, 0.02, 0.001, 0.001, 0.001, 0.01, 0.01, 0.01, 0.001, 0.001, 0.001),
  fwhm = c(7, 7),
  interp = c("bspline4", "nearestneighbor", "trilinear", paste0("bspline", 2:3),
    paste0("bspline", 5:7)),
  wrap_x = FALSE,
  wrap_y = FALSE,
  wrap_z = FALSE,
  mask = FALSE,
  prefix = "r",
  verbose = TRUE,
  ...
)

build_spm12_coregister_estimate(
  fixed,
  moving,
  other.files = NULL,
  cost_fun = c("nmi", "ecc", "ncc"),
  separation = c(4, 2),
  tol = c(0.02, 0.02, 0.02, 0.001, 0.001, 0.001, 0.01, 0.01, 0.01, 0.001, 0.001, 0.001),
  fwhm = c(7, 7),
  verbose = TRUE,
  ...
)

build_spm12_coregister_reslice(
  fixed,
  moving,
  interp = c("bspline4", "nearestneighbor", "trilinear", paste0("bspline", 2:3),
    paste0("bspline", 5:7)),
  wrap_x = FALSE,
  wrap_y = FALSE,
  wrap_z = FALSE,
  mask = FALSE,
  prefix = "r",
  verbose = TRUE,
  ...
)

spm12_coregister_wrapper(
  ...,
  func = c("build_spm12_coregister", "build_spm12_coregister_reslice",
    "build_spm12_coregister_estimate"),
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  outdir = NULL,
  install_dir = NULL
)

spm12_coregister(
  ...,
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  outdir = NULL,
  install_dir = NULL
)

spm12_coregister_estimate(
  ...,
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  outdir = NULL,
  install_dir = NULL
)

spm12_coregister_reslice(
  ...,
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  outdir = NULL,
  install_dir = NULL
)

Arguments

fixed	File that is assumed fixed
moving	moving file to be registered to fixed space
other.files	Other files to register to fixed, in same space as moving file
cost_fun	Cost function
separation	The average distance between sampled points (in mm). Can be a vector to allow a coarse registration followed by increasingly fine
tol	The accuracy for each parameter. Iterations stop when differences between successive estimates are less than the required
fwhm	Gaussian smoothing to apply to the 256x256 joint histogram. Other information theoretic coregistration methods use fewer bins,
interp	Interpolator for sampling in fixed space
wrap_x	wrap in x-direction
wrap_y	wrap in y-direction
wrap_z	wrap in z-direction
mask	Mask the data. With masking enabled, the program searches through the whole time series looking for voxels which need to be sampled from outside the original images. Where this occurs, that voxel is set to zero for the whole set of images
prefix	Prefix to append to front of image filename
verbose	Print diagnostic messages
...	Additional arguments to pass to run_matlabbatch
func	not used
add_spm_dir	Add SPM12 directory from this package
spmdir	SPM dir to add, will use package default directory
clean	Remove scripts from temporary directory after running
outdir	Directory to copy results. If full filename given, then results will be in dirname(filename)
install_dir	directory to download SPM12

Value

List of output files, the matlabbatch object, and the script

Examples

## Not run: 
fname = paste0("~/Desktop/D2/scratch/", 
"100-318_20070723_0957_CT_3_CT_Head-_SS_0.01_SyN_ROI.nii.gz")
spm = spm12_coregister(
fixed = fname,
moving = fname, 
other.files = fname,
execute = FALSE)

## End(Not run)
if (matlabr::have_matlab()) {
install_dir = tempdir()
dims = rep(10, 3)
fixed = array(rnorm(prod(dims)), dim = dims)
fixed = oro.nifti::nifti(fixed)
moving = array(rnorm(prod(dims)), dim = dims)
moving = oro.nifti::nifti(moving) 
res = build_spm12_coregister(
fixed = fixed, moving = moving,
install_dir = install_dir)
}

muschellij2/spm12r documentation built on Aug. 31, 2022, 9:49 p.m.