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Yes, they are treated as multiple measurements of the b=0 image, so having more of them will reduce the variance in the s0 quantity in the model. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Gary Turner Sent: Thursday, August 27, 2009 4:28 PM To: [log in to unmask] Subject: Re: [FSL] eddy correct & series averaging follow-up Thanks Matt, Does this imply that Dtifit/Bedpostx internally averages the b0s to improve the signal to noise in these reference images and, if not, how are the subsequent b0s (after the initial reference b0) treated? Cheers, Gary On Thu, Aug 27, 2009 at 9:13 AM, Matt Glasser <[log in to unmask]> wrote: It is not necessary to move all the bvalues to the front and average them (unless you plan to use some software that requires it). You should do any averaging after some form of motion correction (which eddy_correct does). Peace, Matt. -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Gary Turner Sent: Thursday, August 27, 2009 10:53 AM To: [log in to unmask] Subject: [FSL] eddy correct & series averaging follow-up Hi all, Just a quick query following up on exchange posted a wile back about the order of EC correct and series averaging ... **** Mike Cohen: "I have a 60-direction DTI scan that is repeated 3x for subsequent averaging ... Is it better to run eddy_correct on each of three acquisitions and then average them, or average them first and then run eddy_correct?" T. Behrens: We have exactly the same data - what we do is merge all data sets into a single big 4D file, run eddy_correct on this big file, then split it up into 3 averages and average these. **** I have the same protocol (only 30 dirs due to time constraints unfortunately). I have interleaved b0s throughout the 30 diffusion weighted scans which I average and move to the beginning of the diffusion weighted scans for subsequent processing. Should I do this before eddy_current correction? Or should I run EC on the whole dataset as acquired, referencing the first b0 acquisition, and then do the averaging for both diffusion and non-diffusion-weighted volumes as per the response above? Many thanks, Gary _______________ Gary Turner, Ph.D. Helen Wills Neuroscience Institute University of California, Berkeley 132 Barker Hall Berkeley, CA 94720-3190 -- Gary Turner, Ph.D. Helen Wills Neuroscience Institute University of California, Berkeley 132 Barker Hall Berkeley, CA 94720-3190 (w) 510.642.3004 (c) 510.407.6750 (fx) 510.643.3516