I created regressors to model when participants made a (1) correct response (2) incorrect response (3) did not respond at all. My regressors are structured as such: (stimulus onset): (duration).
I have time points for the “correct responses” and “incorrect responses” regressors, but sometimes I don’t have any time points for the “did not respond at all” regressors. As a result, my 3dDeconvolve was not running. To alleviate this issue, I inserted “-1:1” for each of my runs in the regressor files without any timing values. With this, I specified “allzero_OK” and 'GOFORIT 10" in my afni_proc script. I just wanted to verify that this was the correct approach?
I also got several error/warnings messages in the 3dDeconvolve.err output as a result of above. I just wanted to make sure that these warnings were “okay” and due to the fact that I specified “-1:1” in my regressors with no actual timing information. Since I specified “GOFORIT 10”, I want to make sure that 3dDeconvolve isn’t bypassing other errors.
Thank you very much,
Tamara
3dDeconvolve.err
*+ WARNING: ‘-stim_times_AM1 19’ didn’t read any good times from file ‘stimuli/NonRevP_perf_NoResp.txt’
*+ WARNING: ‘-stim_times_AM1 20’ didn’t read any good times from file ‘stimuli/NonRevP_perf_NoResp_fed.txt’
*+ WARNING: ‘-stim_times_AM1 23’ didn’t read any good times from file ‘stimuli/RevP_rev_NoResp.txt’
*+ WARNING: ‘-stim_times_AM1 24’ didn’t read any good times from file ‘stimuli/RevP_rev_NoResp_fed.txt’
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 19’ file ‘stimuli/NonRevP_perf_NoResp.txt’ has no good stimulus time values
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 20’ file ‘stimuli/NonRevP_perf_NoResp_fed.txt’ has no good stimulus time values
*+ WARNING: ‘-stim_times_AM1 23’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 23’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 23’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 23’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 23’ file ‘stimuli/RevP_rev_NoResp.txt’ has no good stimulus time values
*+ WARNING: ‘-stim_times_AM1 24’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 24’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 24’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 24’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 24’ file ‘stimuli/RevP_rev_NoResp_fed.txt’ has no good stimulus time values
*+ WARNING: -------------------------------------------------
*+ WARNING: Problems with the X matrix columns, listed below:
*+ WARNING: * Column 34 [NonRevP_perf_NoResp#0] is all zeros
*+ WARNING: * Column 35 [NonRevP_perf_NoResp_fed#0] is all zeros
*+ WARNING: * Column 38 [RevP_rev_NoResp#0] is all zeros
*+ WARNING: * Column 39 [RevP_rev_NoResp_fed#0] is all zeros
*+ WARNING: -------------------------------------------------
*+ WARNING: !! in Signal+Baseline matrix:
Largest singular value=2.26308
4 singular values are less than cutoff=2.26308e-07
Implies strong collinearity in the matrix columns!
*+ WARNING: !! in Signal-only matrix:
Largest singular value=1.41868
4 singular values are less than cutoff=1.41868e-07
Implies strong collinearity in the matrix columns!
*+ WARNING: !! 3dDeconvolve -GOFORIT is set to 10: running despite 6 matrix warnings
*+ WARNING: !! See file 3dDeconvolve.err for all WARNING and ERROR messages !!
*+ WARNING: !! Please be sure you understand what you are doing !!
*+ WARNING: !! If in doubt, consult with someone or with the AFNI message board !!
*+ WARNING: Smallest FDR q [8 NonRevP_learn_incor_fed#0_Tstat] = 0.151891 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [9 NonRevP_learn_incor_fed_Fstat] = 0.151417 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [11 NonRevP_learn_incor#0_Tstat] = 0.102402 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [12 NonRevP_learn_incor_Fstat] = 0.102401 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [53 NonRevP_learn_NoResp_fed#0_Tstat] = 0.143557 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [54 NonRevP_learn_NoResp_fed_Fstat] = 0.14304 ==> few true single voxel detections
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: Smallest FDR q [62 RevP_acq_NoResp#0_Tstat] = 0.214525 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [63 RevP_acq_NoResp_Fstat] = 0.213817 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [65 RevP_acq_NoResp_fed#0_Tstat] = 0.828139 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [66 RevP_acq_NoResp_fed_Fstat] = 0.825204 ==> few true single voxel detections
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
This seems reasonable, however I do not think it is enough to be sure there are no other problems. When I want to check for that, I add minimal event times and see if all the warnings go away.
Thank you very much for the suggestion. I re-ran my pre-processing after adding “real” timing values. Below are the 3dDeconve.err outputs before and after I added these timing values. I think they look okay. Do you think so too?
Thank you very much!!
