Xiaochu Zhang wrote:
> I downloaded the vbm toolbox from "http://dbm.neuro.uni-jena.de/vbm" and
> installed it.
> I tried using this toolbox with my data today. All things looked like ok.
> However, something still comfused me.
> The first one is about customize template. I knew the customize template
> is very important for VBM analysis. However, I didn't find where I can
> make the customize template. Is it done automatically?
Christian Gaser has some notes on customised templates in the docs for
his VBM2 toolbox:
http://dbm.neuro.uni-jena.de/vbm/vbm2-for-spm2/creating-customized-template/
There is also a lot of material in the archives, including some
discussion of how important they are with SPM5. The general view
seemed to be probably not very important for fairly normal data (my
summary sentence here is deliberately vague -- it's very difficult to
be sure about this kind of issue...), possibly important for early
developmental subjects or those with severe pathology.
It's easy to create an average of a bunch of SPM5 segmentations, using
imcalc (e.g. 'mean(X)' with the data matrix (dmtx) flag set). It's not
so easy to decide whether you want modulated or unmodulated normalised
segmentations (though it probably doesn't make too much difference...)
and whether you want to balance groups (e.g. controls and patients)
going into the average, even if your original groups are unbalanced,
or whether to simply weight the averages by group numbers. I can't
remember seeing much of a consensus on these issues in the mailing
list; perhaps others will comment here?
This is probably a longer answer than you really wanted -- sorry! The
short answer is: VBM5 doesn't create custom templates, because they
are less important with SPM5.
> The second, I read several papers about VBM. They usually used 12mm FWHM.
> However, I didn't find any opition related to the FWHM. The only one
> is "Bias FWHM". But the select is from 30-150mm.
I think the VBM5 toolbox is just concerned with the segmentation (and
unified normalisation) not with smoothing. So under the usual SPM GUI,
click the smooth button and then you should see the options you need.
Hope that helps,
Ged.
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