2) Non-linearly warp images into 1x1x1 standard space using  the FSL script "tbss_2_reg" 

The "tbss_2_reg" script uses nonlinear deformation procedures performed by FNIRT \cite{s2007}, specifically a b-spline representation of the registration warp field. The -T option in the code below is a flag to indicate that the FMRIB58_FA template was used as the target.