Hello! I have found a solution for the problem causing the bad registration.
In Freesurfer 5.0, the function mri_robust_template is used for registration creating the output volume rawavg.mgz when using the autorecon1 flag. It turns out, that in Freesurfer 4.0, this step is performed by the function mri_motion_correct.fsl and using this function instead of mri_robust_template, the registration works perfectly! The volumes I use have different intensity levels, and it may be the reason why mri_robust_template fails, since it require that the input images should all have the same intensity level. For other volumes not failing the registration, I have noticed that the resulting volume sometimes are more blurred when using v. 5.0 than v. 4.0. So, why is the registration step more robust in v. 4.0 than v. 5.0? Is it possible to change the autorecon1 script in v. 5.0, such that mri_motion_correct.fsl is used instead of mri_robust_template? Kind regards Nikolas
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