Hello Gang,
Yes, of course. Here are the scripts, starting with the steps necessary to create the interaction regressor:
1deval -a SEED_Neur_C3_5392.1D -b G1Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5392.1D
1deval -a SEED_Neur_C3_5395.1D -b G2Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5395.1D
1deval -a SEED_Neur_C3_5409.1D -b G3Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5409.1D
1deval -a SEED_Neur_C3_5410.1D -b G1Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5410.1D
1deval -a SEED_Neur_C3_5413.1D -b G2Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5413.1D
1deval -a SEED_Neur_C3_5414.1D -b G3Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5414.1D
1deval -a SEED_Neur_C3_5417.1D -b G2Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5417.1D
1deval -a SEED_Neur_C3_5418.1D -b G2Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5418.1D
1deval -a SEED_Neur_C3_5429.1D -b G3Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5429.1D
1deval -a SEED_Neur_C3_5441.1D -b G1Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5441.1D
1deval -a SEED_Neur_C3_5466.1D -b G1Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5466.1D
1deval -a SEED_Neur_C3_5488.1D -b G3Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5488.1D
1deval -a SEED_Neur_C3_5490.1D -b G3Acoding.txt -expr 'a*b' > Inter_neu_C3_A_5490.1D
//there are three different .1D (G1Acoding.txt, G2Acoding.txt, G3Acoding.txt) files because of three different sequences of events. The condition of interest is coded with 1s all other time points have been set to 0. //
for i in 5392 5395 5409 5410 5413 5414 5417 5418 5429 5441 5466 5488 5490
do
waver -GAM -peak 1 -TR 3 -input Inter_neu_C3_A_"$i".1D -numout 420 > Inter_ts_C3_A_"$i".1D
done
//Next, seed and interaction are added to the initial deconvolution script//
3dDeconvolve\
-input ../../../Exam#5395/Results/psc.ssm.tsm.cl.dsp.hpf.reg.ts.1+tlrc ../../../Exam#5395/Results/psc.ssm.tsm.cl.dsp.hpf.reg.ts.2+tlrc\
-mask ../../../Exam#5395/Results/clippedAutomask.1+tlrc\
-censor ../../../Exam#5395/Results/S2G2censor.txt\
-polort A\
-num_stimts 8\
-stim_file 1 ../../../Exam#5395/Results/fmrigroup2.txt[0]\
-stim_label 1 favhigh\
-stim_maxlag 1 5\
-stim_file 2 ../../../Exam#5395/Results/fmrigroup2.txt[1]\
-stim_label 2 neuthigh\
-stim_maxlag 2 5\
-stim_file 3 ../../../Exam#5395/Results/fmrigroup2.txt[2]\
-stim_label 3 lfhigh\
-stim_maxlag 3 5\
-stim_file 4 ../../../Exam#5395/Results/fmrigroup2.txt[3]\
-stim_label 4 favlow\
-stim_maxlag 4 5\
-stim_file 5 ../../../Exam#5395/Results/fmrigroup2.txt[4]\
-stim_label 5 neutlow\
-stim_maxlag 5 5\
-stim_file 6 ../../../Exam#5395/Results/fmrigroup2.txt[5]\
-stim_label 6 lflow\
-stim_maxlag 6 5\
-stim_file 7 SEED_ts_C3_5395.1D\
-stim_label 7 SEED\
-stim_file 8 Inter_ts_C3_A_5395.1D\
-stim_label 8 InteractRegressor\
-fout\
-rout\
-tout\
-bucket deconTR1..5_C3_A_5395\
-xsave\
-tshift\
//In this case I am interested in the connectivity for one condition, which is described by the regressors 1 and 4 (favhigh and favlow, two subconditions for the broader condition I am investigating). The interaction regressor seems to be correlated with these earlier regressors and I get the following collinearity error://
++ N.B.: 3dREMLfit command above written to file deconTR1.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
*+ WARNING: -------------------------------------------------
*+ WARNING: Problems with the X matrix columns, listed below:
*+ WARNING: !! * Column 49 [InteractRegressor#0] is all zeros
*+ WARNING: -------------------------------------------------
++ ----- Signal+Baseline matrix condition [X] (404x50): 5.29254 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=1.97016
* 1 singular value is less than cutoff=1.97016e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
0 0.0703351 0.176143 0.396675 0.479444
0.572321 0.749896 0.784817 0.867844 0.952859
0.969955 0.988798 0.993607 0.999479 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1.01379 1.02119 1.04049
1.0554 1.08551 1.12685 1.18112 1.25747
1.38835 1.40489 1.50432 1.9483 1.97016
++ ----- Signal-only matrix condition [X] (404x38): 1.51212 ++ VERY GOOD ++
*+ WARNING: !! in Signal-only matrix:
* Largest singular value=1.39145
* 1 singular value is less than cutoff=1.39145e-07
* Implies strong collinearity in the matrix columns!
++ Signal-only matrix singular values:
0 0.608547 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1 1 1
1 1 1.39145
++ ----- Baseline-only matrix condition [X] (404x12): 1.56412 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (404x12): 1.56412 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 0.0004 ++ OK ++
++ Matrix setup time = 0.17 s
** 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 !!
All the best,
Jana
