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