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
>
|