Sylvain,
I think you should treat your missing parts as if they were
lesions. I would therefore mask the object images.
However, if you prefer to mask the template SPM allows you to
do so under the default options for Spatial Normalisation.
You'll find two (masking) options there, I quote form the help
facility:
% 'Mask brain when registering?'
% Applies a weighting mask to the template(s) during the parameter
% estimation. By default, weights in and around the brain have
% values of one whereas those clearly outside the brain have values
% of zero. This is an attempt to base the normalization purely upon
% the shape of the brain, rather than the shape of the head (since
% low frequency basis functions can not really cope with variations
% in skull thickness).
% The option is now available for a user specified weighting image.
% This should have the same dimensions and mat file as the template
% images, with values in the range of zero to one.
%
% 'Mask object brain when registering?'
% Applies a weighting mask to the object image(s) during the parameter
% estimation. Weights are as for the template mask (0-1). Used
% (usually) to prevent unusual or abnormal areas of brain (e.g.
% stroke, tumour) influencing normalisation to normal brain
%
Hope this helps,
Emmanuel
> Sylvain Clément wrote:
>
> First I'd like to thank anybody for all the answers I received.
>
> I've understood that I have 2 major possibilities:
> * reducing the number of basis function which may lead to a lower quality
> normalisation
> * using a mask.
>
> I've chosen to try this latter solution. I've read some threads in the
> list's archive. It seems that the solution for my problem is to mask the
> top & the bottom part of the template T1 image (parts that do not exist on
> my images). But the masking image that spm ask for is the one used to mask
> the source images (for exemple avoid normalisation on a lesion) but not the
> one to apply to the template!
> Should I create a personnalized brainmask.img/hdr used by spm by defaults?
> Thanks in advance
>
> Sylvain Clement
>
> ---------------------------
> Sylvain Clément
> Bordeaux, FRANCE
> mailto:[log in to unmask]
--
______________________________________________________________
Emmanuel A Stamatakis PhD Tel: +44 (0) 1786 467 669
Research Fellow Fax: +44 (0) 1786 467 641
Dept of Psychology e-mail: [log in to unmask]
University of Stirling
Stirling FK9 4LA
U.K. http://jura.stir.ac.uk/~stamatak/
|