Hello James,
That's indeed what was disturbing. Thank you so much. The script runs! However, I would have two more questions regarding some warning messages.
(1) When I set polort to 1, I get the following warning:
*+ WARNING: Input polort=1; Longest run=630.0 s; Recommended minimum polort=5
Do you think I should set the polort that high?
(2) The next thing is that script execution stops after 3 warnings. As the script stands now, I have included the six movement parameters into the base model. However, the program tells me that I have collinearity problems.
Script:
3dDeconvolve\
-input psc.ssm.tsm.cl.dsp.hpf.reg.ts.1+orig psc.ssm.tsm.cl.dsp.hpf.reg.ts.2+orig\
-polort 1\
-num_stimts 10\
-global_times\
-stim_times_AM2 1 onsettimes_pleasant_S1.txt 'BLOCK(18,1)'\
-stim_label 1 pleasant\
-stim_times_AM2 2 onsettimes_neutral_S1.txt 'BLOCK(18,1)'\
-stim_label 2 neutral\
-stim_times_AM2 3 onsettimes_unpleasant_S1.txt 'BLOCK(18,1)'\
-stim_label 3 unpleasant\
-stim_times 4 onsettimes_other_S1.txt 'BLOCK(18,1)'\
-stim_label 4 other\
-stim_file 5 mot[0]\
-stim_base 5\
-stim_label 5 Roll\
-stim_file 6 mot[1]\
-stim_base 6\
-stim_label 6 Pitch\
-stim_file 7 mot[2]\
-stim_base 7\
-stim_label 7 Yaw\
-stim_file 8 mot[3]\
-stim_base 8\
-stim_label 8 dS\
-stim_file 9 mot[4]\
-stim_base 9\
-stim_label 9 dL\
-stim_file 10 mot[5]\
-stim_base 10\
-stim_label 10 dP\
-num_glt 6\
-gltsym 'SYM: +pleasant[0] -neutral[0]'\
-glt_label 1 pleasant_vs_neutral\
-gltsym 'SYM: +pleasant[0] -unpleasant[0]'\
-glt_label 2 pleasant_vs_unpleasant\
-gltsym 'SYM: +neutral[0] -unpleasant[0]'\
-glt_label 3 neutral_vs_unpleasant\
-gltsym 'SYM: +pleasant[1] -neutral[1]'\
-glt_label 4 pleasant_vs_neutral_modulation\
-gltsym 'SYM: +pleasant[1] -unpleasant[1]'\
-glt_label 5 pleasant_vs_unpleasant_modulation\
-gltsym 'SYM: +neutral[1] -unpleasant[1]'\
-glt_label 6 neutral_vs_unpleasant_modulation\
-fout\
-rout\
-tout\
-fitts fitts_modulation_S1\
-x1D Xmat.x1D\
-bucket decon_modulation_S1\
Messages:
++ '-stim_times_AM2 1 onsettimes_pleasant_S1.txt' has 1 auxiliary values per time point
++ '-stim_times_AM2 1 onsettimes_pleasant_S1.txt' will have 2 regressors
++ '-stim_times_AM2 2 onsettimes_neutral_S1.txt' has 1 auxiliary values per time point
++ '-stim_times_AM2 2 onsettimes_neutral_S1.txt' will have 2 regressors
++ '-stim_times_AM2 3 onsettimes_unpleasant_S1.txt' has 1 auxiliary values per time point
++ '-stim_times_AM2 3 onsettimes_unpleasant_S1.txt' will have 2 regressors
++ 3dDeconvolve: AFNI version=AFNI_2010_10_19_1028 (Jan 3 2011) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 113,501 bytes (about 114 thousand)
++ loading dataset psc.ssm.tsm.cl.dsp.hpf.reg.ts.1+orig psc.ssm.tsm.cl.dsp.hpf.reg.ts.2+orig
++ current memory malloc-ated = 275,373,813 bytes (about 275 million)
++ Auto-catenated datasets start at: 0 210
*+ WARNING: Input polort=1; Longest run=630.0 s; Recommended minimum polort=5
++ -stim_times using TR=3 s for stimulus timing conversion
++ -stim_times using TR=3 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ -stim_times_AM2 1 using GLOBAL times
++ '-stim_times_AM2 1' average amplitude#1=-0.157895
++ -stim_times_AM2 2 using GLOBAL times
++ '-stim_times_AM2 2' average amplitude#1=-0.588235
++ -stim_times_AM2 3 using GLOBAL times
++ '-stim_times_AM2 3' average amplitude#1=-0.15
++ -stim_times 4 using GLOBAL times
------------------------------------------------------------
GLT matrix from 'SYM: +pleasant[0] -neutral[0]':
0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: +pleasant[0] -unpleasant[0]':
0 0 0 0 1 0 0 0 -1 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: +neutral[0] -unpleasant[0]':
0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: +pleasant[1] -neutral[1]':
0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: +pleasant[1] -unpleasant[1]':
0 0 0 0 0 1 0 0 0 -1 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: +neutral[1] -unpleasant[1]':
0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0
++ Number of time points: 420 (no censoring)
+ Number of parameters: 17 [10 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] (420x17): 10.5741 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=3.81463
* 1 singular value is less than cutoff=3.81463e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
-3.85858e-15 0.0341166 0.0461907 0.0943487 0.175441
0.526968 0.649424 0.862266 0.956003 0.966492
0.984714 1.02573 1.37497 1.63565 1.81902
2.03404 3.81463
++ ----- Signal-only matrix condition [X] (420x7): 1.04909 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (420x10): 8.72671 ++ VERY GOOD ++
*+ WARNING: !! in Baseline-only matrix:
* Largest singular value=3.67404
* 1 singular value is less than cutoff=3.67404e-07
* Implies strong collinearity in the matrix columns!
++ Baseline-only matrix singular values:
-3.88628e-15 0.0482439 0.0973238 0.178736 0.617806
1 1.12656 1.55909 1.6982 3.67404
++ ----- stim_base-only matrix condition [X] (420x6): 7.20644 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (420x4): 1 ++ VERY GOOD ++
*+ WARNING: +++++ !! Matrix inverse average error = 0.366799 ** BEWARE **
++ Matrix setup time = 0.50 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 !!
** Program compile date = Jan 3 2011
If I take the movement parameters out, the script runs fine, though. However, I guess that this is not ideal either. Would you rather use the -GOFORIT option?
Best,
Jana
