Dear Johannes,
> I'm working on a VBM study using the optimised protocol. I've created my own
> GM template.
>
> When I want to determine the optimised normalisation parameters (register
> native space-segmented GM to my GM template) I get the following error message:
>
> This message only appears when using a (default) brainmask. Without a
> brainmask everything works fine.
the brainmask and the template have to be identical with respect to their image properties, i.e. same orientation, same voxel size, same bounding box, same Origin, etc.
So, the best is probably to create your own brainmask, as well. You can either reslice the default brainsmaks by using the coregistration -> reslice only option, defining your template as the 'space defining image', or you use ImCalc to create your brainmask out of you GM template (e.g. use the formula i1>0.01), but this latter brainmask tends to cover a larger area than the default brainmask.
I guess, you got something like a WM template as well, while creating the GM template. In that case, you will get an even better brainmask by combining the GM and WM template with the following ImCalc formula: ((i1>0.05)+(i2>0.05))>0.
Good luck,
Karsten
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Karsten Specht, PhD
Department of Biological and Medical Psychology
University of Bergen
Jonas Lies vei 91
5009 Bergen
Norway
Tel.: +47-555-86279
Fax: +47-555-89872
[log in to unmask]
http://fmri.uib.no/
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