Dear SPMers
I have some questions about the first steps in optimized VBM: the creation
of a customised template and priors. I am an absolute SPM beginner so please
forgive me any stupid questions! After studying protocols that I found in
the archives and in several papers the following points are still unclear to me:
1. Creation of a customized whole brain T1-template (for use in the initial
(implicit) affine registration step in Optimized VBM)
Option a: affine-only registration of all subjects to MNI-152-template,
smoothing (8 mm), mean image
Option b: Do not create customized T1 at all, and use the standard template
for the following steps instead. What would be the advantage of that?
2. Creation of customized GM, WM, and CSF priors and of a customized brainmask:
Option a: Affine-only registration of the images to my customized
T1-template, segmentation, smoothing (8 mm), mean image. The new images are
used as own priors, brainmask, and GM/WM-template (for estimating the
optimized normalization parameters) in Optimized VBM.
Using this option I do not have exactly corresponding prior images in the
segmentation process from above. Would that be a serious drawback? Should I
stick to the MNI-152-template?
Option b: Same as in a, but also affine AND non-affine registration to my
customized T1. Can you comment on that?
Option c: Same as in Option a. but this time all images are registered
(affine-only) to the MNI-152-template. Later I will use my GM/WM-templates
for the estimation of the optimized normalization parameters only. For the
initial (implicit) affine registration step to come in Optimized VBM the
MNI-152-template will be used.
I have some doubts if this process actually does create GM, WM etc. priors
that are customized “enough” as registration is to the MNI152-template.
However, would the standard priors be better suited as in Option a. for the
segmentation process during creation of the customized priors (because they
correspond more exactly with the template)?
Option d: Same as in Option c. However, this time for the initial (implicit)
affine registration step to come in Optimized VBM the customized T1 will be
used! Also, I will use the new images as own priors, brainmask, and
GM/WM-template (for estimating the optimized normalization parameters) in
Optimized VBM, as in Option a.
Being derived from the same template (MNI-152), might the customized priors
created in this option better fit my customized template in the segmentation
steps that follow in Optimized VBM (segmentation before estimating the
optimized normalization parameters etc.) than in Options a and b?
Do you have any recommendations for which protocol to use? I realize there
are scripts available for this but I would like to understand what I’m doing
before proceeding further. Thank you for any comments and suggestions!
Johannes
Johannes Ahrendts
Neuroimaging Research Group
Dept. of Psychiatry and Psychotherapy
Freiburg University Hospital
Germany
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