It sounds like you want to derive metrics based on the shapes of the
images. I would suggest maybe trying the Shoot toolbox in the latest
set of updates of SPM8. To use this, you'd do the segmenting and
importing as for Dartel, then run the registration of GM and WM to a
common average shaped template (similar to Dartel). When this has
finished (for all your images) you can run the option for generating
kernel matrices from velocity fields (v_*.nii). This will generate a
MATLAB file containing inner products between each pair of velocity
fields. A measure of distance (assuming linear approximations around
the template) can then be obtained between each pair of images using
D = sqrt(repmat(diag(K),1,size(K,2)) + repmat(diag(K)',size(K,1),1) - 2*K);
There are many ways of generating such inner products, and the form
that is used should reflect the regularisation used by the nonlinear
registration. The one that I currently use is based on the weighted
sum of these two terms:
1) Decompose the Jacobian matrices throughout the velocity fields into
symmetric and anti-symmetric components, and penalising the sum of
squares of the symmetric elements. The anti-symmetric part encodes
rotations, whereas the symmetric part encodes zooms and shears.
2) The sum of squares of the traces of the Jacobian matrices. These
are the squares of the divergences, and penalise volumetric changes.
I don't know if this helps.
Best regards,
-John
On 7 April 2011 16:18, Joaquin Goni <[log in to unmask]> wrote:
> Hello,
>
> I am using the "new segment toolbox" for both segmentation and normalization
> processes. During normalization, it is possible to obtain a deformation
> field archive (its name by default starts with an "y"). I would like to know
> if it is possible to obtain a global measure of the deformation field
> required. In particular, I would use that to find which of the T1-MRIs of
> certain dataset is closer or more similar to a third one.
>
> Thank you in advance for your help.
>
> Best regards,
>
> Joaquín
>
> --
> --------------------------------
> Joaquín Goñi, Ph.D
> Neuroimaging Lab.
> Dpt. of Neurosciences - CIMA
> University of Navarra
> Pamplona (Spain)
> Phone (+34) 948194700 Ext 2035
> (+34) 948425600 Ext 6634
> Fax (+34) 948194715
> --------------------------------
>
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