Hi there,
I have run my 1st level analysis with FEAT using FLIRT for the registration. Since I'd like to improve my registration, I was considering using FNIRT, running registration only from the FEAT gui and using the feat directories created by my first round of analyses. Just as a background info: since my functional data are acquired as a slab covering only a small part of the brain, I set up my initial struc as the whole brain functional image, the main structural as the T1 and then the corresponding standard space. I understand that for FNIRT to run properly, it needs to have the non-brain-extracted image and that needs to have the extension "*brain.nii". What is not clear to me: do I need to actually select this image, using the FEAT gui, for the main structural image? or does it simply just need to be in the same directory as my brain-extracted T1 image?
Thanks and best regards,
Hannah
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