Hi Giulia,
I would bet my 2 cents that what you see is an issue due to the image
inhomogeneity. Looking at the figures, there are quite evident intensity
fluctuations in the images which makes things harder for the
coregistration algorithm as they may dominate the overlap measure. You
could test that by segmenting the anatomical and the mean EPI in order
to only write out a bias-corrected image in native space, which you
could then use to try coregistration again.
Hope this helps,
Marko
Giulia Dormal wrote:
> Hello,
>
> I encounter a systematical problem when coregistering functional volumes
> (400 nifti files) to the anatomical volume aquired in the same session.
>
> After coregistration, when looking with the check reg button, there is a
> systematical shift of the functional data with respect to the
> anatomical, in the bottom direction. The shift is mostly evident when
> pointing cursor on the intersection between occipital cortex and the
> cerebellum (see PDF attached). Such shift is not apparent before
> coregistration. Batches used for realignement and coregistration are in
> attached as well.
>
>
> I have tried several things, namely by changing the default parameters
> of separation used either in realignment or in coregistration steps in
> order for them to be closer to voxel size (3 x 3 x 3.3). Nothing works..
>
> I would very much appreciate your help on this.
>
> Thanks in advance,
>
> Giulia
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
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http://www.medizin.uni-tuebingen.de/kinder/epn
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