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