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Hi Eugenio,

Thanks for your reply. Just to check if I've understood correctly, these can be the steps by using mri_easyreg:

*Linear (with --affine-only):*

1. Register all the subjects to the MNI (subj_to_MNI_lin_1) 2. Average the subj_to_MNI_lin_1s to reach a new template (MNI_mod_lin_1) 3. Register subj_to_MNI_lin_1s to MNI_mod_lin_1 and achieve subj_to_MNI_lin_2 and MNI_mod_lin_2 (and repeat it 5-6 times)

*NonLinear:*

1. Register subj_to_MNI_lin_5s to MNI_mod_lin_5 nonlinearly to achieve subj_to_MNI_nlin_1 and MNI_modified_nlin_1. 2. Repeat the steps similarly 5 times.

Correct? I also have another question: Should I do the linear-nonlinear in an interleaved manner or first linear registrations iterations and then non-linear?

Best, Amir