Hi,
Yes and no in that order.
All the best,
Mark
On 11 Nov 2009, at 19:54, Shal Hat wrote:
> As long as the data was acquired in that way, I should be fine with
> using the other tools, correct?
>
> Also is there a way to reorient using the GUI?
>
> Thanks !
>
> On Wed, Nov 11, 2009 at 2:20 PM, Mark Jenkinson
> <[log in to unmask]> wrote:
> 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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