Hi AFNI experts,
I don't know how to express this DTI question in proper mathematical terms, but I hope you'll know what I'm getting at.
3dDWItoDT calculates the principal direction tensors from gradient vectors and DWI data. However, since the gradient vectors are expressed in reference to the scanner bore, not the subject's head, the principal direction tensors are also expressed with reference to the scanner, not the subject. If I want the principal direction tensors to be matched to the principal directions of the subject's head, I think I need to use something like 3dWarpDrive in rotation-translation mode to align my subject in space, and apply the matrix from that also to the gradient vectors before using 3dDWItoDT. I was wondering whether you had already written a script to do this, and also whether you could point me to any useful educational materials on DTI that address this question.
I appreciate your help, and please let me know if this question doesn't make sense, or if you think I don't understand what's going on.
Thanks,
Sally