Hello,
thanks for help. Fortunatelly enaugh my patient has asymmetrical
ventricles so I am pretty sure with the orientation. The data are
imported from Siemens "one big image", so the only problem was the
order of the slices. I realized I do not have to swap x, just z and I
did a tiny script for doing
1) dinifti
2) orientace="`fslorient -getqform $tmpdir/$filename$sufix`"
3) fslswapdim x y -z
4) fslorient -swaporient
5) fslorient -setqform
6) fslorient -setsform
and it works. Thank you again for all of the valuable help.
best regards
George
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