Date: Thu, 14 Jul 2016 10:35:43 -0400 (EDT) From: Lilla Zollei lzollei@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] CVS question To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1607121530370.50358@semmelweis.nmr.mgh.harvard.edu Content-Type: text/plain; charset="utf-8"

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

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Thank you, I happened to try that after I had sent this help request, and yes, it works much, much better. The transformation to MNI space is highly warped, that I realize was the problem. Thank you for your help.