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April 21, 2021 05:38PM
I ran afni_proc.py-based analysis and it produced no QC folder. I may have done something wrong in setting up the analysis , but I can't figure out what. I would appreciate suggestions...

Here is the relevant part of the output:
apqc_make_tcsh.py -review_style pythonic -subj_dir . -uvar_json out.ss_review_uvars.json
++ Found 40 files for QCing.
Traceback (most recent call last):
  File "/home/pawel/abin/apqc_make_tcsh.py", line 563, in <module>
    tspace    = lat.get_space_from_dset(ap_ssdict['template'])
  File "/home/pawel/abin/afnipy/lib_apqc_tcsh.py", line 291, in get_space_from_dset
    dset_fullpath = com.so[0]
IndexError: list index out of range


afni_proc call from my script

afni_proc.py                                                              \
        -subj_id                 ${subj}                                      \
        -script                  ${odir_ap}/proc.$subj.${state} -scr_overwrite \
        -out_dir                 ${odir_ap}/${subj}.${state}.results          \
        -blocks                  ${appy_blocks}                 			  \
        ${appy_blur_param}  \
        -dsets                   ${subj_epi}                                  \
        -copy_anat               "${dset_subj_anat}"                          \
        -anat_has_skull          no                                           \
        -anat_uniform_method     unifize                                         \
        -anat_unif_GM            yes                                           \
        -anat_follower_ROI       WMmask epi ${odir_aw}'/'WM_anat_mask         \
        -anat_follower_erode     WMmask                                       \
        -radial_correlate_blocks tcat volreg                                  \
        -radial_correlate_opts   -sphere_rad 14                               \
        -tcat_remove_first_trs   2                                            \
        -volreg_base_dset        "${EPIname}[0]"                              \
	-volreg_align_e2a                                                     \
        -volreg_tlrc_warp                                                     \
	-align_epi_strip_method  3dSkullStrip                                 \
        -align_opts_aea          -cost ${cost_a2e} -feature_size 4            \
                                 -partial_coverage -deoblique on              \
                                 -giant_move -cmass cmass                     \
                                 -check_flip                                  \
	-align_epi_ext_dset      "${EPIname}[0]"                               \
        -tlrc_base               ${refvol}                                    \
        -tlrc_NL_warp                                                         \
        -tlrc_NL_warped_dsets                                                 \
            ${odir_aw}/${subj}*_warp2std_nsu.nii.gz                           \
            ${odir_aw}/${subj}*_composite_linear_to_template.1D               \
            ${odir_aw}/${subj}*_shft_WARP.nii.gz                              \
        -regress_anaticor_fast                                                \
        -regress_anaticor_radius  20                                          \
        -regress_anaticor_label   WMmask                                      \
        -regress_motion_per_run                                               \
        -regress_apply_mot_types  demean deriv                                \
        -regress_censor_motion    ${motion_threshold}                         \
        -regress_censor_outliers  ${outlier_threshold}                        \
        -regress_est_blur_errts                                               \
        -regress_est_blur_epits                                               \
        -regress_run_clustsim     no                                          \
        -html_review_style        pythonic                                    \
        -execute
Subject Author Posted

QC not produced by afni_proc

Pawel April 21, 2021 05:38PM

Re: QC not produced by afni_proc

ptaylor April 21, 2021 07:51PM

Re: QC not produced by afni_proc

Pawel April 21, 2021 11:33PM

Re: QC not produced by afni_proc

ptaylor April 22, 2021 08:39AM

Re: QC not produced by afni_proc

Pawel April 22, 2021 10:08AM

Re: QC not produced by afni_proc

ptaylor April 22, 2021 11:06AM

Re: QC not produced by afni_proc

Pawel April 22, 2021 11:29AM

Re: QC not produced by afni_proc

ptaylor April 22, 2021 11:44AM

Re: QC not produced by afni_proc

Pawel April 22, 2021 12:13PM

Re: QC not produced by afni_proc

ptaylor April 22, 2021 12:26PM

Re: QC not produced by afni_proc

Pawel April 22, 2021 12:32PM

Re: QC not produced by afni_proc

ptaylor April 22, 2021 12:42PM



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