Hi Paul.
did you manually reorient the T1 scan such that it roughly matches your
template, prior to normalization? To me it seems you started out with a
T1 'looking' in the wrong direction, that is, looking to the right
(where the template 'looks' to the left). Your deformed image still
looks' to the right, that is why I have this suspicion. Such a big
difference with the desired template cannot be handled by normalization,
you might have ended up in a local minimum. Start out with an image that
is already roughly in register with your template.
Good luck,
Bas
On 04/02/2012 11:09 AM, Paul Czienskowski wrote:
> Dear all,
>
> I am trying to accomplish a normalization of MR-images with a script,
> using the SPM2-Version of spm_normalise. Unfortunately the
> 'normalized' image does not match what I was expecting, after
> transforming the image with spm_write_sn, but looks gravely distorted
> (see attached image). The code I've used is approximately like the
> following:
>
> mri_template =
> spm_vol(fullfile(cd,'external','spm2','templates','T1.mnc'));
>
> spm_normalise(mri_template,mri_source,deformation_file);
>
> spm_write_sn(mri_source, deformation_file);
>
> I would appreciate very much, if someone has got any clue what went
> wrong.
>
> Tanks in advance,
> Paul
>
--
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
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