Hi Michael,

I want to compare two populations using CVS so I can cross-register multimodal maps (e.g. ASL, FA, QSM) for volumetric comparisons.

I’ve gotten CVS to work very well registering one subject to another, it really is impressive

However, using the --mni option, it doesn’t work so well, perhaps because the atlas is so averaged together and smoothed out, the images look highly warped.

I know I can pick a subject at random, and register everything to that, but that may induce some biases. The following website suggests I might try simply creating my own atlas (under the answers to Nov 2014 course questions): https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers

Seems like they register 40 subjects with each other for multiple iterations, average the brain together, then run recon-all on that. How does one actually do that, however? i.e. 1st round, register everyone to subject 1 … then what? Seems like somehow you would want a registration intermediate point somehow?

Have you tried to use the default cvs atlas? If you do not indicate any explicit targets that is what will get used. I think that might be a solution that you are looking for.

Lilla