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