Federico,
please figure this out yourself by trying different bounding box sizes.
They are given in mm coordinates, and to include cerebellum you will
probably want to include more data in -z direction.
Volkmar
On Thu, 21 Dec 2006, Federico Tubaldi wrote:
> 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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--
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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