Dear Jurgen,
The q-factor can be positive or negative and still be correct. It is only the labels that matter. So look at the labels in FSLView and see if they are correct. If they are fine then you don't need to worry about the details of the nifti qform or sform (as long as at least one has a non-zero code, otherwise it means that there is no information stored, which is dangerous).
If you see something that appears flipped with respect to the labels in FSLView, then that is a problem and you'll need to do something about it in conversion or by modifying the nifti information if you can determine how they should be fixed.
All the best,
Mark
On 11 Jan 2013, at 13:07, Jürgen Hänggi <[log in to unmask]> wrote:
> Dear FSL experts
>
> Please can you confirm that the NIFTI q-factor in the NIFTI header has to be
> negative (e.g. -1) in order to have correct right and left orientation.
>
> When the NIFTI q-factor is positive in my T1-w. and DTI images, then the
> left and the right hemisphere seem to be flipped.
>
> Thanks in advance
> Regards
> Jürgen Hänggi
>
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> Jürgen Hänggi, Ph.D.
> Division Neuropsychology
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