I have some questions concerning denoising procedure in DTIPrep. Denoise is one of good practice. However, I found there is no difference of the excluded gradients between with and without denoising procedure. 
1. I noticed there is *_DenoiseInput.nrrd file created. I wonder whether and how this denoised file is linked to the DTIPrep output.
2. Is Rician noise removal the same as smoothing in DTIPrep?

Originally posted by ameliaqian:
the denoising in DTIPrep is achieved via the Slicer modules for DWI denoising (these are no longer included in the newer versions of Slicer, not sure why).
https://www.slicer.org/wiki/Documentation/4.4/Modules/DWIJointRicianLMMSEFilter
https://www.slicer.org/wiki/Documentation/4.4/Modules/DWIRicianLMMSEFilter

Both are based on Rician noise
Martin