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History of AFNI updates  

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July 23, 2015 11:33AM
Pretty new here.

I'm trying to use 3dDeconvolve but am getting the following error messages before it crashes:

*+ WARNING: '-stim_times_AM2 4 /home/ajames/data/Cognectome/logs/COG.C.010_iowa_planning_advantage.1D' has 0 amplitude modulation parameters; ==> converting to be like -stim_times_AM1
*+ WARNING: '-stim_times_AM2 5 /home/ajames/data/Cognectome/logs/COG.C.010_iowa_planning_disadvantage.1D' has 0 amplitude modulation parameters; ==> converting to be like -stim_times_AM1
*+ WARNING: no -stim_label given for stim #6 ==> label = 'Stim#6'
*+ WARNING: no -stim_label given for stim #7 ==> label = 'Stim#7'
*+ WARNING: no -stim_label given for stim #8 ==> label = 'Stim#8'
*+ WARNING: no -stim_label given for stim #9 ==> label = 'Stim#9'
*+ WARNING: no -stim_label given for stim #10 ==> label = 'Stim#10'
*+ WARNING: no -stim_label given for stim #11 ==> label = 'Stim#11'
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=2.26101
* 1 singular value is less than cutoff=2.26101e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: !! in Signal-only matrix:
* Largest singular value=1.83949
* 1 singular value is less than cutoff=1.83949e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: +++++ !! Matrix inverse average error = 0.00376489 ** BEWARE **
** ERROR: !! 3dDeconvolve: Can't run past 3 matrix warnings without '-GOFORIT 3'
** ERROR: !! Currently at -GOFORIT 0
** ERROR: !! See file 3dDeconvolve.err for all WARNING and ERROR messages !!
** ERROR: !! Be sure you understand what you are doing before using -GOFORIT !!
** ERROR: !! If in doubt, consult with someone or with the AFNI message board !!
** FATAL ERROR: !! 3dDeconvolve (regretfully) shuts itself down !!

Here's my script:

#! /bin/csh

set study = (COG)
set subjs = (C.010) # C.011 C.012 C.013 C.014 C.015 C.016 C.017 C.018 C.020 C.021 C.022 C.023 C.025 C.027 C.028 C.029 C.031 C.032 C.033 C.036 C.038 C.039 C.041 C.043 C.044 C.045 C.046 C.047 C.050 C.052 C.053 C.054 C.056 C.058 C.062 C.063 C.065 C.066 C.067 C.070 C.073 C.074 C.075 C.076 C.079)
set thisdir = pwd
set task = (iowa)
set rootpath = /home/ajames/data/Cognectome/results/${task}
set logpath = /home/ajames/data/Cognectome/logs

cd ${rootpath}
foreach subj (${subjs})
cd ${rootpath}
rm decon.${study}.${subj}.${task}*
rm reml.${study}.${subj}.${task}*
cp /home/ajames/data/Cognectome/scripts/decon/TT_icbm452_automask_resampled+tlrc.* .
3dDeconvolve -input ${study}.${subj}.${task}.scaled.resid+tlrc \
-polort A \
-force_TR 2.00 \
-censor censor.${study}.${subj}.${task}.1D \
-mask TT_icbm452_automask_resampled+tlrc \
-num_stimts 11 \
-stim_times_AM1 1 ${logpath}/${study}.${subj}_${task}_choice_duration.1D 'dmBLOCK(1)' \
-stim_label 1 PreChoice \
-stim_times_AM2 2 ${logpath}/${study}.${subj}_${task}_netwin_AM.1D 'GAM' \
-stim_label 2 Win \
-stim_times_AM2 3 ${logpath}/${study}.${subj}_${task}_netloss_AM.1D 'GAM' \
-stim_label 3 Loss \
-stim_times_AM2 4 ${logpath}/${study}.${subj}_${task}_planning_advantage.1D 'dmBLOCK(1)' \
-stim_label 4 AdvantageousDeck \
-stim_times_AM2 5 ${logpath}/${study}.${subj}_${task}_planning_disadvantage.1D 'dmBLOCK(1)' \
-stim_label 5 DisadvantageousDeck \
-stim_file 6 ${study}.${subj}.${task}.motion.1D'[0]' \
-stim_file 7 ${study}.${subj}.${task}.motion.1D'[1]' \
-stim_file 8 ${study}.${subj}.${task}.motion.1D'[2]' \
-stim_file 9 ${study}.${subj}.${task}.motion.1D'[3]' \
-stim_file 10 ${study}.${subj}.${task}.motion.1D'[4]' \
-stim_file 11 ${study}.${subj}.${task}.motion.1D'[5]' \
-stim_base 6 \
-stim_base 7 \
-stim_base 8 \
-stim_base 9 \
-stim_base 10 \
-stim_base 11 \
-num_glt 6 \
-gltsym 'SYM: +Win[1] +Loss[1]' \
-glt_label 1 WIN+LOSS_AM \
-gltsym 'SYM: +Win[1] -Loss[1]' \
-glt_label 2 WIN-LOSS_AM \
-gltsym 'SYM: 0.5*Win[1] 0.5*Loss[1] -PreChoice[0]' \
-glt_label 3 +WIN_AM+LOSS_AM-PRECHOICE \
-gltsym 'SYM: +Win[1] -PreChoice[0]' \
-glt_label 4 +WIN_AM-PRECHOICE \
-gltsym 'SYM: +Loss[1] -PreChoice[0]' \
-glt_label 5 +LOSS_AM-PRECHOICE \
-gltsym 'SYM: AdvantageousDeck[0] -DisadvantageousDeck[0]' \
-glt_label 6 ADV-DIS \
-x1D matrix.${study}.${subj}.${task}.1D \
-fout -rout -tout \
-errts errts.${study}.${subj}.${task} \
-bucket decon.${study}.${subj}.${task}

3dREMLfit \
-input ${study}.${subj}.${task}.scaled.resid+tlrc \
-mask TT_icbm452_automask_resampled+tlrc \
-matrix matrix.${study}.${subj}.${task}.1D \
-GOFORIT 1 \
-fout -rout -tout \
-Rbuck reml.${study}.${subj}.${task}

end
cd ${thisdir}

How do fix a collinearity issue, or how can I find the specific columns that have the strong collinearity causing the crash?

Thanks so much for any help!
Subject Author Posted

Collinearity issues in 3dDeconvolve

bmartins July 23, 2015 11:33AM

Re: Collinearity issues in 3dDeconvolve

rick reynolds July 23, 2015 12:09PM

Re: Collinearity issues in 3dDeconvolve

bmartins July 23, 2015 12:29PM

Re: Collinearity issues in 3dDeconvolve

rick reynolds July 23, 2015 03:53PM

Re: Collinearity issues in 3dDeconvolve

bmartins July 23, 2015 04:27PM