Hi
I wanted to share a code I picked up at the Afni Bootcamp! One can use fmriprep output with afni_proc to do the following analysis (My example: blur scaling and regressions). The code might throw an error when generating the QC page. But no worries, the main analysis will still wrap up just fine. The QC page is a bit tricky and might need to wait for an update in the future.
Best
#!/usr/bin/env tcsh
# set data directory
set top_dir = /media/test/afni_fmriprep/sub-LM027
# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id sub-LM027 \
-blocks mask blur scale regress \
-radial_correlate_blocks tcat regress \
-copy_anat $top_dir/sub-LM027_ses-T2_desc-preproc_T1w.nii.gz \
-dsets \
$top_dir/sub-LM027_ses-T2_task-Prototype1_space-T1w_desc-preproc_bold.nii.gz \
-blur_size 4.0 \
-regress_motion_file \
$top_dir/afni_sub-LM027_ses-T2_task-Prototype1_confounds.txt \
-regress_stim_times \
$top_dir/afni_sub-LM027_ses-T2_task-Prototype1_allTrials.txt \
# I used the following to transform fsl-type regressor into afni-type. \
# timing_tool.py -fsl_timing_files input -write_timing output \
-regress_stim_labels \
allTrials \
-regress_basis 'BLOCK(5,1)' \
-regress_censor_motion 1.0 \
-regress_censor_outliers 0.05 \
-regress_motion_per_run \
-regress_opts_3dD \
-jobs 1 \
-gltsym 'SYM: allTrials ' -glt_label 1 V-A \
-regress_compute_fitts \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no \
-html_review_style pythonic \
-execute