Thank you for your quick reply!
We collected MP2RAGE and DWI data from 4 year children at T=0, T=4 weeks, and T=8 weeks. I am mapping the DWI to the T1 separately because I do not want to introduce any bias. If I register T=4 weeks DWI to T=0 T1, I think the deformation may be larger than the deformation applied when I register T=0 DWI to T=0 T1. This would be systematically treating the scans differently and might introduce a confound when I look at differences between the scans.
I don't think the problem is that I switched the T1s, because I have now run the correction several times, and each time I started from scratch.
Finally, I used FA in the contrast because on page 24 of the manual it is written that "for a T1, you could also try 'Avg(DWIs)' or 'FA'. Additionally, in this another post in the google group, Alexander Leemans said " 2. The default, "Non-DWI" works best if your reference image is a T2
image. For a T1, I would choose the "FA" or "Avg(DWIs)" contrast as it
looks more similar to the T1." (https://groups.google.com/forum/#!searchin/e_dti/fa$20or$20non$20fa%7Csort:relevance/e_dti/eoVtRDqOZZg/tTwyHTVVdIwJ
I think the strange thing is that I have done this with 60 other participants, but don't have such a problem with the exact same settings.