Hello,

I have been having an issue with 3dDeconvolve not using the local times for the stimuli. I use the -local_times prior to listing the stim_times but the 3dDeconvolve program still tries to guess whether to use local or global times. 3dDeconvolve guesses correctly for most the stimuli. However, for the stimuli with only 1 time point the program guesses to use the global times, which is not desired. I have pasted a portion of the error log below and my script after. Any idea how to fix this? I need 3dDeconvolve to use local times for all stimuli. I could go change all the timing files to global times but that would be a nuisance.

++ ** GUESSED ** -stim_times 32 using LOCAL times
++ ** GUESSED ** -stim_times 33 using LOCAL times
++ ** GUESSED ** -stim_times 34 using LOCAL times
++ ** GUESSED ** -stim_times 35 using LOCAL times
++ ** GUESSED ** -stim_times 36 using LOCAL times
++ ** GUESSED ** -stim_times 37 using GLOBAL times
ESC[7m*+ WARNING:ESC[0m '-stim_times 37' (GLOBAL) has 32 runs and 32 early events; do you want LOCAL times?
ESC[7m*+ WARNING:ESC[0m '-stim_times 37' file 'VideoActions.1D.txt' has 0 duplicate and 39 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
++ ** GUESSED ** -stim_times 38 using GLOBAL times
ESC[7m*+ WARNING:ESC[0m '-stim_times 38' (GLOBAL) has 32 runs and 32 early events; do you want LOCAL times?
ESC[7m*+ WARNING:ESC[0m '-stim_times 38' file 'VideoKnots.1D.txt' has 0 duplicate and 39 near-duplicate times ???
+ Where 'near-duplicate' means within 50% of one TR
+ You are using global times: do you want local times?
++ ** GUESSED ** -stim_times 39 using LOCAL times
++ ** GUESSED ** -stim_times 40 using LOCAL times
++ ** GUESSED ** -stim_times 41 using LOCAL times
++ ** GUESSED ** -stim_times 42 using LOCAL times
++ ** GUESSED ** -stim_times 43 using LOCAL times

singularity run --cleanenv /Shared/lss_kahwang_hpc/opt/afni/afni.sif \
3dDeconvolve -input $(find /Shared/lss_kahwang_hpc/data/MDTB/fmriprep/ -regex "/Shared/lss_kahwang_hpc/data/MDTB/fmriprep/sub-${subject}/\(ses-a1\|ses-a2\|ses-b1\|ses-b2\).*desc-preproc_bold\.nii\.gz") \
-mask combined_mask+tlrc.BRIK \
-polort A \
-censor censor.1D \
-ortvec nuisance.1D \
-local_times \
-num_stimts 43 \
-stim_times 1 AnimatedMovie.1D.txt 'BLOCK(30)' -stim_label 1 AnimatedMovie \
-stim_times 2 NatureMovie.1D.txt 'BLOCK(30)' -stim_label 2 NatureMovie \
-stim_times 3 LandscapeMovie.1D.txt 'BLOCK(30)' -stim_label 3 LandscapeMovie \
-stim_times 4 BiologicalMotion.1D.txt 'BLOCK(3)' -stim_label 4 BiologicalMotion \
-stim_times 5 ScrambledMotion.1D.txt 'BLOCK(3)' -stim_label 5 ScrambledMotion \
-stim_times 6 DigitJudgement.1D.txt 'BLOCK(2.6)' -stim_label 6 DigitJudgement \
-stim_times 7 Math.1D.txt 'BLOCK(2.6)' -stim_label 7 Math \
-stim_times 8 FingerSeq.1D.txt 'BLOCK(4.6)' -stim_label 8 FingerSeq \
-stim_times 9 FingerSimple.1D.txt 'BLOCK(4.6)' -stim_label 9 FingerSimple \
-stim_times 10 Go.1D.txt 'BLOCK(1)' -stim_label 10 Go \
-stim_times 11 NoGo.1D.txt 'BLOCK(1)' -stim_label 11 NoGo \
-stim_times 12 Instruct.1D.txt 'BLOCK(5)' -stim_label 12 Instruct \
-stim_times 13 MentalRotEasy.1D.txt 'BLOCK(3)' -stim_label 13 MentalRotEasy \
-stim_times 14 MentalRotHard.1D.txt 'BLOCK(3)' -stim_label 14 MentalRotHard \
