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April 21, 2022 09:28PM
Hi, Osman-

Thanks for sending a copy of some of the APQC HTML. Attached is the critical part that I suggested looking at---the ve2a, which shows the EPI-anatomical alignment. Because your initial EPI and anatomical are a bit far apart (shown in the vorig block of the APQC), I suggest adding the option "-giant_move" to your afni_proc.py command in the '-align_opts_aea ..' part of controlling alignment of EPI and anatomical (= AEA), like this:

#!/bin/tcsh

afni_proc.py                                                                 \
    -subj_id                  FT.11b.rest                                    \
    -blocks                   despike tshift align tlrc volreg blur mask     \
                              scale regress                                  \
    -copy_anat                anat+orig                                      \
    -dsets                    func+orig.HEAD                                 \
    -tcat_remove_first_trs    2                                              \
    -align_opts_aea           -cost lpc+ZZ   -giant_move                                \
    -tlrc_base                TT_N27+tlrc                                    \
    -tlrc_NL_warp                                                            \
    -volreg_align_to          MIN_OUTLIER                                    \
    -volreg_align_e2a                                                        \
    -volreg_tlrc_warp                                                        \
    -volreg_warp_dxyz         2.5                                            \
    -blur_size                4                                              \
    -mask_segment_anat        yes                                            \
    -mask_segment_erode       yes                                            \
    -mask_import              Tvent template_ventricle_2.5mm+tlrc            \
    -mask_intersect           Svent CSFe Tvent                               \
    -mask_epi_anat            yes                                            \
    -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  0.05                                           \
    -regress_apply_mot_types  demean deriv                                   \
    -regress_est_blur_epits                                                  \
    -regress_est_blur_errts                                                  \
    -regress_run_clustsim     yes

Also, I don't see the motion plots in your QC. I was a bit surprised by that. What is the output of:
afni_system_check.py -check_all

?

--pt


Subject Author Posted

afni_proc.py example 11b

osman April 20, 2022 07:25PM

Re: afni_proc.py example 11b

ptaylor April 21, 2022 09:55AM

Re: afni_proc.py example 11b Attachments

osman April 21, 2022 05:06PM

Re: afni_proc.py example 11b

ptaylor April 21, 2022 05:12PM

Re: afni_proc.py example 11b

osman April 21, 2022 05:48PM

Re: afni_proc.py example 11b Attachments

ptaylor April 21, 2022 09:28PM

Re: afni_proc.py example 11b Attachments

osman April 28, 2022 12:15PM

Re: afni_proc.py example 11b Attachments

ptaylor April 28, 2022 12:42PM

Re: afni_proc.py example 11b

rick reynolds April 28, 2022 01:06PM

Re: afni_proc.py example 11b Attachments

osman April 28, 2022 07:27PM

Re: afni_proc.py example 11b

osman April 28, 2022 07:30PM

Re: afni_proc.py example 11b

ptaylor April 29, 2022 08:49AM

Re: afni_proc.py example 11b

osman April 29, 2022 10:23AM

Re: afni_proc.py example 11b

ptaylor April 29, 2022 02:52PM



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