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Hi Jesper, Unfortunately, the result got even worse. I've added a picture illustrating the problem. The first row shows at left my reference image (181*181*217; 1*1*1mm^3) and at right my target image (256*256*256; 1*1*1 mm^3). The second row shows the result of FLIRT: this is OK. The third row shows at left the result of FNIRT with default settings. At right is the result with the schedule file you provided. How to proceed? Cheers, Ed  On 11 Jun 2013, at 1:00, FSL automatic digest system wrote: Date: Sun, 9 Jun 2013 17:46:52 -0700 From: Jesper Andersson <[log in to unmask]> Subject: Re: Bad registration with FLIRT&FNIRT Dear ed, I am not sure if MJ has replied to this one or not, but in case he hasn't. You still need to use a suitable configuration file. Try the one I have attached here by adding config=T1_2_T1.cnf to the fnirt command and let me know how it goes. Jesper