[Anand Joshi]

The SVReg registration module performs full anatomical alignment of subject to atlas. This alignment is much more accurate than AC-PC alignment. Can you please explain some more about why you want to do AC-PC alignment? Is it for visualization purpose?

[Vinny]

Yes that is correct, my goal is tractography. I’ve seen some process workflows use MIPAV for AC-PC alignment prior to diffusion weighted image preprocessing using TORTOISE, as part of the AFNI distribution.

[Anand Joshi]

For tractography and finding connectivity across regions, we do not need AC PC alignment in BrainSuite.
http://brainsuite.org/processing/diffusion/tractography/

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