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