Hi,
How are you determining that the displayed orientation is neurological?
Are the labels right? That is the most crucial thing. The terms
neurological
and radiological for display get a bit confusing when the brain is not
in the
same orientation as the standard brain.
If the labels are correct (including left and right) then *do not* do
a fslswapdim
as that will muck the labels up. I would also avoid using fslorient
to change
things unless you know the labels are wrong.
Can you explain more about what you see in FSLView, what you expect to
see, and
what the labels are like? Don't worry about the sform values for now,
although it would
be helpful to send us the output of fslhd.
All the best,
Mark
On 22 Apr 2008, at 19:25, Emily Stoneham wrote:
> Hello all,
> I have performed an fslorient -getorient, and it tells me it is
> RADIOLOGICAL, however, when viewed
> in FSLView, it shows it in Neurological orientation. If I run
> fslswapdim, I can change that (albeit I get
> a warning), but I suspect I should be using fslorient to do that
> instead- (i.e., change the header)?
> When I run fslorient -getsform, I get a string of numbers, but I
> don't know what they mean, or
> how/if I should change one or more (and which) of them. Can you help?
>
> Thanks,
> Emily
>
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