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Dear AFNI users-

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Sincerely, AFNI HQ

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MayaSa
July 10, 2022 02:53AM
Hi,
I am running proc.py for 7T multi-echo data and I don't get an output of the QC HTML file.
I will very much appreciate your help in understanding how to fix it.
attached is my proc.py script: 

afni_proc.py \
     -subj_id $subject.$session.$scan.ME.blur \
     -blocks despike tshift align tlrc volreg blur mask combine scale \
     -radial_correlate_blocks tcat volreg                      \
     -blip_forward_dset $subject.$session.AP.ME+orig.HEAD                     \
     -blip_reverse_dset $subject.$session.PA.ME+orig.HEAD                     \
     -copy_anat anatSS.$subject.$session.$scan.ME.nii \
     -anat_has_skull no \
     -dsets_me_run $subject.$session.$scan.ME_00?+orig.HEAD \
     -echo_times 13.2 34.72 56.24 \
     -reg_echo 2                                               \
     -tcat_remove_first_trs 4                                  \
     -tshift_interp -wsinc9                                    \
     -align_opts_aea -cost lpc+ZZ -giant_move            \
     -tlrc_base MNI152_2009_template_SSW.nii.gz               \
     -tlrc_NL_warp                                             \
     -tlrc_NL_warped_dsets anatQQ.$subject.$session.$scan.ME.nii anatQQ.$subject.$session.$scan.ME.aff12.1D anatQQ.$subject.$session.$scan.ME_WARP.nii \
     -volreg_align_to MIN_OUTLIER                              \
     -volreg_align_e2a                                         \
     -volreg_tlrc_warp                                         \
     -blur_size 4												\
     -mask_epi_anat yes                                        \
     -combine_method tedana                                    \
     -html_review_style pythonic \
     -scr_overwrite
     
tcsh -xef proc.$subject.$session.$scan.ME.blur 2>&1 | tee output.proc.$subject.$session.$scan.ME.blur

Thank you in advance!
Maya
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Subject Author Posted

QC file for proc.py with tedana

MayaSa July 10, 2022 02:53AM

Re: QC file for proc.py with tedana

ptaylor July 10, 2022 06:53PM

Re: QC file for proc.py with tedana

MayaSa July 12, 2022 06:06AM

Re: QC file for proc.py with tedana

ptaylor July 12, 2022 08:30AM

Re: QC file for proc.py with tedana

ptaylor July 13, 2022 09:23AM