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Dear Ulrike, > Dear FSL users and FMRIB group, > > I usually use topup for distortion correction of children's DWI data - so far that worked out quite well for me. In my previous analyses, the AP and PA images were always nicely aligned with each other. > > In a newly acquired data set, however, the alignment between both is not so great due to motion. From the TOPUP wiki page I would take that this is not an issue. "Given the two images and knowledge of the acquisition parameters topup will then attempt to estimate the field by finding the field that when applied to the two volumes will maximise the similarity of the unwarped volumes. The similarity is gauged by the sum-of-squared differences between the unwarped images. This measure allows us to use Gauss-Newton for jointly finding the field and any movement that may have occurred between the two acquisitions." > > Just to be sure: Is motion between those two scans really not a problem for topup? this is essentially the case. There is a second order effect in that the field is likely to be slightly different for the two different positions. But that is quite subtle so it is unlikely you would see that by just eye-balling the results. Can you please describe a little more what you see? Jesper > > Thank you so much for any help you can give me on this! > > Cheers, > Ulrike > > -- > Max Planck Institute for Human Cognitive and Brain Sciences > Department of Neuropsychology (A219) > Stephanstraße 1a > 04103 Leipzig > > Mail: [log in to unmask] > Internet: http://www.cbs.mpg.de/employees/kuhl/162350