Hi Rick,
Following up on the previous message, I ran a 3dDeconvolve script with TENTs that included 6 regressors for motion parameters (see script below) and got an error message that I copied below:

3dDeconvolve \
-input 16588.SST.time+orig \
-TR_1D 1.2 \
-automask \
-num_stimts 9 \
-stim_times 1 regressor_CorrectStop.1D 'TENT(0,14.4,7)' \
-stim_label 1 CorrectStop \
-stim_times 2 regressor_CorrectGo.1D 'TENT(0,14.4,7)' \
-stim_label 2 CorrectGo \
-stim_times 3 regressor_IncorrectStop.1D 'TENT(0,14.4,7)' \
-stim_label 3 IncorrectStop \
-stim_file 4 16588motion_output.1D[0] -stim_base 4 -stim_label 4 Roll \
-stim_file 5 16588motion_output.1D[1] -stim_base 5 -stim_label 5 Pitch \
-stim_file 6 16588motion_output.1D[2] -stim_base 6 -stim_label 6 Yaw \
-stim_file 7 16588motion_output.1D[3] -stim_base 7 -stim_label 7 dS \
-stim_file 8 16588motion_output.1D[4] -stim_base 8 -stim_label 8 dL \
-stim_file 9 16588motion_output.1D[5] -stim_base 9 -stim_label 9 dP \
-polort 3 \
-xout \
-fout \
-tout \
-fitts output_model_fitts \
-xjpeg Xmat_jpg.jpg \
-x1D Xmat_1D.x1D \
-bucket 16588.stopsignal.bucket \

*+ WARNING: -------------------------------------------------
*+ WARNING: Problems with the X matrix columns, listed below:
*+ WARNING: !! * Columns 1 [Run#1Pol#1] and 25 [Roll#0] are nearly collinear!
*+ WARNING: -------------------------------------------------
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=5.33021
* 1 singular value is less than cutoff=5.33021e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: !! in Baseline-only matrix:
* Largest singular value=4.02603
* 1 singular value is less than cutoff=4.02603e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: +++++ !! Matrix inverse average error = 0.0889729 ** BEWARE **
** ERROR: !! 3dDeconvolve: Can't run past 4 matrix warnings without '-GOFORIT 4'
** 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 !!

We usually do motion correction with FIASCO software on raw data, but I thought of including also these motion parameters from 3dvolreg. Is that what caused the problem? Once I took the motion regressors out the script ran fine.

My second question is that in the output bucket file we get 12 sub-bricks (6 pairs of Coeff and tstat) for each of the 3 conditions (eg correct stop, incorrect stop, correct go). How do I pick the best fitting curve? It seems that most of the red activation is for sub-bricks 3-4 and 5-6, but what sub-brick would give the MSE?


Third question is: will the best fitting curve vary by subject or should I just pick one pair of sub-bricks and be consistent across subjects?
Sorry for the long e-mail and multiple questions, and thank you very much for your input,
Alessandra