Hello,
I think the switch might be partly due to the inputs being in a different orientation than the target. This shouldn't normally be a problem - the test would be to make sure that everything looks OK in the merged FA image. As a precautionary step, it is often worth running fslreorient2std on each input image before running an analysis - this just makes sure that all images start in the same rough orientation, and can make it easier to spot registration problems.
Hope this helps,
Kind Regards
Matthew
> Hi Matthew,
>
> When running fslorient I get the following for Sub1=does not switch and Sub2=switch:
>
> fslorient Sub1_FA_FA_to_target.nii.gz RADIOLOGICAL
>
> fslorient Sub2_FA_FA_to_target.nii.gz RADIOLOGICAL
>
> fslorient Sub1_FA.nii.gz NEUROLOGICAL
>
> fslorient Sub1_FA.nii.gz NEUROLOGICAL
>
> fslorient target.nii.gz RADIOLOGICAL
>
> Since my last post we have switched all subjects' *_FA.nii.gz from inferior-to-superior and all tbss stages have run well. But I still would like to know why this was happening in the first place and if there's a bigger problem in the initial stages e.g. when converting the dicoms to nifti.
>
> Thanks for your help.
> Veronika
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