If you have the time you get an advantage of SNR with two reversed phase encoding directions and they will also even out the signal pileup and rarefaction that occurs together with distortion. As for half vs whole sphere, as I recall the recommendation originally for eddy was for the whole sphere, but that may have changed with newer versions.

Matt.

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Wagshul <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Thursday, July 11, 2019 at 1:58 PM
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] Advice for topup/DTI acquisition strategy

Dear FSL experts,

Hi. I have seen a number of posts about this, but was hoping one of the FSL experts could provide some insight/suggestions.

We are setting up a new DTI/NODDI protocol, and I would like to make sure that the acquisition strategy is optimal for FSL processing.

We plan on collecting three shells with a strategy similar to the ADNI protocol (this is in an elderly patient and control population), i.e. b = 500, 1000, and 2000, on 16, 32, and 64 directions respectively. What would you recommend collecting with respect to directions and/or reversed phase encodes? My initial thought was to collect two full data sets of A and P phase encodes for the entire data set, but I saw a recent post from Jesper indicating that there was not much advantage to collecting anything above just the b=0 acquisition with reversed phase encodes, at least with respect to topup.

Secondly, if you do recommend only collecting reversed b=0’s, what is the optimum strategy for the distribution of the individual shells, distributed over a half or whole sphere? The information on the FSL wiki would seem to indicate that it is preferable to collect over the whole sphere for large N’s, but I is this may only be relevant for tractography, not for standard DTI or NODDI processing?

Thanks for any suggestions of insights!

Best,

Mark

____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: [log in to unmask]

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