Sorry to repose the same question, but I haven't, yet, received a response.
I am trying to run the non-linear registration of the dti FA files using the second script: tbss_2_reg -T
I get the response error: No such file or directory exists. I assume it is referring to FMRIB58_FA which does exist and is located in fsl/data/standard/* which is where I believe it should be.