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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