topup - calling FSL topup — topup • fslr

A tool for estimating and correcting susceptibility induced distortions

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