> I am new to SPM, and I have downloaded SPM5b. I have some questions about
> how to do the normalization and coregistration of my SPECT and MRI images.
> I have a single SPECT image and its corresponding T2 MRI image.
>
> 1) Normalization: should I simply normalize the structural MRI image, and
> then coregister it to the functional SPECT image (unnormalized)? Or should
> I normalize both images and then coregister them? I am not sure what is
> normally done here.
Coregistration must be done on images that have not been distorted in any way.
This is because it estimates a rigid body transformation. If the data have
been distorted, then they can no longer be registered by a rigid body
transform.
I would suggest coregistering the data first, and then normalising afterwards.
You would either estimate the spatial transformation from the SPECT and apply
it to both, or estimate it from the MR and apply it to both. Personally, I
would estimate from the MR image (using the Segment button).
>
> 2) Segmentation: is it normal practice to segment the structural MRI image
> and then coregister?
Do any rigid body registrations before you introduce any nonlinear warping
(i.e. spatial normalisation).
> Do I normalize the MRI first, segment, and then
> coregister with the SPECT?
No.
> Also, which segmented image do I use?
What do you want to use them for? I would suggest using the Segment button to
estimate your spatial normalisation parameters. You can then use the
Normalise button to apply the spatial transformations to your data.
>
> 3) Image display: when I display my SPECT image, the top two boxes show a
> squished up picture, but the axial direction looks okay. Do I just play
> around with the resize x & y options? I attached a SPECT image to this
> email.
You need to get the image file format correct before doing anything with SPM.
This includes ensuring that you have the correct voxel sizes (so that
rigid-body transformations can take them into account). I suspect that these
are wrong for your data. If you know what the voxel sizes should be, then
you may be able to use the resize options to correct them.
Best regards,
-John
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