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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