# 	name of reference image
--ref=/cluster/tract/ayendiki/hcps/mgh_1035/dmri/dtifit_FA
# 	name of input image
--in=/usr/pubsw/packages/fsl/current/data/standard/FMRIB58_FA_1mm
# 	name of file containing affine transform
--aff=/autofs/space/hercules_001/users/ggrisot/hcps/mgh_1035/dmri/xfms/mni2fa.mat
# 	name of output file with field coefficients
--cout=/autofs/space/hercules_001/users/ggrisot/hcps/mgh_1035/dmri/xfms/mni2fa_warp
# If =1, use implicit masking based on value in --ref image. Default =1
--imprefm=1
# If =1, use implicit masking based on value in --in image, Default =1
--impinm=1
# Value to mask out in --ref image. Default =0.0
--imprefval=0
# Value to mask out in --in image. Default =0.0
--impinval=0
# sub-sampling scheme, default 4,2,1,1
--subsamp=8,4,2,2
# 	Max # of non-linear iterations, default 5,5,5,5
--miter=5,5,5,5
# FWHM (in mm) of gaussian smoothing kernel for input volume, default 6,4,2,2
--infwhm=12,6,2,2
# FWHM (in mm) of gaussian smoothing kernel for ref volume, default 4,2,0,0
--reffwhm=12,6,2,2
# Weight of regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
--lambda=300,75,30,30
# Estimate intensity-mapping if set, deafult 1 (true)
--estint=1,1,1,0
# (approximate) resolution (in mm) of warp basis in x-, y- and z-direction, default 10,10,10
--warpres=10,10,10
# Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
--splineorder=3
# If set (=1), lambda is weighted by current ssq, default 1
--ssqlambda=1
# Allowed range of Jacobian determinants, default 0.01,100.0
--jacrange=0.01,100
# Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
--regmod=bending_energy
# Model for intensity-mapping [none global_linear global_non_linear local_linear global_non_linear_with_bias local_non_linear]
--intmod=global_linear
# Order of poynomial for mapping intensities, default 5
--intorder=5
# Resolution (in mm) of bias-field modelling local intensities, default 50,50,50
--biasres=50,50,50
# Weight of regularisation for bias-field, default 10000
--biaslambda=10000
# Precision for representing Hessian, double or float. Default double
--numprec=double
# Image interpolation model, linear or spline. Default linear
--interp=linear
# If =1, ref image is used to calculate derivatives. Default =0
--refderiv=0