> we do most of our fMRI analyses in AFNI but would like to use SPM's nifty
> automatic coregistration and normalisation tools to align our functional
> images to the anatomical images and to standardise or anatomical images to
> tailarach space.
>
> following the documentation i have read, i do not reslice during
> coregistration (as it downgrades the resolution of the anatomies when the
> target image is the functional image). according to the documentation,
> reslicing should be done only after the normalisation. however, i can't
> work out how to get the output writing during normalisation to use the
> matrix output of the coregistration step! how do you do this?
The headers of the images are modified so that they include the rigid-body
transformations estimated by the realignment, or any coregistration step.
You therefore don't need to do anything else.
>
> from what i understand, the template images that come SPM are MNI
> templates. are there Talairach ones available as well?
I don't have any in T&T space, although in principle, it should be possible to
transform the images using Matthew Brett's estimated transformation
parameters.
>
> i have been using spm2b. i have also tried running the coregistration tool
> in spm5b on the same data but i get this error and the calculation
> suspends:
>
> "Incorrect number of right hand side elements in dot name assignment."
I haven't seen this error. What were the rest of the error messages? Having
the full stack of errors would allow me to narrow down the cause of the
problem.
Best regards,
-John
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