> I have a little dummy questions about preprocessings step under SPM99.
> Usually, I used two registration steps using mutual information option:
> 1) between a 3D anatomical image as a target and an axial anatomical image
> covering the same cerebral thickness as the functional data, taking as
> other objects all the functional images;
> 2) for each functional session, between the 3D anatomical image as a target
> and a mean image created in each functional session before any
> preprocessing step taking as other objects all the functional images of the
> considered session.
> These two steps creates .mat files used in my last normalisation step to
> reslice images.
> As the first step of the preprocessings should be the motion correction, is
> it necessary to reslice images before the coregister steps or is th
> einformation contained in this files after motion correction taken into
> account for the mutual information coregistration?
All rigid-body motion infrmation is carried in the .mat files. These
rigid-body transformations are easy to combine, invert etc, using simple
matrix multiplications, and are combined with the affine part of the
spatial normalisation. This means that there is often no need to reslice.
In fact, reslicing can cause problems because of the missing data in
resliced files, which normally have a value of zero, and appear as edges.
Remember that the target/template/reference image remains stationary, and
the source image ("object image" in SPM99) gets moved to match. "Other
images" are moved the same way as the source image.
If you realign images F1, F2 and F3, then they are all aligned with F1
(which I assume is the first image selected). If a mean M is created
by Realign->Reslice, then this is also in the space of F1.
So, if in a coregister step, image A is the target, M is the source, and
F1, F2 and F3 are other images (which are in register with M), then the
result should be all images registered with each other, but moved to the
initial space of A.
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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