afni.nimh.nih.gov

Hi pt,

Thanks for the response! I have attached the output here. It looks like the initial alignment is not great. I tested using "-init_xform AUTO_CENTER" with the @auto_tlrc command just to check, but the same result occurred (convergence not being reached and output being warped). And yes, this is an fMRI processing pipeline. I think the "-xform shift_rotate_scale" option works well for us, my main question is whether it can be applied automatically like it says in the help file (since it would save a lot of time re-running subjects!).

Sincerely,
Ian