Thanks a lot for your input.
I think that there might be a hole in my knowledge about view vs. space.
The output below is from @auto_tlrc which was first applied to the structural and then I input the stats file into @auto_tlrc with the output of the previous step (transformed structural) being specified under option -apar.
*+ WARNING: Changing the space of an ORIG view dataset may cause confusion!
*+ WARNING: NIFTI copies will be interpreted as TLRC view (not TLRC space).
*+ WARNING: Consider changing the view of the dataset to TLRC view also
++ 3drefit processed 1 datasets
Changing view of xformed volumes
Based on this terminal output it seems that my view was marked as TLRC but not the space. If I am correct the space determines the coordinates (xyz) and if it is set to an atlas the coordinates you get from AFNI correspond with those from the atlas specified under space. What does the view really mean (I know it is marked in the header)?
