I am running the latest version of AFNI (AFNI_2007_05_29_1644). However, despite the warning, the orientation of the dataset seems fine. Is it then safe to simply disregard this warning?
I've uploaded a single run of the raw data and the script that I used for BRIK creation in case you wanted to have a look. The filename is to3d_warningData.tgz.
thanks again