Hi Konstantinos, 

May I follow up with this string?  
Since DTITK re-set the origin to the center and reorients the tensor to LPI, in order to transform back to MNI coordinates, I need to apply "flirt" using "-applyxfm -init" with the  matrix, [-1 0 0 90; 0 1 0 -126; 0 0 1 -72; 0 0 0 1], correct? 

However, the transformed image did not overly with MNI  template. Did I miss anything? 

Thank you, 

Ping