Hi,
It is a bit hard to diagnose the problem from this info.
Can you upload the data to our upload site at:
http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
It is certainly possible that highly variable signals
in the ventricles or other places could cause problems.
This shouldn't affect FLIRT though, so that problem
seems even more strange to me.
Anyway, if you upload the data we can give you a
better idea of what might be going wrong and what to do.
All the best,
Mark
On 17 Feb 2010, at 16:38, Jennifer Evans wrote:
> Hi,
>
> This is a really basic question about getting mcflirt/flirt to do
> what I
> expect. I just wanted to do simple motion correction to one of my
> fMRI
> timeseries, but mcflirt seems to add "motion" rather than correcting
> for
> what little motion there is. I checked the data by running another
> motion
> correction algorithm and the data seem fine. I'm wondering whether
> the
> algorithm is being biased by the intensities in the ventricles... I
> just
> ran mcflirt -in <dataset>.
>
> This is only a problem because I would like to run multi session
> temporal
> concatenation in Melodic which requires a flirt registration step
> that does
> similar odd things to my data (like shrinking the brain so it's really
> small) and the ICA fails.
>
> Any insight into what might be the problem would be appreciated.
>
> Thanks,
> Jen
>
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