AFNI version info (afni -ver): AFNI_24.0.17 'Caracalla'
I was at the recent bootcamp at the NIH and want to first say thank you for hosting such a helpful workshop - I really enjoyed it and learned a lot!
I am attempting to run the final pre-processing steps and first level analysis on subjects from a data set on Open Neuro (link if it is useful). We did the initial round of pre-processing through fMRIprep. I think I got all of my timing files and confound files converted correctly (thanks to y'alls help in person yesterday!)
This is the script I ran:
#!/usr/bin/env tcsh
# set subject and group identifiers
set subj = 006
set ses = T1
set task = Num
# set data directory
set top_dir = /Volumes/ITALY/derivatives/sub-${subj}
# run afni_proc.py to create a single subject processing script
afni_proc.py -subj_id $subj \
-blocks tcat blur mask scale regress \
-copy_anat $top_dir/anat/sub-${subj}_space-MNI152NLin2009cAsym_res-2_desc-preproc_T1w.nii.gz \
-dsets \
$top_dir/ses-${ses}/func/sub-${subj}_ses-${ses}_task-${task}_run-01_space-MNI152NLin2009cAsym_res-2_desc-preproc_TR1570_bold.nii \
$top_dir/ses-${ses}/func/sub-${subj}_ses-${ses}_task-${task}_run-02_space-MNI152NLin2009cAsym_res-2_desc-preproc_TR1570_bold.nii \
-tcat_remove_first_trs 0 \
-regress_motion_per_run \
-regress_motion_file \
$top_dir/ses-${ses}/func/sub-${subj}_ses-${ses}_task-${task}_mvt-confounds.txt \
-regress_censor_motion 0.5 \
-regress_censor_outliers 0.05 \
-regress_censor_prev yes \
-regress_extra_ortvec \
$top_dir/ses-${ses}/func/sub-${subj}_ses-${ses}_task-${task}_aCompCor-confounds.txt \
-regress_extra_ortvec_labels 5aCompCor \
-regress_reml_exec \
-regress_stim_times \
$top_dir/ses-${ses}/func/num_hard_ses-T1.1D \
$top_dir/ses-${ses}/func/num_medium_ses-T1.1D \
$top_dir/ses-${ses}/func/num_easy_ses-T1.1D \
$top_dir/ses-${ses}/func/num_control_ses-T1.1D \
-regress_stim_times_offset -0.785 \
-regress_stim_labels \
NumHard NumMedium NumEasy NumControl \
-regress_basis 'BLOCK(2,1)' \
-regress_opts_3dD \
-bout \
-gltsym 'SYM: NumHard -NumControl' -glt_label 1 NumH-C \
-gltsym 'SYM: NumMedium -NumControl' -glt_label 2 NumM-C \
-gltsym 'SYM: NumEasy -NumControl' -glt_label 3 NumE-C \
-gltsym 'SYM: NumHard NumMedium NumEasy -3*NumControl' -glt_label 4 NumHME-C \
-regress_est_blur_epits \
-regress_est_blur_errts \
-write_3dD_prefix NumFirstLevel \
-html_review_style pythonic \
-execute
It seemed like my script ran almost all the way through until it got this error at the very end:
++ Done making (executable) GV pbrun script:
run_graphview_pbrun.tcsh
++ APQC create: qc_00_vorig_anat
++ APQC create: qc_01_mot_enormoutlr
++ APQC create: qc_02_mot_VR6
++ APQC create: qc_03_mot_grayplot
++ APQC create: qc_04_regr_ideal
++ APQC create: qc_05_regr_stims
++ APQC create: qc_06_regr_df
++ APQC create: qc_07_radcor_rc_regress
Traceback (most recent call last):
File "/Users/fmriprep/abin/apqc_make_tcsh.py", line 957, in <module>
rcname, rcdir, ith_run=ii )
File "/Users/fmriprep/abin/afnipy/lib_apqc_tcsh.py", line 5712, in apqc_radcor_rcvol
all_ulay = [ap_ssdict['main_dset']] # bc errts makes a poor ulay
KeyError: 'main_dset'
I opened up the scripts that are referenced in the error, but I am not a proficient enough coder to understand exactly what is going wrong so hopefully someone here can help!