Hi,
Have you tried running fslreorient2std on all the images before vbm?
That should fix this sort of thing.
All the best,
Mark
On 14 Apr 2014, at 15:51, "Hoi Fong, Chan" <[log in to unmask]> wrote:
> FSL expert,
> currently i am running a VBM study on 2 group patient T1 MPRAGE on 1.5T siemens magnetom MRI. I have checked the quality of BET, which is fine. However, after i finished the fslvbm_2_template -a, the template_GM_4D looks upside down. After running fslvbm_3_proc, the GM_mod_merg shows about half of the MRI did not affine well.
> It would be nice if i could upload the data for you to check .
> thanks !!
> hoifong
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