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Hi, as a follow up, you may want to clarify what you mean by "matching". For the template and the T1 to be in rough alignment (same orientation), you can do as Donald suggested below, or try coregistration. A closer matching, so that regions in the original brain can be considered (well... ;) to correspond to regions in the template, is called spatial normalization. You will find loads of information on either procedure in the spm manual, the list's archive, and the online spm bibliography, which are the usual places to start. Cheers, Marko MCLAREN, Donald wrote: > Set the origin and rotation to match the template. The origin should > be at the AC. > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Research Fellow, Department of Neurology, Massachusetts General Hospital and > Harvard Medical School > Postdoctoral Research Fellow, GRECC, Bedford VA > Website: http://www.martinos.org/~mclaren > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at (773) > 406-2464 or email. > > > On Thu, Nov 22, 2012 at 7:53 PM, SUBSCRIBE SPM Palermo > <[log in to unmask]> wrote: >> Hello all >> Relative beginner to SPM and fMRI in general. One participant's activation is quite considerably off the atlas. The preprocessed T1 images seem to be falsely aligned. How can I reorient all T1 and activation images to match the templates? >> Any help is greatly appreciated. > -- ____________________________________________________ PD Dr. med. Marko Wilke Facharzt für Kinder- und Jugendmedizin Leiter, Experimentelle Pädiatrische Neurobildgebung Universitäts-Kinderklinik Abt. III (Neuropädiatrie) Marko Wilke, MD, PhD Pediatrician Head, Experimental Pediatric Neuroimaging University Children's Hospital Dept. III (Pediatric Neurology) Hoppe-Seyler-Str. 1 D - 72076 Tübingen, Germany Tel. +49 7071 29-83416 Fax +49 7071 29-5473 [log in to unmask] http://www.medizin.uni-tuebingen.de/kinder/epn/ ____________________________________________________