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History of AFNI updates  

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November 12, 2021 03:53PM
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
Subject Author Posted

afni_proc.py EPI strip

Doughboys November 11, 2021 10:23AM

Re: afni_proc.py EPI strip

Peter Molfese November 12, 2021 02:17PM

Re: afni_proc.py EPI strip

ptaylor November 12, 2021 02:42PM

Re: afni_proc.py EPI strip

Daniel Glen November 12, 2021 03:23PM

Re: afni_proc.py EPI strip

Doughboys November 12, 2021 03:53PM

Re: afni_proc.py EPI strip

rick reynolds November 12, 2021 04:12PM



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