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(...)| 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 | 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 |