Hello James,

The -polort 5 option does not change anything, just that it goes further to another warning message.

Here is just the message section after the gtl section on the contrasts:
++ Number of time points: 420 (no censoring)
+ Number of parameters: 25 [18 baseline ; 7 signal]
++ Memory required for output bricks = 306,708,480 bytes (about 307 million)
++ Wrote matrix values to file Xmat.x1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:

3dREMLfit -matrix Xmat.x1D \
-input "psc.ssm.tsm.cl.dsp.hpf.reg.ts.1+orig psc.ssm.tsm.cl.dsp.hpf.reg.ts.2+orig" \
-fout -tout -rout -Rbuck decon_modulation_S1_REML -Rvar decon_modulation_S1_REMLvar \
-Rfitts fitts_modulation_S1_REML -verb

++ N.B.: 3dREMLfit command above written to file decon_modulation_S1.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ ----- Signal+Baseline matrix condition [X] (420x25): 11.979 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=3.85309
* 1 singular value is less than cutoff=3.85309e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
-3.60823e-15 0.0268516 0.0313338 0.0458836 0.155161
0.356533 0.379377 0.559979 0.666904 0.768592
0.80873 0.900131 0.965943 0.998517 1.03599
1.07417 1.16096 1.25975 1.30095 1.4496
1.57257 1.71527 1.87147 2.04224 3.85309
++ ----- Signal-only matrix condition [X] (420x7): 1.04909 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (420x18): 10.4221 ++ VERY GOOD ++
*+ WARNING: !! in Baseline-only matrix:
* Largest singular value=3.70981
* 1 singular value is less than cutoff=3.70981e-07
* Implies strong collinearity in the matrix columns!
++ Baseline-only matrix singular values:
-3.72563e-15 0.0341541 0.0466142 0.161136 0.403044
0.844159 0.959479 0.965982 0.975082 1
1.02574 1.03128 1.05007 1.05728 1.29222
1.65526 1.78868 3.70981
++ ----- stim_base-only matrix condition [X] (420x6): 7.20644 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (420x12): 1.05251 ++ VERY GOOD ++
*+ WARNING: +++++ !! Matrix inverse average error = 0.169608 ** BEWARE **
++ Matrix setup time = 0.44 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 !!




If I run 1d_tool.py -infile Xmat.1D -show_cormat_warnings, as you suggested, it cannot open the file, because it was just not created (below nonetheless the error message)

failed to open 1D file Xmat.1D
** failed to read text data file Xmat.1D
** failed to read 1D data from 'Xmat.1D'


Best,
Jana