Hi Colm,
> Does that mean that right of the brain should be on the left
> of the screen and vice versa? (I let to3d figure out the
> orientation of the data from the IMA files itself.)
This is controllable (from your ~/.afnirc file), so it depends
on whether you've set the AFNI_LEFT_IS_LEFT variable. But the
bottom of each image window says "left=SOMETHING", so it is not
ambiguous. The coronal and axial images should say "left=left",
if you have that variable set to "YES", otherwise, "left=right".
- rick