Thank you for the response Sandor Kovacs. It actually turns out the issue was not my naming conventions but actually my brain orientations. The brain was not rotated to match the reference brain which ended up causing a warp failure. Unfortunately the aligment was not perfect and my aligned brains have several dark gaps in them especially on the early and later layers. I am not sure if you know why that may be but I will try it with the new CMTK GUI integration which might fix the issues I currently have.