Hi,

I have questions when I run afni_proc.py example 11b since I am trying to use MNI space instead of Talairach space

This is my afni_proc.py

afni_proc.py -subj_id FT.11b.rest \
-blocks despike tshift align tlrc volreg blur mask regress \
-copy_anat My_anat+orig \
-dsets My_epi+orig.HEAD \
-tcat_remove_first_trs 2 \
-align_opts_aea -cost lpc+ZZ \
-tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \
-volreg_tlrc_warp \
-volreg_warp_dxyz 2.5 \
-mask_segment_anat yes \
-mask_segment_erode yes \
-mask_import Tvent template_ventricle_2.5mm+tlrc \
-mask_intersect Svent CSFe Tvent \
-regress_motion_per_run \
-regress_ROI_PC Svent 3 \
-regress_ROI_PC_per_run Svent \
-regress_make_corr_vols WMe Svent \
-regress_anaticor_fast \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.1 \
-regress_apply_mot_types demean deriv \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim yes


I just changed input datasets(epi and anat) and tlrc_base to MNI space.
For the Talairach space,
3dcalc -a ~/abin/TT_desai_dd_mpm+tlrc \
-expr 'amongst(a,152,170)' -prefix template_ventricle
3dresample -dxyz 2.5 2.5 2.5 -inset template_ventricle+tlrc \
-prefix template_ventricle_2.5mm

I need to use these command. But for MNI space, how can I modify these commands and afni_proc.py?
and why do we need to resample them in 2.5mm?


Thanks