Hello AFNI gurus!
What is the best way to preprocess data such that I have slice-time corrected, aligned, motion corrected, scaled, and blurred EPIs in both the subject's native space as well as standard space? I need to run 3dDeconvolve in native space (to extract Betas for a Representational Similarity Analysis) and standard space (to do whole-brain group-level contrasts).

Using the following afni_proc command doesn't save the preprocessed data in native space.

afni_proc.py -subj_id $sid -script proc.$sid -scr_overwrite        \
      -blocks tshift align tlrc volreg mask blur scale regress     \
      -copy_anat $anat_ss                                          \
      -anat_has_skull no                                           \
      -anat_follower anat_w_skull anat $anat_orig                  \
      -dsets $EPI_files                                            \
      -tcat_remove_first_trs 0                                     \
      -tshift_opts_ts -tpattern alt+z2                             \
      -radial_correlate yes                                        \
      -align_opts_aea -giant_move -cost lpc+ZZ -check_flip         \
      -tlrc_base MNI152_2009_template_SSW.nii.gz                   \
      -tlrc_NL_warp                                                \
      -tlrc_NL_warped_dsets $anat_std $anat_warp_aff $anat_warp_nl \
      -volreg_align_to MIN_OUTLIER                                 \
      -volreg_align_e2a                                            \
      -volreg_tlrc_warp                                            \
      -mask_epi_anat yes                                           \
      -blur_size 6                                                 \
      -blur_in_mask yes

But if I change the order of the block (like in the following command), it doesn't run the tlrc block at all.

afni_proc.py -subj_id $sid -script proc.$sid -scr_overwrite        \
      -blocks tshift volreg align  blur mask scale tlrc			   \
      -copy_anat $anat_ss                                          \
      -anat_has_skull no                                           \
      -anat_follower anat_w_skull anat $anat_orig                  \
      -dsets $EPI_files                                            \
      -tcat_remove_first_trs $dummy_scans                          \
      -tshift_opts_ts -tpattern $stc_pattern                       \
      -radial_correlate yes                                        \
      -align_opts_aea -giant_move -cost lpc+ZZ -check_flip         \
      -tlrc_base MNI152_2009_template_SSW.nii.gz                   \
      -tlrc_NL_warp                                                \
      -tlrc_NL_warped_dsets $anat_std $anat_warp_aff $anat_warp_nl \
      -volreg_align_to MIN_OUTLIER                                 \
      -volreg_align_e2a                                            \
      -volreg_tlrc_warp                                            \
      -mask_epi_anat yes                                           \
      -blur_size $blur_size                                        \
      -blur_in_mask yes                                            \

Should I just run Option 1 once with, and once without the tlrc block?
Thank you,
Mrinmayi