Dear Charlotte,
If you have a registration problem then we suggest you try the various options
with FLIRT to improve your registration (e.g. crop the image if there is a
lot of neck present, try using -nosearch/"Already virtually aligned" in the GUI,
etc - see the FSL course on registration). Once you have a registration
that is good then you can feed the registration matrix into run_first_all
using the -a option.
All the best,
Mark
On 8 Feb 2011, at 16:55, SUBSCRIBE FSL Anonymous wrote:
> Dear FSL users,
>
> I have a problem with two of my 164 subjects with FIRST in the registration. With the option -d, I have identified the step of the error. It is in the step two. With the slicesdir, I can see a misalignement between the 3D of my subject and the MNI152 template.
> I try to find how to correct this error, but I don't see any option to change that.
> Somebody can help me?
> Thanks!
> Charlotte
>
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