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Dear AFNI users-

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Sincerely, AFNI HQ

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Michael Amlung
May 05, 2009 12:54PM
We are trying to solve an issue we're having with our analysis. We have 4 individual runs that we concatenated together prior to 3dDeconvolve. However, for 2 of our participants, we do not have behavioral responses because of computer error. So we cannot build regressors for that run because we cannot classify trials based on responses.

We're trying to figure out the best approach to handle this. Originally, we thought to include a censor in 3dDeconvolve that will just censor that entire run from the concatenated dataset (all 0's for those TRs). However, when we do that, 3dDeconvolve dies (see error message pasted below). It appears as if the error is caused by the baseline for run 2 being all 0's. Censoring an entire run must not be the best approach.

Any suggestions on how to handle this run? I'm happy to answer follow-up questions.



++ 3dDeconvolve: AFNI version=AFNI_2008_07_18_1710 (Oct 29 2008) [32-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 244485 bytes (about 244 thousand)
++ loading dataset s01_ddcat_3.0bl_reg+orig
++ current memory malloc-ated = 148880133 bytes (about 149 million)
++ Imaging duration=270.0 s; Automatic polort=2
------------------------------------------------------------
GLT matrix from 'SYM: +control +impulsive +restrained':
0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +impulsive -control':
0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +restrained -control':
0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +restrained -impulsive':
0 0 0 0 0 0 0 0 0 0 0 0 -1 1 0 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +0.5*impulsive +0.5*restrained -control':
0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -1 0 0 0 0 0 0 0

++ Memory required for output bricks = 11698176 bytes (about 12 million)
++ Wrote matrix values to file s01_dd.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:

3dREMLfit -matrix s01_dd.xmat.1D -input s01_ddcat_3.0bl_reg+orig \
-tout -Rbuck s01_dd.buc_REML -Rvar s01_dd.buc_REMLvar -verb

++ N.B.: 3dREMLfit command above written to file s01_dd.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 3 [Run#2Pol#0] is all zeros
*+ WARNING: !! * Column 4 [Run#2Pol#1] is all zeros
*+ WARNING: !! * Column 5 [Run#2Pol#2] is all zeros
*+ WARNING: -------------------------------------------------
++ ----- Signal+Baseline matrix condition [X] (324x22): 19.6497 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=3.50151
* 3 singular values are less than cutoff=3.50151e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
-1.59887e-17 7.05225e-19 2.2856e-17 0.0090687 0.0102398
0.013958 0.0474944 0.10613 0.175108 0.25851
0.495027 0.727015 0.944588 1.00116 1.04528
1.26255 1.29771 1.45356 1.91461 2.21577
2.52071 3.50151
++ ----- Signal-only matrix condition [X] (324x3): 1.00461 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (324x19): 19.0944 ++ VERY GOOD ++
*+ WARNING: !! in Baseline-only matrix:
* Largest singular value=3.40441
* 3 singular values are less than cutoff=3.40441e-07
* Implies strong collinearity in the matrix columns!
++ Baseline-only matrix singular values:
-1.64608e-16 6.3181e-17 1.75585e-16 0.00933746 0.0102513
0.0139954 0.0500744 0.121147 0.18367 0.600652
1 1 1.00688 1.04673 1.39996
1.70463 2.006 2.44226 3.40441
++ ----- stim_base-only matrix condition [X] (324x7): 8.64427 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (324x12): 1 ++ VERY GOOD ++
*+ WARNING: !! in polort-only matrix:
* Largest singular value=1
* 3 singular values are less than cutoff=1e-07
* Implies strong collinearity in the matrix columns!
++ polort-only matrix singular values:
0 0 0 1 1
1 1 1 1 1
1 1
*+ WARNING: +++++ !! Matrix inverse average error = 0.00619835 ** BEWARE **
++ Matrix setup time = 0.11 s
** ERROR: !! 3dDeconvolve: Can't run past 7 matrix warnings without '-GOFORIT 7'
** 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 !!
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Subject Author Posted

3ddeconvolve concat runs

Michael Amlung May 05, 2009 12:54PM

Re: 3ddeconvolve concat runs

rick reynolds May 05, 2009 02:15PM