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Dear AFNI users-

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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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DeLab
March 31, 2021 10:30PM
Running a script generated by afni_proc.py called proc.s3. Goes up to 3dDeconvolve, runs 3dDeconvolve, in about 4 hrs generates the stats.s3 file, then appears to hang. The 3dDeconvolve process is running 6 hrs after saving the stats file but nothing seems to be happening no new files being generated in 6 hours. The last few lines of output.proc.s3 file are

...
++ Smallest FDR q [74 LP+LN+MP+MN-2AP-2AN_GLT#0_Tstat] = 6.6892e-08
++ Smallest FDR q [75 LP+LN+MP+MN-2AP-2AN_GLT_Fstat] = 6.68918e-08
++ Wrote bucket dataset into ./stats.s3+tlrc.BRIK
+ created 51 FDR curves in bucket header

The fitts and errts files are not generated and appears to stall. The 3dDecon command in proc.s3 file is

# ------------------------------
# run the regression analysis
3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \
-censor censor_${subj}_combined_2.1D \
-ortvec ROI.CSFe_rall.1D ROI.CSFe \
-ortvec mot_demean.r01.1D mot_demean_r01 \
-ortvec mot_demean.r02.1D mot_demean_r02 \
-ortvec mot_demean.r03.1D mot_demean_r03 \
-ortvec mot_demean.r04.1D mot_demean_r04 \
-ortvec mot_demean.r05.1D mot_demean_r05 \
-ortvec mot_demean.r06.1D mot_demean_r06 \
-ortvec mot_demean.r07.1D mot_demean_r07 \
-ortvec mot_demean.r08.1D mot_demean_r08 \
-ortvec mot_demean.r09.1D mot_demean_r09 \
-polort 3 \
-num_stimts 8 \
-stim_times 1 stimuli/abstract_negative_timing.1D 'SPMG1(2.5)' \
-stim_label 1 abstract_negative_timing \
-stim_times 2 stimuli/abstract_positive_timing.1D 'SPMG1(2.5)' \
-stim_label 2 abstract_positive_timing \
-stim_times 3 stimuli/filler_negative_timing.1D 'SPMG1(2.5)' \
-stim_label 3 filler_negative_timing \
-stim_times 4 stimuli/filler_positive_timing.1D 'SPMG1(2.5)' \
-stim_label 4 filler_positive_timing \
-stim_times 5 stimuli/literal_negative_timing.1D 'SPMG1(2.5)' \
-stim_label 5 literal_negative_timing \
-stim_times 6 stimuli/literal_positive_timing.1D 'SPMG1(2.5)' \
-stim_label 6 literal_positive_timing \
-stim_times 7 stimuli/metaphor_negative_timing.1D 'SPMG1(2.5)' \
-stim_label 7 metaphor_negative_timing \
-stim_times 8 stimuli/metaphor_positive_timing.1D 'SPMG1(2.5)' \
-stim_label 8 metaphor_positive_timing \
-jobs 4 \
-num_glt 17 \
-gltsym 'SYM: abstract_positive_timing -abstract_negative_timing' \
-glt_label 1 AP-AN \
-gltsym 'SYM: literal_positive_timing -literal_negative_timing' \
-glt_label 2 LP-LN \
-gltsym 'SYM: metaphor_positive_timing -metaphor_negative_timing' \
-glt_label 3 MP-MN \
-gltsym 'SYM: literal_positive_timing -abstract_positive_timing' \
-glt_label 4 LP-AP \
-gltsym 'SYM: metaphor_positive_timing -abstract_positive_timing' \
-glt_label 5 MP-AP \
-gltsym 'SYM: literal_negative_timing -abstract_negative_timing' \
-glt_label 6 LN-AN \
-gltsym 'SYM: metaphor_negative_timing -abstract_negative_timing' \
-glt_label 7 MN-AN \
-gltsym 'SYM: literal_positive_timing -metaphor_positive_timing' \
-glt_label 8 LP-MP \
-gltsym 'SYM: literal_negative_timing -metaphor_negative_timing' \
-glt_label 9 LN-MN \
-gltsym 'SYM: literal_positive_timing +metaphor_positive_timing \
+abstract_positive_timing -literal_negative_timing \
-metaphor_negative_timing -abstract_negative_timing' \
-glt_label 10 LP+MP+AP-LN-MN-AN \
-gltsym 'SYM: literal_positive_timing -literal_negative_timing \
-abstract_positive_timing +abstract_negative_timing' \
-glt_label 11 LP-LN-AP+AN \
-gltsym 'SYM: metaphor_positive_timing -metaphor_negative_timing \
-abstract_positive_timing +abstract_negative_timing' \
-glt_label 12 MP-MN-AP+AN \
-gltsym 'SYM: literal_positive_timing -literal_negative_timing \
+metaphor_positive_timing -metaphor_negative_timing \
-2*abstract_positive_timing +2*abstract_negative_timing' \
-glt_label 13 LP-LN+MP-MN-2AP+2AN \
-gltsym 'SYM: literal_positive_timing -literal_negative_timing \
-metaphor_positive_timing +metaphor_negative_timing' \
-glt_label 14 LP-LN-MP+MN \
-gltsym 'SYM: literal_positive_timing +literal_negative_timing \
-abstract_positive_timing -abstract_negative_timing' \
-glt_label 15 LP+LN-AP-AN \
-gltsym 'SYM: metaphor_positive_timing +metaphor_negative_timing \
-abstract_positive_timing -abstract_negative_timing' \
-glt_label 16 MP+MN-AP-AN \
-gltsym 'SYM: literal_positive_timing +literal_negative_timing \
+metaphor_positive_timing +metaphor_negative_timing \
-2*abstract_positive_timing -2*abstract_negative_timing' \
-glt_label 17 LP+LN+MP+MN-2AP-2AN \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.${subj} \
-bucket stats.$subj



3dDecon process itself is running without taking any CPU resources. There is no error, no flag, and it is not out of disk space. Afni version is the latest from complied on March 24 'Titus'. Running on OSX Catalina 10.15.7. Thanks!



Edited 2 time(s). Last edit at 03/31/2021 10:51PM by DeLab.
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Subject Author Posted

3dDeconvolve hangs?

DeLab March 31, 2021 10:30PM

Re: 3dDeconvolve hangs?

DeLab April 01, 2021 08:53AM

Re: 3dDeconvolve hangs?

rick reynolds April 01, 2021 11:50AM

Re: 3dDeconvolve hangs?

DeLab April 02, 2021 01:33PM

Re: 3dDeconvolve hangs?

rick reynolds April 09, 2021 05:19PM