Thanks - I had actually been looking at the 'users' manual & didn't realise that there was a separate developer's manual!

I have been following the steps from the developer's manual today and I am stuck on orientation - my atlas file is oriented such that the front of the brain is pointing towards the right and the MNI_T1.nii is facing the left!

Doing manual reorientation in 'display' in SPM12 doesn't work as I need to flip or invert the image rather that just rotate it (which results in the image being upside down!). I have also tried 'reorient' in the batch window & it says for a left-right orientation you enter the vector [-1 0 0 0; 0 1 0 0; 0 0 1 0; 0 0 0 1] but I want to orient it from right to left - any tips? (also when I try their left-right vector on a left facing image, e.g. the MNI_T1.nii, it looks exactly the same afterwards when I do a check reg?

I have attached the atlas I am trying to reorient - just in case you wanted to view it. 

Thank you in advance for your help!