Hello,

If we are using the moco (motion corrected) series output from a Siemens 3T Trio, is it okay to still run motion correction on the images during preprocessing (i.e. 3dvolreg) or will this be introducing unnessary interpolation? Do the motion parameters from the moco series get accounted for in the motion output file from afni_proc.py? Would you recommend continuing to use the motion corrected images from the scanner or would it be better to use the original raw files and do all preprocessing post scanning session? We are combining multiple runs and currently use the following script (stim times/labes and glms removed for ease of reading):

afni_proc.py -subj_id $subj \
-script proc.$subj -scr_overwrite \
-out_dir ~/Desktop/Imaging/${study}_PDD/${subj}.PDD \
-move_preproc_files \
-blocks tshift despike align tlrc volreg blur mask scale regress \
-copy_anat $anat_dir/$subj.MPRAGE+orig \
-tcat_remove_first_trs 0 \
-dsets $epi_dir/${subj}.EPI?m+orig.HEAD \
-align_opts_aea -giant_move \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_size 4.0 \
-test_stim_files no \
-regress_stim_times \
-regress_stim_labels \
-regress_local_times \
-regress_basis 'BLOCK5(1,1)' \
-regress_stim_types \
AM2 AM2 AM2 AM2 times AM2 AM2 \
-regress_opts_3dD \
-jobs 5 \
-GOFORIT 5 \
-regress_reml_exec \
-regress_opts_reml -GOFORIT \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts

Any advice would be much appreciated as we cannot find very much information about what the Moco series is doing.

Thank you!