> 6. I proceeded to reorient my anatomical (via translation) using the
> reorient tool on the display window, and saved the reorientation.
> 7. I tried to do segmentation on my anatomical image again, and this worked
> 8. I attempted to normalize my functionals using the new *seg_sn.mat. This
> time, my normalized functionals were not distorted (a big improvement!),
> however these functionals were cut-off on one side.
I think you need to apply the reorientation parameters that you needed
for your anatomical to all of the coregistered functionals, before you
apply the seg_sn transformation to them.
Also, when using normalise-write, you can select the bounding box of
the output. Setting this to nan(2,3) will reproduce the bounding box
of the original template image, which is probably what you want.
Do either/both those points fix things?