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
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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