From the error that you posted earlier
Error: target image /usr/share/fsl/data/standard/FMRIB58_FA_1mm not valid
Usage: tbss_2_reg [options]
Target-selection options - choose ONE of:
-T : use FMRIB58_FA_1mm as target for nonlinear registrations (recommended)
-t <target> : use <target> image as target for nonlinear registrations
-n : find best target from all images in FA
I think "tbss_2_reg" couldnt locate the FMRIB58_FA template as the target. So I think the source of the problem lies here.