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I don't think it's an installation problem. I think you just need to make sure you have the original anatomical in the same folder as the skull-stripped anatomical that ends in "_brain". Example: anat.nii.gz anat_brain.nii.gz Hope this helps, David -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Ariana Anderson Sent: Monday, January 19, 2009 11:21 PM To: [log in to unmask] Subject: Re: [FSL] Nonlinear Registration "FEAT cannot find the whole-head image" Hello, I'm having a bit of trouble using the non-linear registration option in FSL, and I'm wondering if anyone has experienced this problem before. I was told this may be an installation problem. I'm using FSL 4.1.1 I'm getting the error: ======================= Warning: nonlinear registration is turned on but FEAT cannot automatically find the whole-head image related to the selected brain-extracted structural image 1 (this needs to end in "_brain"). If this is not changed, the non-linear registration will use brain-extracted images instead of whole-head images; this is suboptimal. =========== This happens when I use the FSL GUI and use Melodic. It doesn't seem to depend on the file I'm using, as I've received it with a few datasets. Thank you, Ariana