spm12_coregister: Batch SPM12 Coregister (Estimate and Reslice)

Description Usage Arguments Value Examples

View source: R/zzz_batch_spm12_coregister.R

Description

Performs SPM12 coregistration estimation and reslicing on an Image

Usage

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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

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## 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)
}

neuroconductor-devel/spm12r documentation built on April 30, 2019, 1:13 p.m.