Hi Javier,
I still find it a bit hard to see what is going on as your scan is behind the atlas image. Would you mind adding a screenshot with the actual scan on top?
Thanks,
Eelke
> On 17 Jun 2015, at 23:19, Javier Sanz Perez <[log in to unmask]> wrote:
>
> Hi Eelke,
>
> Thank you for your answer. I ran flirt -in ${anatomic_dir}/anatomic_brain.nii.gz -ref ${template} -dof 6 -out ${anatomic_dir}/anatomic_tostandard.nii.gz -omat ${anatomic_dir}/anatomic_tostandard_transform.mat.
> I attach two screenshots: one with 6 degrees of freedom and the other with 12 degrees of freedom.
>
> Best regards,
>
> Javier
>
>
> 2015-06-18 3:27 GMT+02:00 Eelke Visser <[log in to unmask]>:
> Hi Javier,
>
> The anisotropy is not necessarily a problem for FLIRT, but it is a bit hard to guess what is going on without seeing the images. Would it be possible to share some screenshots along with the options you used when running it?
>
> Cheers,
> Eelke
>
>
> > On 17 Jun 2015, at 10:48, Javier Sanz Perez <[log in to unmask]> wrote:
> >
> > Hi everyone,
> >
> >
> >
> > I’m having problems trying to register anisotropic anatomic rat images (0.2x0.2x1 mm3) to an isotropic template (1.25x1.25x1.25 mm3) with FLIRT, 6 and 12 DoF. The resulting image is not properly registered to the template.
> >
> >
> >
> > I was wondering if the problem was due to the high anisotropy of the images (1/0.2=5) compared to the isotropy of the template. How can the registration improve?
> >
> >
> >
> > Thank you,
> >
> > All the best,
> >
> >
> >
> > Javier
> >
>
>
> <FLIRT_6dof.png><FLIRT_12dof.png>
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