> 1. Once an image has been reoriented to approximate Talairach space,
> should be be further fine-tuned (e.g. shifted/tilted) to match T1.img?
> Please see an example of this in the attached spgr.doc in which brain
> is shifted down and tilted compared to T1.img (as per attached T1.doc).
It should only need to be in approximate registration. Ideally within
about 5cm and 45 degrees for spatial normalisation to work. Images
should be more closely aligned for mutual information coregistration to
work (about 3cm and 15 degrees).
> 2. Three windows with coronal (upper left window), saggital (upper
> right window), and axial (lower window) views in Talairach space
> display in SPM. Which of these represents the correct image
> orientation? It seems that the lower window does, though I could not
> find it in the help function.
See: http://www.fil.ion.ucl.ac.uk/spm/spm2b.html#Compat
Check that when using the Display facility (possibly after specifying
some rigid-body rotations) that:
* The top-left image is coronal with the top (superior) of the
head displayed at the top and the left shown on the left.
This is as if the subject is viewed from behind.
* The bottom-left image is axial with the front (anterior) of
the head at the top and the left shown on the left. This is
as if the subject is viewed from above.
* The top-right image is sagittal with the front (anterior) of
the head at the left and the top of the head shown at the
top. This is as if the subject is viewed from the left.
> 3. The default is Radiological convention for SPM (and it can be
> changed via defaults). Is there a way to check whether images are in
> radiological or neurological convention in SPM?
No. You need to know which side of your image is which. This will
involve checking with whoever wrote the conversion software. If your
original data is DICOM format, then try the DICOM conversion routines
from the Toolbox pulldown.
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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