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Hi Jasper, We tried your suggestion of using the T2 instead of having a blip-up and blip-down b0. However, we have some concerns because the "eddy" data appears to be distorted. Given that we acquired our images using right to left encoding, our acqparams.txt had to be changed to reflect this. The fourth element was also changed using the formula suggested on FSL website (the "dwell time" multiplied by "number of PE steps -1"). This is what our acqparams.txt file looks like. -1 0 0 0.113 1 0 0 0.113 Is this correct? Should the top row have a positive 1 because we don't have a blip up and down, but have a t2 instead? Thank you for all of your help, Colleen -----Original Message----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Jesper Andersson Sent: Friday, October 07, 2016 6:56 AM To: [log in to unmask] Subject: Re: [FSL] Can eddy be used on our DTI data? Dear Colleen, > I would like to know if it is possible to use "eddy" on our data. Our DTI images were acquired with single-shot EPI (SENSE factor 2.5) on a 3T 'Acheiva' scanner (Philips, Best, the Netherlands). Two runs were collected in each subject, with 32 gradient directions (b = 800 s/mm3) and one b0 in each run. Sixty 2.2-mm axial slices were acquired for each volume, with 0.9 mm in-plane reconstructed resolution. We also acquired a non-EPI axially acquired T2-weighted image. Is it possible to average the two runs together and then run eddy? Can we still use eddy even though we do not have opposite phase encoding directions? yes, eddy does not require opposing PE directions. How well it works will depend a little on how your b-vecs are distributed. I know that some Phillips protocols have a rather funny distribution of b-vecs and I have seen problems with running eddy on such data sets. You do need at least one pair of b0 volumes with opposing PE directions if you want to run topup in order to estimate the susceptibility induced off-resonance field. If you have that, you can then pass the topup output (field estimate) into eddy, which means that eddy will correct the data also for susceptibility distortions. If you don't have that, you can still run eddy and correct your data for eddy currents and movement. In your case, if the contrast in your T2-image is sufficiently similar to the b0-images, you may be able to use your T2 in lieu of a reversed-PE b0. In that case you stick one of your b0:s followed by the T2 image in a 4D file and make an acqparams.txt file looking something like 0 1 0 0.05 0 -1 0 0.00005 provided that the PE-direction in your EPI images is A<->P (if it is in the L<->R direction you put the 1 and -1 in the first column instead). Jesper > Thanks, > Colleen Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.