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I assume that you mean bringing scans from lots of subjects into a common alignment. I'd suggest the following paper as a starting point: Klein, Arno, Jesper Andersson, Babak A. Ardekani, John Ashburner, Brian Avants, Ming-Chang Chiang, Gary E. Christensen et al. "Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration." *Neuroimage* 46, no. 3 (2009): 786-802. The old SPM algorithms did not do so well in the above comparison (ie the Normalise button in anything prior to SPM12). SPM's Dartel did well with some of the datasets, but less well on others where the SPM segmentation had struggled with scans that were too closely skull-stripped. A more recent evaluation of Dartel (with some of the same data as in Klein et al) is presented in: Ashburner, John, and Karl J. Friston. "Diffeomorphic registration using geodesic shooting and Gauss–Newton optimisation." *NeuroImage* 55, no. 3 (2011): 954-967. Best regards, -John On 30 October 2015 at 11:47, Raphael F.C. <[log in to unmask]> wrote: > Dear all, > > What is the best method to register images? > > FreeSurfer traditional > FreeSurfer CVS > SPM coregistration > FSL FLIRT/FNIRT > ANTs SyN > Another one that I did not mention? > > I just would like to position a seed in the template (e.g., the anterior > nucleus of the thalamus) and be sure that it is going to be (at least a > little) in that structure for every person. Am I being too ambitious? > > I found some papers on the web, but maybe it was a shallow research and I > did not find a winner. It seems that SyN and FreeSurfer's traditional > method are better than the others, but I am not sure of it, specially for > subcortical areas. > > Any ideas? > > Sorry for such a basic/controversial question, > All the best > -- > Raphael F. Casseb > Medical Physicist, Ph.D. Student > Medical Physics Lab - University of Campinas > Contact: +55 19 3521-8246 >