BEFORE REAL TIMING VALUES ADDED (These just included -1:1 * per run)
*+ WARNING: ‘-stim_times_AM1 19’ didn’t read any good times from file ‘stimuli/NonRevP_perf_NoResp.txt’
*+ WARNING: ‘-stim_times_AM1 20’ didn’t read any good times from file ‘stimuli/NonRevP_perf_NoResp_fed.txt’
*+ WARNING: ‘-stim_times_AM1 21’ didn’t read any good times from file ‘stimuli/RevP_acq_NoResp.txt’
*+ WARNING: ‘-stim_times_AM1 22’ didn’t read any good times from file ‘stimuli/RevP_acq_NoResp_fed.txt’
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 19’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 19’ file ‘stimuli/NonRevP_perf_NoResp.txt’ has no good stimulus time values
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 20’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 20’ file ‘stimuli/NonRevP_perf_NoResp_fed.txt’ has no good stimulus time values
*+ WARNING: ‘-stim_times_AM1 21’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 21’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 21’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 21’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 21’ file ‘stimuli/RevP_acq_NoResp.txt’ has no good stimulus time values
*+ WARNING: ‘-stim_times_AM1 22’ (LOCAL) run#1 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 22’ (LOCAL) run#2 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 22’ (LOCAL) run#3 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: ‘-stim_times_AM1 22’ (LOCAL) run#4 has 1 times outside range 0 … 380 [PSFB syndrome]
*+ WARNING: !! ‘-stim_times_AM1 22’ file ‘stimuli/RevP_acq_NoResp_fed.txt’ has no good stimulus time values
*+ WARNING: -------------------------------------------------
*+ WARNING: Problems with the X matrix columns, listed below:
*+ WARNING: * Column 34 [NonRevP_perf_NoResp#0] is all zeros
*+ WARNING: * Column 35 [NonRevP_perf_NoResp_fed#0] is all zeros
*+ WARNING: * Column 36 [RevP_acq_NoResp#0] is all zeros
*+ WARNING: * Column 37 [RevP_acq_NoResp_fed#0] is all zeros
*+ WARNING: -------------------------------------------------
*+ WARNING: !! in Signal+Baseline matrix:
Largest singular value=2.37259
4 singular values are less than cutoff=2.37259e-07
Implies strong collinearity in the matrix columns!
*+ WARNING: !! in Signal-only matrix:
Largest singular value=1.37407
4 singular values are less than cutoff=1.37407e-07
Implies strong collinearity in the matrix columns!
*+ WARNING: !! 3dDeconvolve -GOFORIT is set to 10: running despite 6 matrix warnings
*+ WARNING: !! See file 3dDeconvolve.err for all WARNING and ERROR messages !!
*+ WARNING: !! Please be sure you understand what you are doing !!
*+ WARNING: !! If in doubt, consult with someone or with the AFNI message board !!
*+ WARNING: Smallest FDR q [2 NonRevP_learn_corr_fed#0_Tstat] = 0.30516 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [3 NonRevP_learn_corr_fed_Fstat] = 0.30426 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [17 NonRevP_perf_corr#0_Tstat] = 0.184234 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [18 NonRevP_perf_corr_Fstat] = 0.183724 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [29 RevP_acq_corr#0_Tstat] = 0.288842 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [30 RevP_acq_corr_Fstat] = 0.288011 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [32 RevP_acq_incor_fed#0_Tstat] = 0.267437 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [33 RevP_acq_incor_fed_Fstat] = 0.266408 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [35 RevP_acq_incor#0_Tstat] = 0.109113 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [36 RevP_acq_incor_Fstat] = 0.108714 ==> few true single voxel detections
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: mri_fdrize: will not process only 0 values (min=20)
*+ WARNING: Smallest FDR q [68 RevP_rev_NoResp#0_Tstat] = 0.171038 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [69 RevP_rev_NoResp_Fstat] = 0.170431 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [71 RevP_rev_NoResp_fed#0_Tstat] = 0.999893 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [72 RevP_rev_NoResp_fed_Fstat] = 0.996062 ==> few true single voxel detections
OUTPUT AFTER “REAL” TIMING VALUES ARE ADDED
*+ WARNING: Smallest FDR q [2 NonRevP_learn_corr_fed#0_Tstat] = 0.229716 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [3 NonRevP_learn_corr_fed_Fstat] = 0.22905 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [17 NonRevP_perf_corr#0_Tstat] = 0.117249 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [18 NonRevP_perf_corr_Fstat] = 0.116927 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [29 RevP_acq_corr#0_Tstat] = 0.468379 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [30 RevP_acq_corr_Fstat] = 0.466964 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [32 RevP_acq_incor_fed#0_Tstat] = 0.261584 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [33 RevP_acq_incor_fed_Fstat] = 0.260554 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [71 RevP_rev_NoResp_fed#0_Tstat] = 0.999898 ==> few true single voxel detections
*+ WARNING: Smallest FDR q [72 RevP_rev_NoResp_fed_Fstat] = 0.996063 ==> few true single voxel detections
Sure, that looks good. And it seems like the classes with no events are the ones that are now shown to have basically no significant effect, which is expected.
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
Health (NIH), a component of the U.S. Department of Health and Human
Services.