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Hi Rosalia (see my last email regarding the rendered_thresh files). Did you select non-linear registration when you set up Feat? If so, you should have a file 'reg/example_func2standard_warp.nii.gz'. Pass this file to the 'applywarp' command to transform from the subject functional space to MNI152 space. For example: applywarp -i thresh_zstat1 -r $FSLDIR/data/standard/MNI152_T1_2mm -o thresh_zstat1_standard -w reg/example_func2standard_warp Cheers, Paul On 20 November 2016 at 21:43, Rosalia Dacosta Aguayo <[log in to unmask]> wrote: > Dear FSL experts, > > I have finally solved the problem regarding seeing the activations...just > was a problem with setting min and max values. > > The problem now is that I am trying to make a non linear registration with > fnirt setting the following: > > fnirt --ref=MNI152_T1_2mm_brain.nii.gz --in=rendered_thresh_zstat1.nii.gz > -aff=example_func2standard.mat --iout= rendered_thresh_zstat1_fnirted > > But it seems that there is something that does not work.... > > Any one of you could help me with this problem? > > Kind regards, > > Rosalia >