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Hello An other alternative would be to apply the affine transform to the nifti header in all the raw data before running topup. This is the way spm handel coregistration. (so if you use spm coregister, the header is change without interpolation). I can understand that in some case it may be confusing to change the header (and not to have an external transformation) but it is convenient to easily avoid several interpolation. I do not know if there is in fsl a way to apply an affine transformation to the nifti header (without changing the data) but it would be nice to have it Cheers Romain Le 15/10/2013 11:22, Jesper Andersson a écrit : > Dear Jan, > >> >> thank you for providing such great tools as topup and eddy! >> I have 2 questions: >> >> 1. Are my data interpolated only once when I feed the results from topup into eddy? > yes. > >> 2. Is it possible to align my diffusion data with a T1 or T1 weighted scan without adding an additional interpolation step? >> If not, would it theoretically be possible to extend eddy to do so with a reference image and affine transform? (That would be nice to know before I tried…) >> I guess when combining the exported fields from eddy with an affine transform from flirt (would that work?) > It is a good idea and something I will keep in mind for future releases. It is certainly possible, but it would take a bit of coding on your side. The field that you can get as output would need to be combined with the rigid body parameters in the text file. > >> then I would miss the correction of corrupted slices. > The correction of corrupted slices is not "activated" in the current release (unless I have somehow done that by mistake) as we need to do more testing of that before we are happy with people using it. So you'll miss that right now anyway. > > Jesper > > >> Thanks, >> Jan