Dear Wen Miao,
I would run fslreorient2std on all your images
to put them in a standard orientation to begin with.
As long as the labels are all correct then this
will work.
Once you've done this, run the vbm process as usual.
All the best,
Mark
On 7 Jul 2011, at 16:20, wen miao wrote:
> Dear Mark,
>
> Thanks a lot for your quick reply.
> The result from fslvbm_1_bet seems are not in the same orientation, but the orientation label(R,L,I,S,A,P) are right when check by fslview. The attached file BM.jpg is an example showing different orientations from the standard template but have right orientation labels. The corresponding subject got wrong orientation and wrong orientation labels in the template_GM_4D file. And the BX.jpg is a right result example.
> Seems change the orientation can fix this error. How can I change the orientation while leave the orientation labels unchanged?
>
> Thank you.
>
> Wen Miao
>
> On Thu, Jul 7, 2011 at 5:38 PM, Mark Jenkinson <[log in to unmask]> wrote:
> Dear Wen Miao,
>
> Did you check the brain extraction results from fslvbm_1_bet ?
> Did they all look fine?
> And are they all in the same orientation at this point?
>
> What you are describing sounds like a failure in the linear registration
> component which could be due to failure in BET or failure of the
> segmentation (FAST) or a failure in the registration (FLIRT). It is
> highly unusual for the registration to fail if (1) the images were all
> originally in similar orientations, (2) the brain extraction worked OK,
> and (3) the segmentations were fine. So I would double-check these
> issues first.
>
> All the best,
> Mark
>
>
> On 7 Jul 2011, at 02:26, wen miao wrote:
>
> > Hi FSL experts,
> >
> > Im' running FSL-VBM analyses. By following the instructions, I was able to run the first step successfully using fslvbm_1_bet -N. Everything seems right utill I check the "template_GM_4D" image after the 'fslvbm_2_template -n' script using fslview. About half of the brains get wrong orientations. The "_struc_GM_to_T" images of each subject get right orientations. And "_struc_GM_to_T_init" get wrong orientations, same as the corresponding image in "template_GM_4D".
> >
> > I notice that this problem has been posted on the mailing list, as you can see here:https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1009&L=FSL&F=&S=&P=194531. But it was not solved or at least the solution was not posted.
> >
> > Can anyone give some help ?
> >
> > Thanks in advance.
> >
> > Wen Miao
> > --
> > State Key Laboratory of Intelligent Control and Management of Complex Systems
> > Institute of Automation,Chinese Academy of Sciences(CASIA)
> > Beijing, 100190, P.R.CHINA
> > -----
> > http://nica.ia.ac.cn/?q=wenmiao
> >
>
>
>
> --
> State Key Laboratory of Intelligent Control and Management of Complex Systems
> Institute of Automation,Chinese Academy of Sciences(CASIA)
> Beijing, 100190, P.R.CHINA
> -----
> http://nica.ia.ac.cn/?q=wenmiao
>
> <BM.jpg><BX.jpg>
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