AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Doughboys
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
Reply Quote
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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