Generating QC HTML report without running regress block in afni_proc

AFNI Message Board
1

Hi there,

I would like to apply some minimal preprocessing to my functional data using AFNI and afni_proc as a first step before fitting a special model outside AFNI using my own custom code. Therefore, I have no need for the regress block in my afni_proc script. However, I've discovered that removing the regress block means that the many beautiful QC figures/reports never get generated. Is there a way I can get afni_proc to generate the (indispensable) QC reports (for purposes of judging alignment, motion, tSNR, etc) without conducting any regression?

Below is my afni_proc script:

afni_proc.py -subj_id $subj                                                   \
	    -out_dir ER_${ses}                                                        	\
		-script proc.${ses}.${subj} -scr_overwrite                             	    \
		-blocks tshift align volreg surf scale                                      \
		-radial_correlate_blocks tcat volreg                                        \
		-copy_anat $anat_dir/${subj}_ses-01_T1w.nii.gz                              \
		-dsets  $epidata                                                            \
		-blip_forward_dset $fmap_dir/${subj}_${ses}_fmap-AP_bold.nii.gz	            \
		-blip_reverse_dset $fmap_dir/${subj}_${ses}_fmap-PA_bold.nii.gz	            \
		-volreg_align_to MEDIAN_BLIP	                                              \
		-blip_opts_qw  -noXdis -noZdis -Qfinal                                      \
		-tcat_remove_first_trs 0                                                    \
		-tcat_remove_last_trs 0			                                                \
		-tshift_opts_ts -tpattern @/data1/2021_R01/scripts/slice-timing-se.txt      \
		-align_opts_aea -giant_move                                                 \
		                -cost lpc+ZZ                                                \
				        -check_flip                                                 \
		-volreg_align_to MIN_OUTLIER                                                \
		-volreg_align_e2a                                                           \
		-volreg_interp -Fourier						                                          \
		-volreg_post_vr_allin yes                                                   \
	        -volreg_pvra_base_index MIN_OUTLIER                                         \
		-volreg_compute_tsnr yes                                                    \
		-surf_anat ${top_dir}/derivatives/fs/${subj}/surf/SUMA/${subj}_SurfVol.nii     \
		-surf_spec ${top_dir}/derivatives/fs/${subj}/surf/SUMA/std.141.${subj}_?h.spec  \
		-html_review_style pythonic

Many thanks!
Daniel

AFNI version info (afni -ver): 23.3.12

2

Hi Daniel,

That is why we include the regress block in the ap_run_simple_rest* versions, for the QC block. Just keep the regress block but ignore those outputs, or even delete those resulting datasets. But still, it should be okay to keep that block, treating the data as if it were rest.
-rick

1 Like
3

Thanks for pointing me to the ap_run_simple_rest demo, Rick! For some reason, I didn't consider you can run a regression without specifying a stimulus. I decided to keep the resultant error time series data with the nuisance predictors projected out, just in case I have a need for them. Given the file size, though, I might decide to delete it. Easy enough. It's great to have the QC reports back!

Thanks again,
Daniel