My "hifi" data is 30 directions, 2x2x2, whole brain.

Your website says the following: "topup is a tool for estimating the susceptibility induced field. In order to estimate and correct also for EC-induced distortions one will either need to run a tool like e.g. eddy_correct prior to running applytopup. Or one can feed the output from topup into the eddy tool."

Elsewhere, I have read that eddy is for data with more than 30 directions.

So, my question is, should I be running eddy_correct before topup and applytopup

That would work.

OR
eddy_correct after topup/applytopup

That would NOT work as eddy_correct knows nothing about topup.

OR
eddy after topup/applytopup

That would work, provided you have enough directions and diffusion has been sampled on the whole sphere. You can search the archives for an explanation of the difference between sampling on the whole sphere and the half sphere.

I think that with 30 directions you might struggle with eddy, but it can never hurt to test.

Good luck Jesper

OR
something else?

Thanks for all your help...I want to make sure I make optimal use of these new tools.

-Dianne

--
Dianne Patterson, Ph.D.
Research Scientist
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University of Arizona
Speech and Hearing Science 314
1131 E 2nd Street, Building #71
(Just East of Harvill)
621-9877

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