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Dear Mark, I see, thank you so much for this clarification! All the best, Julia On 06/23/2014 05:22 PM, Mark Jenkinson wrote : > Dear Julia, > > If your fieldmap and FMRI images are already in alignment then you can use applytopup directly (and this is usually done for DWI scans where the fieldmap pair is derived from the same sequence as the DWI scans). However, if you want to account for any potential shift between the FMRI and DWI (which could happen if you changed FOV or resolution, as well as due to subject motion) then you are better off using epi_reg. > > Also, if you want to register your FMRI to your structural then you will need to use epi_reg as applytopup does not perform this registration. > > All the best, > Mark > > > > On 21 Jun 2014, at 18:03, julia <[log in to unmask]> wrote: > >> Hi, >> >> I would like to ask for clarification about statements concerning topup and applytopup for fMRI data on this list. >> >> In the course of a previous discussion, Mark told me in order to use topup for distortion correction in fMRI images I would have to use the field derived from it like a fieldmap in epireg: >> Item 061269 >> 2014-05-06 Re: flirt-bbr -fieldmap comapred to flirt -bbr / freesurfer bbregister >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1405&L=FSL&P=R14389&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4) >> >> But in another question about topup correction for r-fMRI, Jesper said applytopup can be used for this purpose with the jac method: >> Item 058727 >> 2014-01-23 Re: TOPUP for r-fMRI >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1401&L=FSL&P=R108610&1=FSL&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4) >> >> So if I have fMRI data and two se-epi scans just as described in the latter thread, can I use topup+applytopup to correct my fMRI data or do I have to use topup+epireg? >> >> Many thanks! >> Julia