I am now working in converting cortical labels from freesurfer to volumetric masks. First i gained the registration matrix by bbregister, then applied those matrix to tranform ROI labels into native space using label2vol. However, when i got the final .NII results, both of them turn out to be L-R fliped. (left ROI on the right hemisphere). From my understanding, freesurfer will automaticly recognize the head direction of the original T1 images and my original T1 data contains the flip information due to the way we scaned.