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What happens when there is movement between the beginning of the acquisition and the end? The field determined by the first top-up pair should no longer be valid.... What if one has multiple b=0 pairs interspersed in the acquisition sequence....is there some value to checking for movement and applying top-up inputs to several subseries of images separately? Stefano Marenco, MD NIMH/CBDB 10 Center Drive, Bldg 10 room 3C103 Bethesda MD 20892 Tel 301 435-8964 Fax 301 480-7795 Email: [log in to unmask] -----Original Message----- From: Jesper Andersson [mailto:[log in to unmask]] Sent: Tuesday, March 05, 2013 5:24 AM To: [log in to unmask] Subject: Re: [FSL] topup processing time Hi again Brian, > If one were to use topup to do all images (b=0 + 256 directions) with their blip reversed "partner", would combining these in one large acquisition file be the best way to do this in topup or would it be best to do each volume (i.e., direction or b=0) separately with it's reversed pair and then combine them all together in the end for input into eddy? at the moment (and probably for the future) eddy only takes a single topup-input (i.e. a single susceptibility off-resonance field). That means that if you use all pairs to calculate that field, there is till only that single field going in. The advantage of using more than a single pair of images for topup is only SNR, and that advantage rapidly disappears as you add more pairs. No matter how poor your SNR I don't think there is ever a case (in practice) for using more than five pairs as input into topup. As for eddy, note that it is the UNcorrected images that should be used as input to eddy. Jesper > > I understand that this is not the recommended approach, but I am trying to wrap my head around all the various possibilities and their relative impact. > > Thanks again. > Brian >