SPM12 Segment

Performs SPM12 Segmentation on an Image

spm12_segment(
  filename,
  set_origin = TRUE,
  biasreg = 0.001,
  biasfwhm = 60,
  native = TRUE,
  dartel = FALSE,
  modulated = FALSE,
  unmodulated = FALSE,
  bias_field = FALSE,
  bias_corrected = FALSE,
  n_gaus = c(1, 1, 2, 3, 4, 2),
  smoothness = 0,
  sampling_distance = 3,
  regularization = c(0, 0.001, 0.5, 0.05, 0.2),
  affine = c("mni", "eastern", "subj", "none"),
  mrf = 1,
  def_inverse = TRUE,
  def_forward = TRUE,
  warp_cleanup = c("light", "none", "thorough"),
  retimg = TRUE,
  add_spm_dir = TRUE,
  spmdir = spm_dir(verbose = verbose, install_dir = install_dir),
  clean = TRUE,
  verbose = TRUE,
  reorient = FALSE,
  install_dir = NULL,
  ...
)

Arguments

filename	File to be segmented
set_origin	Run acpc_reorient on image first. Warning, this will set the orientation differently
biasreg	Amount of bias regularization
biasfwhm	FWHM of Gaussian smoothness of bias.
native	Keep tissue class image (c*) in alignment with the original.
dartel	Keep tissue class image (rc*) that can be used with the Dartel toolbox .
modulated	Keep modulated images. Modulation is to compensate for the effect of spatial normalisation.
unmodulated	Keep unmodulated data
bias_field	save a bias corrected version of your images
bias_corrected	save an estimated bias field from your images
n_gaus	The number of Gaussians used to represent the intensity distribution for each tissue class. Can be 1:8 or infinity
smoothness	FWHM of smoothing done
sampling_distance	smoothness of the warping field. This is used to derive a fudge factor to account for correlations between neighbouring voxels. Approximate distance between sampled points when estimating the model parameters.
regularization	parameters for warping regularization
affine	Space to register the image to, using an affine registration
mrf	strength of the Markov random field. Setting the value to zero will disable the cleanup.
def_inverse	keep the inverse deformation field
def_forward	keep the forward deformation field
warp_cleanup	Level of cleanup with the warping. If you find pieces of brain being chopped out in your data, then you may wish to disable or tone down the cleanup procedure.
retimg	Logical indicating if image should be returned or result from run_matlab_script
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
verbose	Print diagnostic messages
reorient	if retimg=TRUE pass to readNIfTI
install_dir	directory to download SPM12
...	Arguments passed to run_spm12_script

Value

List of output files (or niftis depending on retimg), output matrix, and output deformations.