topup: topup - calling FSL topup

In neuroconductor-devel/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Description

A tool for estimating and correcting susceptibility induced distortions

Usage

topup(
  infile,
  datain,
  out = NULL,
  fout = NULL,
  iout = NULL,
  logout = NULL,
  warpres = 10,
  subsamp = 1,
  fwhm = 8,
  config = NULL,
  miter = 5,
  lambda = NULL,
  ssqlambda = 1,
  regmod = c("bending_energy", "membrane_energy"),
  estmov = 1,
  minmet = c(0, 1),
  splineorder = c(3, 2),
  numprec = c("double", "float"),
  interp = c("spline", "linear"),
  scale = c(0, 1),
  regrid = c(0, 1),
  verbose = TRUE
)

fsl_topup(...)

Arguments

infile	name of 4D file with images
datain	name of text file with PE directions/times
out	base-name of output files (spline coefficients (Hz) and movement parameters)
fout	name of image file with field (Hz)
iout	name of 4D image file with unwarped images
logout	Name of log-file
warpres	(approximate) resolution (in mm) of warp basis for the different sub-sampling levels, default 10
subsamp	sub-sampling scheme, default 1
fwhm	FWHM (in mm) of gaussian smoothing kernel, default 8
config	Name of config file specifying command line arguments
miter	Max # of non-linear iterations, default 5
lambda	Weight of regularisation, default depending on ssqlambda and regmod switches. See user documentation.
ssqlambda	If set (=1), lambda is weighted by current ssq, default 1
regmod	Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
estmov	Estimate movements if set, default 1 (true)
minmet	Minimisation method 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient, default 0 (LM)
splineorder	Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
numprec	Precision for representing Hessian, double or float. Default double
interp	Image interpolation model, linear or spline. Default spline
scale	If set (=1), the images are individually scaled to a common mean, default 0 (false)
regrid	If set (=1), the calculations are done in a different grid, default 1 (true)
verbose	Print diagnostic information while running
...	arguments passed to topup if using fsl_topup

neuroconductor-devel/fslr documentation built on May 6, 2021, 1:44 p.m.