Hi Alex & Teemu:
It looks like Teemu has different versions of FSLView installed - I
suggest redownloading the macos version and installing in both
/usr/local/fsl and /Applications/fslview.app
We've tested the current release version here and it works fine on our
files. It looks like your problem is most likely a neurological convention
image; see http://www.fmrib.ox.ac.uk/fslfaq/#general_lr - in particular,
"we do not recommend storing in neurological convention" as we don't yet
support that properly.
You can easily check the orientation, e.g.:
> avworient -getorient dodgyimage
NEUROLOGICAL
Cheers, Steve.
On Wed, 16 Feb 2005, KORB,ALEX S wrote:
> I am running Mac OS 10.3.8. I changed the FSLOUTPUTTYPE to NIFTI, and
> still have the same problem (whether the input image is NIFTI or Analyze)
> Everytime I save a mask it gets flipped, so if I save it twice then it's
> back in it's original orientation. Apparently though it's just me, as my
> boss tried to replicate the problem from his account and could not. Is
> there some sort of environment variable that has an effect on
> orientation, or a flag for fslview? I noticed that when I'm saving
> analyze files, the header does not change at all, the data just gets
> written out in the .img in the flipped orientation. I don't know how to
> read NIFTI headers, so I don't know if it's the header that's getting
> changed, or the image. So if anyone has any more ideas that would be
> great, otherwise I guess I'll just use the old fslview or AFNI. Thanks,
> Alex
>
--
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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