> What you want to do is change the sform and/or qform
> associated with your image as these are incorrect. For that
> you want to use fslorient. So, use fslswapdim to make it
> look the "correct" way around in fslview (ignoring the labels)
> and then modify the sform/qform with fslorient to fix the labels.
>
> Note that copying the "old" sform/qform prior to using
> fslswapdim and then replacing the "new" ones with the
> old values (using fslorient) can achieve what I think you
> want to do.
I am bit confused. I was playing with the orientation of test.nii and
ended with swapdim2. Now I do not know what should I set manually (and
where -61.xx came from).Here is fslorient output:
--screenshot--
jirka@ICD:/tmp$ fslorient -getsform -getqform swapdim2
-1.79688 0 0 72.9902 0 -1.79688 0 136.59 0 0 -4 46.5783 0 0 0 1
jirka@ICD:/tmp$ fslorient -getsform swapdim2
-1.79688 0 0 72.9902 0 -1.79688 0 136.59 0 0 -4 46.5783 0 0 0 1
jirka@ICD:/tmp$ fslorient -getqform swapdim2
-1.79688 0 -0 72.9902 0 -1.79688 -0 136.59 0 0 -4 46.5783 0 0 0 1
jirka@ICD:/tmp$ fslorient -getqform test
-1.79688 0 0 72.9902 0 -1.79688 0 136.59 0 0 4 -61.4217 0 0 0 1
jirka@ICD:/tmp$ fslorient -getsform test
-1.79688 0 0 0 0 1.79688 0 0 0 0 4 0 0 0 0 1
--screenshot--
many thanks
George
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