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