Hello Zack
I’m going to write my answer assuming we’re thinking of the same dataset, namely the HCP young adult 1200 subjects release. If not, then you should probably disregard this answer as I don’t know about all the other HCP data releases…
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The HCP data does include a transform file for registering the dMRI data to MNI space, although it’s not completely obvious. Here are two threads (files, transform) that should help you get your dMRI data into MNI space.
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The diffusion data is already preprocessed (incl. motion, EPI distortion, eddy current corrections etc.; the manual has the exact details), so you shouldn’t need to do any further preprocessing. But in general, resampling should be done after preprocessing, and definitely after
dwidenoiseandmrdegibbs.
If you’re referring to e.g. tensor fitting or running CSD, then I would personally resample the DWI data before any model fitting, but mainly for reasons of storage and processing efficiency (in the current case of downsampling high resolution data). I’ve seen work specifically justifying upsampling before model fitting instead of after, but I don’t know of any scientific considerations about when to downsample…
Hope that’s helpful!
Fiona