Sure the command
afni_proc.py -subj_id Oliver2019_02_02 -script \
proc.Oliver2019_02_02
-scr_overwrite -out_dir \
/Oliver2019_02_02.results \
-blocks tshift align tlrc volreg blur mask regress -dsets \
BOLD_rs_tshift_deob_RECEN.nii.gz \
-copy_anat \
Oliver2019_02_02/anatT1_deob.nii.gz \
-anat_has_skull no -align_opts_aea -cost lpc+zz -check_flip -giant_move \
-epi_strip None -mask_dilate 1 -volreg_align_to MIN_OUTLIER \
-volreg_align_e2a -volreg_tlrc_warp -mask_epi_anat yes -tlrc_base \
anatT1_deob_in_stdy_template.nii.gz \
-tlrc_NL_warp -tlrc_NL_warped_dsets \
anatT1_deob_in_stdy_template.nii.gz \
identity.aff12.1D \
concate_linear_and_WARP.nii.gz \
-regress_motion_per_run -regress_apply_mot_types demean deriv \
-blur_size 3 -mask_import WMa \
atlas_to_study_template/WM2mm.nii.gz \
-regress_make_corr_vols WMa -regress_anaticor_fast \
-regress_run_clustsim yes -regress_est_blur_errts -html_review_style \
pythonic -execute -tcat_remove_first_trs 5
generates:
align_epi_anat.py -anat2epi -anat anatT1_deob+orig \
-suffix _al_junk \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-anat_has_skull no \
-cost lpc+zz -check_flip -giant_move -epi_strip None \
-volreg off -tshift off
When :
afni_proc.py -subj_id Oliver2019_02_02 -script \
proc.Oliver2019_02_02 \
-scr_overwrite -out_dir \
Oliver2019_02_02.results \
-blocks tshift align tlrc volreg blur mask regress -dsets \
BOLD_rs_tshift_deob_RECEN.nii.gz \
-copy_anat \
Oliver2019_02_02/anatT1_deob.nii.gz \
-anat_has_skull no -align_opts_aea -cost lpc+zz -check_flip -giant_move \
-epi_strip None -align_epi_strip_method None -mask_dilate 1 \
-volreg_align_to MIN_OUTLIER -volreg_align_e2a -volreg_tlrc_warp \
-mask_epi_anat yes -tlrc_base \
Oliver2019_02_02/anatT1_deob_in_stdy_template.nii.gz \
-tlrc_NL_warp -tlrc_NL_warped_dsets \
Oliver2019_02_02/anatT1_deob_in_stdy_template.nii.gz \
identity.aff12.1D \
Oliver2019_02_02/concate_linear_and_WARP.nii.gz \
-regress_motion_per_run -regress_apply_mot_types demean deriv \
-blur_size 3 -mask_import WMa \
atlas_to_study_template/WM2mm.nii.gz \
-regress_make_corr_vols WMa -regress_anaticor_fast \
-regress_run_clustsim yes -regress_est_blur_errts -html_review_style \
pythonic -execute -tcat_remove_first_trs 5
generates:
align_epi_anat.py -anat2epi -anat anatT1_deob+orig \
-suffix _al_junk \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip None \
-anat_has_skull no \
-cost lpc+zz -check_flip -giant_move -epi_strip None \
-volreg off -tshift off
