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Hi Giuseppe, Are you using 7 degrees of freedom? If so, you should use 6 dof for epi to T1 registration. The assumption is that the brain did not grow or shrink between the time you acquired the two scans. Thus you can register with translation and rotation, but no scaling. If this is not the problem then try 6 dof with mutual info. I always get significant registration errors in my brains when I use correlation ratio. cheers, jack ------------------------------ Jack Grinband, PhD Center for Mind & Brain Columbia University 518 PI Annex W. 168th St. NY, NY 10032 >Hi all > >I am trying to get an EPI registered to a T1 (both preprocessed with BET) >and no matter how many parameters I try to change, the results are not good: >the global whole-brain overlapping of the resulting images does not look bad >at first, but at a closer inspection, checking the ventricles and the gyry >overlapping, the registered EPI always ends up lying around 10 mm below the >T1. The images are of reasonable quality (at least to my eye), they cover >most of the brain and have a fairly high resolution (EPI=3x3x3mm, >T1=1x1x1mm). I could try and make a mask out of the ventricles, but I really >see no reason why the registration would fail with normal parameters under >such a standard situation. Did anybody come across the same problem? I'd >hate to have to resort to 'manual' registration....! > >thanks for any help > > giuseppe