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Dear Jesper and FSL colleagues, Thank you for your help on this one, the distortion artefact was mitigated through this approach: I found a post relating to this, https://www.jiscmail.ac.uk/cgi-bin/webadmin?A3=ind1303&L=FSL&E=quoted-printable&P=4254046&B=--B_3446959459_95180&T=text%2Fhtml;%20charset=UTF-8&pending= I ran: topup --imain=T2w_images_topup.nii.gz --datain=topup_dti_params.txt --config=b02b0.cnf --out=my_topup_results --fout=my_field --iout=my_unwarped_images -v and passing the output from this to eddy through the --topup flag. I do however notice some warping problems in eddy, they are visible on the FA image, I am attaching an axial slice (image left with warping error). Is there a way to fix this? Thank you very much, Best wishes, Barbara On Fri, Oct 16, 2015 at 4:49 PM, Barbara Kreilkamp <[log in to unmask]> wrote: > Dear Jesper, > > Thanks a lot, this helps. > I will try what you suggest on my already collected data and report back, > as I don't have b0 with opposing PE. > > All the best wishes, > Barbara > > > > > On 16/10/2015 15:31, Jesper Andersson wrote: > >> Hi again, >> >> I forgot to mention in my earlier reply that in the, unfortunate, case >> that you have already acquired your data and you don’t have data with >> opposed PE directions you _may_ be able to use your T2 structural. >> >> You would then pass your EPI-b0 and your T2 into topup and specify a very >> low readout value (implying no distortions) for the T2 volume. If the >> contrast of your T2 struct and your b0 is similar enough this might give >> you a reasonably good estimate of the field. I have seen this work in the >> past. >> >> That field you can then pass into eddy to the --topup parameter. >> >> For the future I strongly recommend acquiring b0 with opposing PE as part >> of your DTI protocol. >> >> Jesper >> >> Dear Barbara, >>> >>> it is not sufficient to pass a corrected b0 image to eddy. You need to >>> pass it a susceptibility field as calculated by the FSL tool topup. topup >>> requires at least two volumes acquired with different PE-directions in >>> order to estimate the field. This would typically be two b0 images acquired >>> with PE A->P and PE P->A, but can also be for example two b0 acquired A->P >>> and L->R. We also recommend using the first b0 images acquired as part of >>> your DTI protocol as the first image of the pair that is passed to topup. >>> >>> There is more informations and recommendations on the wikihelp. >>> >>> Jesper >>> On 16 Oct 2015, at 14:44, Barbara Kreilkamp < >>> [log in to unmask]> wrote: >>> >>> Dear FSL list, >>>> >>>> Could you please advise me on how to incorporate a b0 geometric >>>> distortion correction procedure? >>>> >>>> My workflow has been like this: >>>> (1) I use eddy_correct (flirt with 6 dof) on the b0 images >>>> (2) I take the mean of these co-registered b0 images >>>> (3) I extract this mean b0 image and register it to the T2-w structural >>>> scan I have (using Bspline co-registration in Slicer) >>>> (4) I bring the image to diffusion space (running flirt -dof 6 >>>> -nosearch on the new b0 to bring it to the original raw first b0 space) and >>>> merge with the raw DWI, now I run eddy. >>>> >>>> I noticed in some participants the b0 and DWI images don't overlap very >>>> well after running eddy, especially where the geometric distortions had >>>> been previously. Although for all DWI the eddy currents and gross motion is >>>> corrected for beautifully in eddy. >>>> >>>> Could you please explain why eddy does not seem to perform very well in >>>> terms of non-linear alignment of DWI to my new b0 image? >>>> Would you recommend I run my steps in a different order? >>>> Would you please point me to a publication on eddy? >>>> >>>> Thank you so much, >>>> Best wishes, >>>> Barbara >>>> >>> >