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Hi Christiane, What you can do is may be manual edit the MPRAGE and take out part out of the brain which is redundant. We had similar problems likes this but when we edited our MPRAGE especially by taking out fat bone marrow signal around dura we indeed got better registratio.This all can be done in FSL. Regards Sachin -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Christiane Jockwitz Sent: Tuesday, February 07, 2012 10:41 AM To: [log in to unmask] Subject: Re: [FSL] Linear vs. nonlinear registration Dear Mark, Unfortunately field maps were not acquired at the time of imaging. I tried to improve the brain extraction on the highres but I still have problems with the example_func to standard as well as the fMRI to standard space(see link). Is there any other possibility to better adjust the bold images to the structural images? Thank you very much. http://registrationchristianej.blogspot.com/2012/02/registration2.html Best regards, Christiane The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.