All options with a double minus need an equals sign between the option and the argument, with no space. On 20 Dec 2011, at 14:04, Burzynska, Aga wrote: > > Dear experts, > I need to apply a transformation to my filtered_func_data to MNI standard space. > > The registration using FLIRT+FNIRT was done in the following way: > > Functional -> initial highres -> highres -> standard (MNI) > > I found help here > http://www.fmrib.ox.ac.uk/fsl/fnirt/combining_warps.html > > tried the command: > applywarp -i / /filtered_func_data.nii -r /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz -o MNIfnirt_filtered_func_data.nii -w / /reg/highres2standard_warp.nii --premat / /reg/example_func2highres.mat > > Which should combine the affine transformation from functional to highres, and then nonlinear warping from highres to standard. > > I get the error: > --premat: Missing non-optional argument! > > It also did not accept other format of arguments(I had to change from --in to -i), but I see no alternative for--premat. > > Can you help me with this? > > Thank you a lot! > Aga > --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------