>
> I created a custom template with John's script and now I would like to run
> the vbm script and use the custom template and the respective priors.
>
> I notice that the output image of the customized template creation script
> is in img format. I assume that to keep things consistent I should flip
> this image and then transform it into mnc format. I should also do this for
> all the priors.
You shouldn't need to - providing you do not plan to mix these data with
any other template data in MINC format. For example, if you select more than
one template, or if you use the "brain weighting" (which uses the brainmask.mnc
file). SPM2b needs all templates and brain-weighting images to be in exactly
the same space (i.e. each voxel should correspond to the exact same location
in all these images).
>
> Besides changing the defaults to allow reading of the new apriori files, I
> imagine I should change the vbm script where it defines VG0 to point to the
> new template.
Yes.
>
> Is this all correct? Anything else I need to worry about?
You may want to do some manual editing of the CSF image in order to remove
some of the low intensity the non-CSF.
Smooth the images by 8mm before using them as templates.
Best regards,
-John
--
Dr John Ashburner.
Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
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