Hi, I find myself in a situation where my collaboration provides only preprocessed eddy-corrected dwi data (no denoising/deringing).
I’m aware that based on this post andthis post the recommended preprocessing order seems to be
- dwidenoise
- (mrdegibbs)
- dwipreproc
- dwibiascorrect
Nevertheless, I wonder if there are any definite arguments against running
- eddy
- dwidenoise
- mrdegibbs
- dwibiascorrect
in a situation where only eddy-corrected data is accessible. I understand that dwidenoise operates based on the uncorrelated noise assumption in p and q space, so it will perform worse due to some possible interpolation from the previous command. Visual inspection shows an improvement after the denoising, so I think it should still be better than not running it at all. Would be very interested in experiences or opinions on the topic.