I am surprised that does not throw an error or at least a warning. The warps produced by population template are actually 4 warps (“warp_full”) stored in one 5D file, you’ll need to convert this to a single deformation field from template to subject space and apply that warp to tcktransform. I think the following should work:
C01_dir=
warpconvert ~/Desktop/data/ctrl/frontalparc/ctrl_template_t1Brain/warps/C01.mif warpfull2deformation -from 1 -template ~/Desktop/data/ctrl/frontalparc/ctrl_template_t1Brain/C01.mif - | tcknormalise "$C01_dir"/dti/frontal_parc/tckgen_l_drtc_rnmask_5mseeds_bi.tck - C01_l_drtc_warped.tck