| 1. Imaging the brainstem. I would like to use spm99 to analyze the data. Is
| it possible to use the pre processing steps in SPM (realignment,
| normalization, etc.) given that I will not be doing whole brain imaging.
| Are there templates available for the brainstem that would enable me to do
| the normalization?
A lot of the spatial stuff was designed for whole brain images, so may not
be optimal for smaller higher resolution images. For example, the realignment
algorithm samples the data roughly every 4.5mm, so if you have a smaller FOV,
then there will be less samples used. I can't really say how well the
spatial normalisation is likely to work for your data. However, if you have
a limited FOV, then it may be worth repositioning the images (via the Display
button) so that the image is roughly lined up with the templates. Hopefully
the templates currently released with SPM cover the part of the brainstem that
you are interested in.
Good luck,
-John
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