Thanks.
So this establishes that this is not related to BET then.
As I said before, FSLView shows the images in the
way in which they were acquired. Most tools will work
fine with the data like this, but if you want to reslice
your images into axial format then you can use fslswapdim.
If your images are in the nifti format, the labels are shown
in FSLView and these labels are anatomically correct then
the simple command:
fslswapdim invol RL PA IS outvol
will convert the image "invol" to "outvol" where outvol is
in the standard axial format.
If you do not have nifti images, or you do not see labels
in FSLView or the labels are incorrect then you should
not use this command.
All the best,
Mark
On 11 Nov 2009, at 18:58, Shal Hat wrote:
> No they are not..
>
>
> On Wed, Nov 11, 2009 at 12:15 PM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Yes, but is it *different*?!?
> Mark
>
>
> On 11 Nov 2009, at 17:06, Shal Hat wrote:
>
> yeah it is actually upside down before BET..
>
> On Wed, Nov 11, 2009 at 11:53 AM, Mark Jenkinson
> <[log in to unmask]> wrote:
> Hi,
>
> You haven't answered my original question:
>
> Is the orientation different *after* BET than it is *before* BET??
>
> All the best,
> Mark
>
>
>
>
> On 11 Nov 2009, at 16:47, Shal Hat wrote:
>
> Thanks,, is their a way to do the reorientation using the GUI? If
> not, what should the inputs x,y,z be for the fslswapdim command ?
> Again, I acquired
> the slices in a sagital direction.
>
> Thanks,
>
>
>
> On Wed, Nov 11, 2009 at 10:42 AM, Ignacio Letelier <[log in to unmask]
> > wrote:
>
>
> 2009/11/11 *Shal Hat* <[log in to unmask]>
>
> Hi
>
> Before doing BET, I use the dcm2niigui.ex software to reorient the
> images in an orthogonoal view. I am not sure if this option does
> exists in fsl, but sure what I'm telling you will work.
>
> best regards.
>
>
>
> --
> Ignacio Letelier Aguirre.
> Estudiante Ingeniería Civil Biomédica
> Universidad de Valparaíso, Viña del Mar.
> Teléfono: 97139955
>
>
>
>
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