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Hi Paul! Thanks for your input! However, we did use fslreorient2std before so both the functional and structural brains *should* be in the correct orientation. But I guess you are right and we need to verify the labels a bit more. Thanks! Paul On Mon, Feb 12, 2018 at 2:24 PM, paul mccarthy <[log in to unmask]> wrote: > Hi Paul, > > It looks to me like your functional/structural images might be left-right > flipped with respect to each other. Try running fslreorient2std on both > of them before registration and seeing if that fixes things. > > Cheers, > > Paul > > On 12 February 2018 at 12:52, Paul Zhutovsky <[log in to unmask]> > wrote: > >> Dear FSL experts, >> >> We are trying to register a data set to MNI space by using BBR for the >> co-registration between the functional (medium volume) and brain-extracted >> T1 image, followed by a FLIRT/FNIRT normalization of the T1 image to MNI >> space through FEAT. >> >> This works well for most of the subjects but for one of the subjects the >> co-registration seems to fail (see links to the pngs in dropbox. The >> failure can be seen in *example_func2highres.png* >> <https://www.dropbox.com/s/uvomedtnwa0tdwj/example_func2highres.png?dl=0> >> and propagates to the final normalization in *example_func2standard.png* >> <https://www.dropbox.com/s/67xft3r2xre4afd/example_func2standard.png?dl=0> >> ). >> >> Do you maybe have some suggestions how we could try to fix this? >> >> Thank you very much! >> Paul & Filipa >> >> >