Hi Jack,
We tested this idea when we first wrote mcflirt.
Somewhat counter-intuitively it did worse (though not hugely) than
using the single volume. So we went for the simple, and better, approach.
One reason that it might not help is that some artefacts in the images may
end up blurring the images over a greater area than you'd get from just any
one instance.
As for your commands, they look just fine.
Is there a problem with the motion correction results?
If so, then the average won't be too nice.
All the best,
Mark
Jack Grinband wrote:
>Hi Mark,
>Would you get a better registration if you used the mean volume of the functional
>data (after motion correction) instead of a single volume (before motion correction)?
>
>I'm trying to create a mean volume from my functional data, but I think I'm doing
>something wrong:
>
>mcflirt -in func -out func_mc
>avwmaths func_mc -Tmean func_mc_mean
>
>I'm averaging 127 volumes, so I expect that func_mc_mean should look better than
>example_func, but that's not the case.
>
>jack
>
>
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