Thanks. For now I am using -regress_no_fitts and that seems to be working. Is there a similar option for -regress_no_errts if you don't want to add -errts to 3dDecon? Could not find it in afni_proc.py help.
Now there is another strange problem. This may be a minor silly scripting thing, not sure. Most of the proc.s1 script seems to have run correctly, and all the corresponding files are generated. Then it never seems to finish. Last files were generated 14 hrs ago, but the script is still running for some reason. The last few lines of the proc.s1 script are
-------------
# if the basic subject review script is here, run it
# (want this to be the last text output)
if ( -e @ss_review_basic ) then
./@ss_review_basic |& tee out.ss_review.$subj.txt
# generate html ss review pages
# (akin to static images from running @ss_review_driver)
apqc_make_tcsh.py -review_style basic -subj_dir . \
-uvar_json out.ss_review_uvars.json
tcsh @ss_review_html |& tee out.review_html
apqc_make_html.py -qc_dir QC_$subj
echo "\nconsider running: \n\n afni_open -b $subj.results/QC_$subj/index.html\n"
endif
# return to parent directory (just in case...)
cd ..
echo "execution finished: `date`"
-------------------
All of the commands seem to have run. The @ss_review_basic is run and there is output in the output.proc.s1 file. There are out.review_html and out.ss_review_uvars.json files generated 14 hrs ago. The QC_s1 folder was also generated, and there are files inside indicating apqc_make_html.py ran fine. But the "consider running:.." message is never printed. "execution finished" is also never printed. The last few lines of output.proc.s1 are
TSNR average : 206.017
global correlation (GCOR) : 0.0374245
anat/EPI mask Dice coef : 0.909886
anat/templ mask Dice coef : 0.953539
maximum F-stat (masked) : 216.554
blur estimates (ACF) : 0.644382 5.29497 13.4468
blur estimates (FWHM) : 0 0 0
which as printed 14 hrs ago. After this, nothing.
'ps' still shows that proc.s1 is still running, 'tee out.review_html' is still running, doing what I am not sure. Any thoughts on why would the script not finish?
