I am getting only zeros in my .csv file due to poor registration

Greetings, do you know how to get these inputs:  ATLAS: Atlas file in standard space (in NIFTI format)
WARP_STD2STRUCT: Warp of the transformation from standard space to structural space (in NIFTI format)? I used AAL90 and WARP_STD2STRUCT from FSL (using T1 and AAL90), but I am getting only zeros due to poor registration. Thank you