Dear Kirk,

I'm running into the same problem as the original poster. Whenever I try to run the first step of TBSS (tbss_1_preproc) with the produced fa maps, I get the message "ERROR: Inconsistent left-right order stored in sform and qform in file fa Using sform instead of qform values". I tried using fslreorient2std as suggested to put them in an FSL-friendly orientation, but still got the same error message. I tried to register the maps to MNI space, still same error.

FSL just refuses to to handle any DKE output files. I tested my input files with FSL dtifit, and produced regular FA maps which I was able to feed into the TBSS pipeline, so my input files definitely have no orientation issue (I think!).

Is there any solution to that problem? I was so excited to finally produce DKI maps, but now I have no idea how to handle them.... 

Thanks for the help.

Cheers,

Shereif