Hi,
I'm afraid it is impossible to diagnose your alignment from
that image. If you upload your data we can have a look at
it and see if there anything that can be done to improve it.
All the best,
Mark
On 2 Nov 2009, at 20:28, Anastasia A Ford wrote:
> Hi,
>
> Im trying to register my FA map to T1 weighted image. I tried using
> 12, 9,
> and 7 DOF, but for each registration the brainstem does not seem to
> align
> very well between the T1 and the FA registered to the T1. Could you
> recommend any alterations to the flirt command line in order to
> correct for
> this? I attached a screen shot of the mis-alignment.
>
> Thank you,
>
> Anastasia
>
> <brainstem_mis_reg_axial.png>
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