Hi Mark,
I don't know if this is perhaps in development, but there would be much
less need to bother with swapping orientation to RAS or LAS if fslview
had an option for *displaying* images in a standard radiological
presentation regardless of the underlying orientation (as FreeSurfer's
tkmedit does for example). I'm not very good at viewing the brain
upside-down or sideways, so even though all the FSL tools should work
regardless of which way the image is stored (assuming the labels are in
the correct places), I find myself using 'fslswapdim' to change to an
RAS/LAS orientation if I ever want to take advantage of 'fslview' for
viewing my images.
cheers,
-Mike H.
On Wed, 2010-05-05 at 00:10 +0200, Mark Jenkinson wrote:
> Hi,
>
> I'm not quite sure how you are defining RAS, or similar, for fslview
> *display*.
>
> Anyway, all that *really* matters is that the labels are in the
> correct places on
> the image. It doesn't really matter which way the image is
> displayed. All the
> FSL tools should work, regardless of which way the image is stored and
> displayed, as long as the labels are correct. However, if the
> different images
> are very differently oriented then you should check the registrations
> carefully
> to make sure that they all work correctly.
>
> So, in summary, I wouldn't worry about swapping anything.
>
> As for FreeSurfer problems, you should email the FreeSurfer list about
> that.
>
> All the best,
> Mark
>
> On 4 May 2010, at 09:11, chen wrote:
>
> > Hello FSLers,
> >
> > I may be asking a stupid question but it really troubled me a while.
> >
> > I converted dicom files to nift using dcm2niigui (MRIcron). In
> > fslview, it displayed in RAS coordinates, but template of FSL are in
> > LAS coordinates. Should I filp L-R before doing any further analysis?
> > Besides, my structrual imagews were scanned in sagittal view, and
> > after dcm2niigui transforation, it's in PIL coordinates in fslview.
> > Should I reorient the image to LAS coordinates too?
> > But the letters L R I S A P are labled correctly (at least A-P and I-
> > S are correct), which means FSL can read in orientation information
> > correctly. So I am confused whetehr I should reorient my data or not?
> > I also processed strucutre images with Freesurfer, and the results
> > between reoriented and not-reoriented images are different, so which
> > one is correct?
> >
> > Any help is appreciated,
> > Thanks!
> > --
> > Chunhui Chen
> >
> >
> > 网易为中小企业免费提供企业邮箱(自主域名)
|