-stim_times 15 MentalRotMed.1D.txt 'BLOCK(3)' -stim_label 15 MentalRotMed \
-stim_times 16 MotorImagery.1D.txt 'BLOCK(30)' -stim_label 16 MotorImagery \
-stim_times 17 SpatialImagery.1D.txt 'BLOCK(30)' -stim_label 17 SpatialImagery \
-stim_times 18 Objects.1D.txt 'BLOCK(1.6)' -stim_label 18 Objects \
-stim_times 19 Object2Back.1D.txt 'BLOCK(1.6)' -stim_label 19 Object2Back \
-stim_times 20 Verbal2Back.1D.txt 'BLOCK(1.6)' -stim_label 20 Verbal2Back \
-stim_times 21 PermutedRules.1D.txt 'BLOCK(7.3)' -stim_label 21 PermutedRules \
-stim_times 22 PleasantScenes.1D.txt 'BLOCK(1.6)' -stim_label 22 PleasantScenes \
-stim_times 23 UnpleasantScenes.1D.txt 'BLOCK(1.6)' -stim_label 23 UnpleasantScenes \
-stim_times 24 HappyFaces.1D.txt 'BLOCK(1.6)' -stim_label 24 HappyFaces \
-stim_times 25 SadFaces.1D.txt 'BLOCK(1.6)' -stim_label 25 SadFaces \
-stim_times 26 PredictScram.1D.txt 'BLOCK(4.8)' -stim_label 26 PredictScram \
-stim_times 27 PredictViol.1D.txt 'BLOCK(4.8)' -stim_label 27 PredictViol \
-stim_times 28 RespAltEasy.1D.txt 'BLOCK(4.6)' -stim_label 28 RespAltEasy \
-stim_times 29 RespAltHard.1D.txt 'BLOCK(4.6)' -stim_label 29 RespAltHard \
-stim_times 30 RespAltMed.1D.txt 'BLOCK(4.6)' -stim_label 30 RespAltMed \
-stim_times 31 SpatialMapEasy.1D.txt 'BLOCK(4.8)' -stim_label 31 SpatialMapEasy \
-stim_times 32 SpatialMapHard.1D.txt 'BLOCK(4.8)' -stim_label 32 SpatialMapHard \
-stim_times 33 SpatialMapMed.1D.txt 'BLOCK(4.8)' -stim_label 33 SpatialMapMed \
-stim_times 34 StroopCon.1D.txt 'BLOCK(1.6)' -stim_label 34 StroopCon \
-stim_times 35 StroopIncon.1D.txt 'BLOCK(1.6)' -stim_label 35 StroopIncon \
-stim_times 36 TheoryOfMind.1D.txt 'BLOCK(14.6)' -stim_label 36 TheoryOfMind \
-stim_times 37 VideoActions.1D.txt 'BLOCK(14)' -stim_label 37 VideoActions \
-stim_times 38 VideoKnots.1D.txt 'BLOCK(14)' -stim_label 38 VideoKnots \
-stim_times 39 VisualSearchEasy.1D.txt 'BLOCK(1.6)' -stim_label 39 VisualSearchEasy \
-stim_times 40 VisualSearchHard.1D.txt 'BLOCK(1.6)' -stim_label 40 VisualSearchHard \
-stim_times 41 VisualSearchMed.1D.txt 'BLOCK(1.6)' -stim_label 41 VisualSearchMed \
-stim_times 42 WordRead.1D.txt 'BLOCK(1.6)' -stim_label 42 WordRead \
-stim_times 43 VerbGen.1D.txt 'BLOCK(1.6)' -stim_label 43 VerbGen \
-iresp 1 AnimatedMovie_FIR_MIN.nii.gz \
-iresp 2 NatureMovie_FIR_MIN.nii.gz \
-iresp 3 LandscapeMovie_FIR_MIN.nii.gz \
-iresp 4 BiologicalMotion_FIR_MIN.nii.gz \
-iresp 5 ScrambledMotion_FIR_MIN.nii.gz \
-iresp 6 DigitJudgement_FIR_MIN.nii.gz \
-iresp 7 Math_FIR_MIN.nii.gz \
-iresp 8 FingerSeq_FIR_MIN.nii.gz \
-iresp 9 FingerSimple_FIR_MIN.nii.gz \
-iresp 10 Go_FIR_MIN.nii.gz \
-iresp 11 NoGo_FIR_MIN.nii.gz \
-iresp 12 Instruct_FIR_MIN.nii.gz \
-iresp 13 MentalRotEasy_FIR_MIN.nii.gz \
-iresp 14 MentalRotHard_FIR_MIN.nii.gz \
-iresp 15 MentalRotMed_FIR_MIN.nii.gz \
-iresp 16 MotorImagery_FIR_MIN.nii.gz \
-iresp 17 SpatialImagery_FIR_MIN.nii.gz \
-iresp 18 Objects_FIR_MIN.nii.gz \
-iresp 19 Object2Back_FIR_MIN.nii.gz \
-iresp 20 Verbal2Back_FIR_MIN.nii.gz \
-iresp 21 PermutedRules_FIR_MIN.nii.gz \
-iresp 22 PleasantScenes_FIR_MIN.nii.gz \
-iresp 23 UnpleasantScenes_FIR_MIN.nii.gz \
-iresp 24 HappyFaces_FIR_MIN.nii.gz \
-iresp 25 SadFaces_FIR_MIN.nii.gz \
-iresp 26 PredictScram_FIR_MIN.nii.gz \
-iresp 27 PredictViol_FIR_MIN.nii.gz \
