Thank you for you precise and well-timed answer. I can be interest in
cerebellum activations because I've a motor task so is it better edit
bounding box values? If yes, which values do I specify? You consider that
I'm interest also in cortical motor areas activations so is it possibile
that changing bounding box values to include also cerebellum I have some
problems to detect activations in cortical motor areas so the best choice
are the defaut values?
Best,
Federico.
-----Messaggio originale-----
Da: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] Per
conto di Volkmar Glauche
Inviato: giovedì 21 dicembre 2006 10.11
A: [log in to unmask]
Oggetto: Re: [SPM] Normalise: VOXEL SIZE and BOUNDING BOX
On Thu, 21 Dec 2006, Federico Tubaldi wrote:
> Dear John and dear Experts,
>
> I acquired functional images (EPI) with an isotropic voxel size 3.5 x
> 3.5 x
> 3.5 and a slice gap equal to 0.5 mm. When I use MRIcro or SPM Display
> utility to display these images I get a no-isotropic voxel size 3.5 x
> 3.5 x 4. My questions are:
>
> 1) Do MRIcro and SPM compute a new voxel size as 3.5 x 3.5 x (3.5+0.5)?
Yes. NIfTI or Analyze image file formats have no concept to express gaps
between slices. Therefore, the gap is just added to your measured slice
thickness, but the voxel intensity values are not changed/interpolated etc.
> 2) What should I specify in Normalise-Write options-Voxel sizes in
> spm5 (or in Defaults for writing normalised in spm2)? 2 x 2 x 2
> (default) or 3.5 x
> 3.5 x 3.5 or 3.5 x 3.5 x 4?
> 3) What should I specify in Normalise-Write options-Bounding box in
> spm5 (or in Defaults for writing normalised in spm2)? Are default values
ok?
This depends only on your decision ;-). If you don't have any other reason,
I would go for voxel sizes that are quite close to your original ones
(3.5x3.5x3.5 or 3.5x3.5x4 would not make much of a difference). The default
bounding box is usually ok, but it does not include cerebellum.
Note, that you need to keep voxel size and bounding box setting constant for
all subjects in your study, otherwise you will not be able to do a group
analysis.
Volkmar
--
Volkmar Glauche
-
Department of Neurology [log in to unmask]
Universitaetsklinikum Freiburg Phone 49(0)761-270-5331
Breisacher Str. 64 Fax 49(0)761-270-5416
79106 Freiburg http://fbi.uniklinik-freiburg.de/
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