1. Is there a registration procedure in DTIPrep that performs an affine registration of the diffusion-weighted images prior to motion and eddy-currents correction?
2.When correcting for subject motion, if there is a rotation of the image involved in the image registration, then the same rotation must be applied to the encoding vectors. I wonder whether rotations that are applied to a given diffusion-weighted volume are also applied to the encoding vectors in DTIPrep automatic pipelines?
3. If SNR is not low, is denoising still recommended?

Originally posted by ameliaqian: 1. No, the affine registration happens during motion & eddy current correction. There is a rigid registration that happens for the baseline motion correction and averaging (just before the motion & eddy current correction).

2. of course, otherwise it would be incorrect. The motion & eddy current correction in DTIPrep is built on the same principles as FSL 5 (only the baseline motion correction is slightly different). (note, FSL 6 does things quite a bit differently)

3. We rarely do it, and it is off by default for DTIPrep, but it's available if users wish to do denoising. Older, low SNR diffusion data would probably benefit from denoising.