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Hi again Steve et al I have a little bit more evidence related to the problem that I thought I would share, given that you mentioned you are surprised that the dofs are changing the end-slice behaviour. -sometimes increasing the paddingsize helps, but sometimes it doesn't -even when I use dof = 7, the end slices look fine (the problem only occurs for dof = 6) -it is always the most inferior slice -the problem is worsened at higher b-values (larger parts of the most inferior slice are cut off, again only with dof = 6) Given the last point, I am wondering if this is more of a problem with using flirt on volumes with very low signal, rather than a problem with movement in my data? I'm very interested to hear any thoughts people might have. Would it be better to just run flirt on my b = 0 images, and interpolate the motion corrections on the intervening diffusion weighted images? Thanks again! Erin ================================================================================================ Hi - I'm a little surprised that you would get different end-slice behaviour in the dof=6 and 12 cases, but if this is just due to very slight rotations out of volume then you can reduce that with the - paddingsize option. I would not use mcflirt as it is not at all optimised for this scenario. Cheers. On 9 Mar 2009, at 20:53, Mazerolle, Erin wrote: > Hi Steve et al > > Thanks very much. I tried this but I find that it results in parts > of my > most inferior slices being cut off. I checked using mcflirt and it > doesn't appear that I have motion that is larger than my slice > thickness > (3mm slices versus 0.002 radians & 0.6mm motion params). Do you > think it > would be reasonable to use mcflirt instead of the flirt call in > eddy_correct? I am worried that mcflirt might get confused by the > differences in intensity between diffusion weighted versus b=0, but I > don't understand how eddy_correct 's flirt call handles these > intensity > differences either. > > I should also note that when I use 12 DOF (i.e., eddy_correct 's > default > flirt call), my inferior slices are not cut off. Basically the only > problem with using the 12 DOF is conceptual - there shouldn't be any > shearing & stretching caused by eddy currents in my spiral data (I > believe eddy currents are more likely to appear as blurring in spiral > acquisitions). > > Thanks for any ideas! > > Erin > > > >> Hi - you're mostly right, you won't get eddy correction in this case >> but you can still correct for head motion. However, you may as well >> constrain the degrees-of-freedom to be rigid body in this case, so >> take a local copy of eddy_correct and add the following flag to the >> flirt call (just before the ">>"): >> >> -dof 6 >> >> Cheers. > > > > On 16 Feb 2009, at 18:37, Mazerolle, Erin wrote: > >> Hello, >> I was hoping someone could tell me if it is valid to run FSL's eddy >> current correction with diffusion data collected using a spiral >> trajectory. I don't imagine it would be able to correct for eddy >> currents due to the difference in trajectory, but can it still do >> the motion correction across images with different bvalues? >> Thanks! >> Erin