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.
[size=small]++ ** 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[/size]
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: +1AnimatedMovie” -glt_label 1 AnimatedMovie
-gltsym “SYM: +1NatureMovie" -glt_label 2 NatureMovie
-gltsym "SYM: +1LandscapeMovie” -glt_label 3 LandscapeMovie
-gltsym “SYM: +1BiologicalMotion" -glt_label 4 BiologicalMotion
-gltsym "SYM: +1ScrambledMotion” -glt_label 5 ScrambledMotion
-gltsym “SYM: +1DigitJudgement" -glt_label 6 DigitJudgement
-gltsym "SYM: +1Math” -glt_label 7 Math
-gltsym “SYM: +1FingerSeq" -glt_label 8 FingerSeq
-gltsym "SYM: +1FingerSimple” -glt_label 9 FingerSimple
-gltsym “SYM: +1Go" -glt_label 10 Go
-gltsym "SYM: +1NoGo” -glt_label 11 NoGo
-gltsym “SYM: +1Instruct" -glt_label 12 Instruct
-gltsym "SYM: +1MentalRotEasy” -glt_label 13 MentalRotEasy
-gltsym “SYM: +1MentalRotHard" -glt_label 14 MentalRotHard
-gltsym "SYM: +1MentalRotMed” -glt_label 15 MentalRotMed
-gltsym “SYM: +1MotorImagery" -glt_label 16 MotorImagery
-gltsym "SYM: +1SpatialImagery” -glt_label 17 SpatialImagery
-gltsym “SYM: +1Objects" -glt_label 18 Objects
-gltsym "SYM: +1Object2Back” -glt_label 19 Object2Back
-gltsym “SYM: +1Verbal2Back" -glt_label 20 Verbal2Back
-gltsym "SYM: +1PermutedRules” -glt_label 21 PermutedRules
-gltsym “SYM: +1PleasantScenes" -glt_label 22 PleasantScenes
-gltsym "SYM: +1UnpleasantScenes” -glt_label 23 UnpleasantScenes
-gltsym “SYM: +1HappyFaces" -glt_label 24 HappyFaces
-gltsym "SYM: +1SadFaces” -glt_label 25 SadFaces
-gltsym “SYM: +1PredictScram" -glt_label 26 PredictScram
-gltsym "SYM: +1PredictViol” -glt_label 27 PredictViol
-gltsym “SYM: +1RespAltEasy" -glt_label 28 RespAltEasy
-gltsym "SYM: +1RespAltHard” -glt_label 29 RespAltHard
-gltsym “SYM: +1RespAltMed" -glt_label 30 RespAltMed
-gltsym "SYM: +1SpatialMapEasy” -glt_label 31 SpatialMapEasy
-gltsym “SYM: +1SpatialMapHard" -glt_label 32 SpatialMapHard
-gltsym "SYM: +1SpatialMapMed” -glt_label 33 SpatialMapMed
-gltsym “SYM: +1StroopCon" -glt_label 34 StroopCon
-gltsym "SYM: +1StroopIncon” -glt_label 35 StroopIncon
-gltsym “SYM: +1TheoryOfMind" -glt_label 36 TheoryOfMind
-gltsym "SYM: +1VideoActions” -glt_label 37 VideoActions
-gltsym “SYM: +1VideoKnots" -glt_label 38 VideoKnots
-gltsym "SYM: +1VisualSearchEasy” -glt_label 39 VisualSearchEasy
-gltsym “SYM: +1VisualSearchHard" -glt_label 40 VisualSearchHard
-gltsym "SYM: +1VisualSearchMed” -glt_label 41 VisualSearchMed
-gltsym “SYM: +1WordRead" -glt_label 42 WordRead
-gltsym "SYM: +1VerbGen” -glt_label 43 VerbGen
-rout
-tout
-bucket FIRmodel_MNI_stats
-errts FIRmodel_errts.nii.gz
-noFDR
-nocout
-jobs 16
-ok_1D_text