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We use skull stripped data, and we have attempted to create a stripped version of the single subject T1 canonical template with which to create a study-specific template from our images. We converted the original canonical .mnc T1 image, using mnc2ana, to Analyze format, stripped the skull, and coverted back to .mnc format using ana2mnc. The file was restored to its original orientation after we stripped it in Analyze. We ran the available script, cg_create_template.m, substituting our stripped template for T1.mnc in the script. We get the error message during the affine registration step in that program. Is there a problem occuring in the analyze to .mnc conversion that might have changed the orientation of the image? We cannot detect any other reason for this problem. In SPM2 Display, the stripped template looks the same as the original template provided by SPM2. We'd appreciate any ideas about this problem.