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History of AFNI updates  

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March 18, 2021 07:31PM
Hello AFNI gurus!
I am running preprocessing on some data and was hoping to generate the the HTML quality control reports using:
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
as suggested here [afni.nimh.nih.gov].

But I'm getting the following error:
++ Found 39 files for QCing.
** ERROR: radcor number of ulays (0) doesn't match number of olays (6)

Why might this be happening? I have BRIK/HEAD files for all runs in radcor.pb00.tcat/ and radcor.pb02.volreg/ that are called epi.ulay.r0?. Should these be used as underlays?

Here is the afni_proc.py command I'm using:
afni_proc.py -subj_id sub-001 -script proc.sub-001 -scr_overwrite           \
            -blocks tshift align tlrc volreg mask blur scale regress                   \
            -radial_correlate yes                                                                       \
            -radial_correlate_blocks tcat volreg                                                \
            -copy_anat /raid-09/LS/hannula/mrinmayi/ConcealMemory/derivatives/AFNI_01_Search_SSwarper/sub-001/anatSS.sub-001.nii                                             \
            -anat_has_skull no                                                                           \
            -anat_follower anat_w_skull anat /raid-09/LS/hannula/mrinmayi/ConcealMemory/derivatives/AFNI_01_Search_SSwarper/sub-001/anatU.sub-001.nii                     \
            -dsets /raid-09/LS/hannula/mrinmayi/ConcealMemory/rawdata/sub-001/func/sub-001_task-exp_run-01_bold.nii /raid-09/LS/hannula/mrinmayi/ConcealMemory/rawdata/sub-001/func/sub-001_task-exp_run-02_bold.nii /raid-09/LS/hannula/mrinmayi/ConcealMemory/rawdata/sub-001/func/sub-001_task-exp_run-03_bold.nii /raid-09/LS/hannula/mrinmayi/ConcealMemory/rawdata/sub-001/func/sub-001_task-exp_run-04_bold.nii /raid-09/LS/hannula/mrinmayi/ConcealMemory/rawdata/sub-001/func/sub-001_task-exp_run-05_bold.nii /raid-09/LS/hannula/mrinmayi/ConcealMemory/rawdata/sub-001/func/sub-001_task-exp_run-06_bold.nii                                               \
            -tcat_remove_first_trs 4                                                                   \
            -tcat_remove_last_trs 0                                                                   \
            -tshift_opts_ts -tpattern alt+z2                                                         \
            -align_opts_aea -big_move -cost lpc+ZZ -check_flip                      \
            -tlrc_base MNI152_2009_template_SSW.nii.gz                              \
            -tlrc_NL_warp                                                                                  \
            -tlrc_NL_warped_dsets /raid-09/LS/hannula/mrinmayi/ConcealMemory/derivatives/AFNI_01_Search_SSwarper/sub-001/anatQQ.sub-001.nii /raid-09/LS/hannula/mrinmayi/ConcealMemory/derivatives/AFNI_01_Search_SSwarper/sub-001/anatQQ.sub-001.aff12.1D /raid-09/LS/hannula/mrinmayi/ConcealMemory/derivatives/AFNI_01_Search_SSwarper/sub-001/anatQQ.sub-001_WARP.nii    \
            -volreg_align_to MIN_OUTLIER                                                      \
            -volreg_align_e2a                                                                            \
            -volreg_tlrc_warp                                                                             \
            -mask_epi_anat yes                                                                        \
            -blur_size 4                                                                                      \
            -blur_in_mask yes                                                                           \
            -regress_motion_per_run                                                                \
            -regress_censor_motion 0.3                                                            \
            -regress_censor_outliers 0.05                                                         \
            -regress_apply_mot_types demean deriv                                       \
            -html_review_style pythonic

And here is the output for afni -ver
Precompiled binary linux_openmp_64: Jul 3 2019 (Version AFNI_19.2.01 'Claudius')

Just fyi, the QC scripts aren't being run on their own in the afni_proc.py command because I'm running the preprocessing on a cluster, and we have to source a bunch of additional modules outside the job scheduler for it to be able to generate these plots.
Thank you,
Mrinmayi
Subject Author Posted

Error with generating HTML QC reports

mrinmayik March 18, 2021 07:31PM

Re: Error with generating HTML QC reports

ptaylor March 18, 2021 09:19PM

Re: Error with generating HTML QC reports

mrinmayik March 18, 2021 10:05PM

Re: Error with generating HTML QC reports

ptaylor March 18, 2021 10:26PM

Re: Error with generating HTML QC reports

rick reynolds March 18, 2021 11:28PM

Re: Error with generating HTML QC reports

mrinmayik March 19, 2021 12:13AM

Re: Error with generating HTML QC reports

ptaylor March 19, 2021 12:57PM

Re: Error with generating HTML QC reports

mrinmayik March 19, 2021 02:14PM