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I have two ROIs in MNI space, one is the seed mask and the other is the target. I can get the matrix from MNI to DTI space by using the registration tool in FDT. Is this matrix from nonlinear or linear registration? All I can see is 12 DOF between MNI and DTI, does that mean it only do the affine transformation?  

If I wanna give the nonlinear registration between MNI and DTI, so can the registation tool do that and what should I do?

Thanks.

Ran