Dear Charis,
> a:Am I correct in putting everything into Talairach orientation in the
> begginning, since I do not normalise? How does that affect
I had this problem too, when opening Analyze files. The registration
process, or at least the normalisation process, uses standard guesses
for the transformation. Switching from radiological to neurological
means changing the x direction from -1 to 1. I don't know if the
registration process also uses standard guesses for the transformation,
but you could try switching the z-direction to -1 as well.
Another solution is to produce .mat files at the beginning. In the
'display' window you can edit the spm co-ordinate matrix. Setting the
z-direction to -1 instead of 1 might work. After that, you can check
your result visually in the display window and 'rewrite header' or
'reorient' to turn the head upside down.
> segmentation and coregistration? (what do these routines 'assume'
Not at all, i presume, as long as you do this consistently.
> concerning orientation?,what do I answer to the 'are these MRIs
> spatially normalised?' prompt in 'spm_segment'- I have always
> answered 'no' until now . )
If you didn't normalise, put 'no'. Yes would mean it is in the tailarach
space.
> b:Where do my rendering/display problems stem from?Are there
> other routines/functions in spm that are affected?What would be a
> good remedy?
If your images are shown upside down, the same will happen in the
rendering. I think rewriting the .mat file will also solve your
rendering problem.
Hope this helps,
Alle Meije
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