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Dear Jesper, Thanks for your complete guide. By the way, using topup and then eddy preserved the phase encoding images, that resulted in 2 sets of images (LR and RL phase encoding), while performing apply topup made just one set images. I really dont know which one is better ? I mean one corrected set or 2 corrected set with phase encoding? I would appreciate if you could help me. Thanks From: Jesper Andersson <[log in to unmask]> To: [log in to unmask] Date: Wed, 2 Jan 2019 10:36:18 +0000 Subject: Re: [FSL] What is the order of applying top-up and eddy correction? Dear Mahshid, if you intend to run eddy you don’t need to run applytopup at all. eddy does everything that applytopup does, and a lot more (such as also correcting for eddy currents and subject movement). The main reason that applytopup exists at all is because topup was written and released well before eddy was released, so there needed to be some way of applying the field estimated by topup. Jesper On 29 Dec 2018, at 23:46, Mahshid Fouladivanda <[log in to unmask]> wrote: Dear FSL Experts, I have just started to analyze an unprocessed data which contains 2 set of images (one set constitutes of 1 b0 volume and 80 dwi volume with right to left and the other set has the same volumes but with inverse phase encoding (totally, 81 volume R2L and 81 L2R)). First of all, I should have preprocessed them using top up and eddy correction in order to have a corrected distortion and movement data that is usefull for other process in future as registration with structural images. Thus, I ran the top up and determined the field of distortion. In continue I was wonder to apply the "eddy correction" on the 4D unprocesse image (merging b0, volume of RL, b0 and volume of LR) with corresponding index, bvecs, bvals and topup result, then applying "apply topup" on the output of the eddy???? or applying "apply topup" on the unprocesse images then just performing eddy correction???? finally I decided to perform the second solution (topup>>applytopup>>eddy correction), unfortunately there was a problem. Using GUI for eddy correction needs my topup results (distortion field) as input that caused in sever deformation on the output. So I used the terminal to perform command (eddy) in order to delete --topup basename input, then I faced with error said: command eddy not found !!!!!!!!!!!! That was odd, since before I have ran the topup command in terminal and it worked! By the way, as I read in the archive of the mailing list, "eddy correction" and "apply topup" should not be applied sequentially on a data set. I don't really know why??!! I would appreciated if anybody could help me. Regards Mahshid To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1