-iresp 28 RespAltEasy_FIR_MIN.nii.gz \
-iresp 29 RespAltHard_FIR_MIN.nii.gz \
-iresp 30 RespAltMed_FIR_MIN.nii.gz \
-iresp 31 SpatialMapEasy_FIR_MIN.nii.gz \
-iresp 32 SpatialMapHard_FIR_MIN.nii.gz \
-iresp 33 SpatialMapMed_FIR_MIN.nii.gz \
-iresp 34 StroopCon_FIR_MIN.nii.gz \
-iresp 35 StroopIncon_FIR_MIN.nii.gz \
-iresp 36 TheoryOfMind_FIR_MIN.nii.gz \
-iresp 37 VideoActions_FIR_MIN.nii.gz \
-iresp 38 VideoKnots_FIR_MIN.nii.gz \
-iresp 39 VisualSearchEasy_FIR_MIN.nii.gz \
-iresp 40 VisualSearchHard_FIR_MIN.nii.gz \
-iresp 41 VisualSearchMed_FIR_MIN.nii.gz \
-iresp 42 WordRead_FIR_MIN.nii.gz \
-iresp 43 VerbGen_FIR_MIN.nii.gz \
-num_glt 43 \
-gltsym "SYM: +1*AnimatedMovie" -glt_label 1 AnimatedMovie \
-gltsym "SYM: +1*NatureMovie" -glt_label 2 NatureMovie \
-gltsym "SYM: +1*LandscapeMovie" -glt_label 3 LandscapeMovie \
-gltsym "SYM: +1*BiologicalMotion" -glt_label 4 BiologicalMotion \
-gltsym "SYM: +1*ScrambledMotion" -glt_label 5 ScrambledMotion \
-gltsym "SYM: +1*DigitJudgement" -glt_label 6 DigitJudgement \
-gltsym "SYM: +1*Math" -glt_label 7 Math \
-gltsym "SYM: +1*FingerSeq" -glt_label 8 FingerSeq \
-gltsym "SYM: +1*FingerSimple" -glt_label 9 FingerSimple \
-gltsym "SYM: +1*Go" -glt_label 10 Go \
-gltsym "SYM: +1*NoGo" -glt_label 11 NoGo \
-gltsym "SYM: +1*Instruct" -glt_label 12 Instruct \
-gltsym "SYM: +1*MentalRotEasy" -glt_label 13 MentalRotEasy \
-gltsym "SYM: +1*MentalRotHard" -glt_label 14 MentalRotHard \
-gltsym "SYM: +1*MentalRotMed" -glt_label 15 MentalRotMed \
-gltsym "SYM: +1*MotorImagery" -glt_label 16 MotorImagery \
-gltsym "SYM: +1*SpatialImagery" -glt_label 17 SpatialImagery \
-gltsym "SYM: +1*Objects" -glt_label 18 Objects \
-gltsym "SYM: +1*Object2Back" -glt_label 19 Object2Back \
-gltsym "SYM: +1*Verbal2Back" -glt_label 20 Verbal2Back \
-gltsym "SYM: +1*PermutedRules" -glt_label 21 PermutedRules \
-gltsym "SYM: +1*PleasantScenes" -glt_label 22 PleasantScenes \
-gltsym "SYM: +1*UnpleasantScenes" -glt_label 23 UnpleasantScenes \
-gltsym "SYM: +1*HappyFaces" -glt_label 24 HappyFaces \
-gltsym "SYM: +1*SadFaces" -glt_label 25 SadFaces \
-gltsym "SYM: +1*PredictScram" -glt_label 26 PredictScram \
-gltsym "SYM: +1*PredictViol" -glt_label 27 PredictViol \
-gltsym "SYM: +1*RespAltEasy" -glt_label 28 RespAltEasy \
-gltsym "SYM: +1*RespAltHard" -glt_label 29 RespAltHard \
-gltsym "SYM: +1*RespAltMed" -glt_label 30 RespAltMed \
-gltsym "SYM: +1*SpatialMapEasy" -glt_label 31 SpatialMapEasy \
-gltsym "SYM: +1*SpatialMapHard" -glt_label 32 SpatialMapHard \
-gltsym "SYM: +1*SpatialMapMed" -glt_label 33 SpatialMapMed \
-gltsym "SYM: +1*StroopCon" -glt_label 34 StroopCon \
-gltsym "SYM: +1*StroopIncon" -glt_label 35 StroopIncon \
-gltsym "SYM: +1*TheoryOfMind" -glt_label 36 TheoryOfMind \
-gltsym "SYM: +1*VideoActions" -glt_label 37 VideoActions \
-gltsym "SYM: +1*VideoKnots" -glt_label 38 VideoKnots \
-gltsym "SYM: +1*VisualSearchEasy" -glt_label 39 VisualSearchEasy \
-gltsym "SYM: +1*VisualSearchHard" -glt_label 40 VisualSearchHard \
-gltsym "SYM: +1*VisualSearchMed" -glt_label 41 VisualSearchMed \
-gltsym "SYM: +1*WordRead" -glt_label 42 WordRead \
-gltsym "SYM: +1*VerbGen" -glt_label 43 VerbGen \
-rout \
-tout \
-bucket FIRmodel_MNI_stats \
-errts FIRmodel_errts.nii.gz \
-noFDR \
-nocout \
-jobs 16 \
-ok_1D_text