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
>
>
> ------------------------------------------------------------------------
> ---
> 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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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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