Hi AFNI Users,
This is our first attempt at AM regression and we are coming up with "strong collinearity" error messages - here's a sampling:

Largest singular value =4.54934
1 singular value is less than cutoff=4.54934-e07
Implies strong collinearity in the matrix columns!.....

For the full output, please see below. I am suspecting the event files. Is it possible that this is something we can push past with a larger GOFORIT?

thanks in advance
Brenda

Output:
++ '-stim_times_AM1 1 stimuli/20617-1fraf1.txt' has 1 auxiliary values per time point
++ '-stim_times_AM1 1': basis function model 'dmBLOCK' uses 1 parameters,
out of the 1 found in timing file 'stimuli/20617-1fraf1.txt'
++ '-stim_times_AM1 2 stimuli/20617-1fraf2.txt' has 1 auxiliary values per time point
++ '-stim_times_AM1 2': basis function model 'dmBLOCK' uses 1 parameters,
out of the 1 found in timing file 'stimuli/20617-1fraf2.txt'
++ '-stim_times_AM1 3 stimuli/20617-1frbf1.txt' has 1 auxiliary values per time point
++ '-stim_times_AM1 3': basis function model 'dmBLOCK' uses 1 parameters,
out of the 1 found in timing file 'stimuli/20617-1frbf1.txt'
++ '-stim_times_AM1 4 stimuli/20617-1frbf2.txt' has 1 auxiliary values per time point
++ '-stim_times_AM1 4': basis function model 'dmBLOCK' uses 1 parameters,
out of the 1 found in timing file 'stimuli/20617-1frbf2.txt'
++ '-stim_times_AM1 5 stimuli/20617-1vwait.txt' has 1 auxiliary values per time point
++ '-stim_times_AM1 5': basis function model 'dmBLOCK' uses 1 parameters,
out of the 1 found in timing file 'stimuli/20617-1vwait.txt'
++ 3dDeconvolve: AFNI version=AFNI_2008_07_18_1710 (Sep 16 2009) [32-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset pb04.20617.r01.scale+orig.HEAD pb04.20617.r02.scale+orig.HEAD
++ Auto-catenated datasets start at: 0 362
++ misfit/FDR automask has 219148 voxels (out of 331776 = 66.1%)
++ Input polort=6; Longest run=832.6 s; Recommended minimum polort=6 ++ OK ++
++ -stim_times using TR=2.3 s for stimulus timing conversion
++ -stim_times using TR=2.3 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ -stim_times_AM1 1 using LOCAL times
++ -stim_times_AM1 2 using LOCAL times
++ -stim_times_AM1 3 using LOCAL times
++ -stim_times_AM1 4 using LOCAL times
++ -stim_times_AM1 5 using LOCAL times
------------------------------------------------------------
GLT matrix from 'SYM: +rrfr -rnfr':
0 0 0 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: +rnfr -rrfr':
0 0 0 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: +rrfr -rrfn':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 1 0 0 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +rrfn -rrfr':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +rnfr -rnfn':
0 0 0 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: +rnfn -rnfr':
0 0 0 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: +rrfr +rnfr -rrfn -rnfn':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 1 -1 1 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +rrfr +rrfn -rnfr -rnfn':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 -1 -1 0 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +rrfr -baseline':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 -1 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +rrfn -baseline':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 -1 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +rrfr +rnfr -2*baseline':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 -2 0 0 0 0 0 0

------------------------------------------------------------
GLT matrix from 'SYM: +rrfn +rnfn -2*baseline':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 -2 0 0 0 0 0 0

*+ WARNING: -stim_file 6: file length is 1051, longer than expected 703 (from dataset)
*+ WARNING: -stim_file 7: file length is 1051, longer than expected 703 (from dataset)
*+ WARNING: -stim_file 8: file length is 1051, longer than expected 703 (from dataset)
*+ WARNING: -stim_file 9: file length is 1051, longer than expected 703 (from dataset)
*+ WARNING: -stim_file 10: file length is 1051, longer than expected 703 (from dataset)
*+ WARNING: -stim_file 11: file length is 1051, longer than expected 703 (from dataset)
++ Memory required for output bricks = 1934917632 bytes (about 1.9 billion)
++ Wrote matrix image to file X.jpg
++ Wrote matrix values to file X.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:

3dREMLfit -matrix X.xmat.1D \
-input "pb04.20617.r01.scale+orig.HEAD pb04.20617.r02.scale+orig.HEAD" \
-fout -tout -Rbuck stats.20617_REML -Rvar stats.20617_REMLvar \
-Rfitts fitts.20617_REML -Rerrts errts.20617_REML -verb

++ N.B.: 3dREMLfit command above written to file stats.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ ----- Signal+Baseline matrix condition [X] (495x25): 1623.54 ++ OK ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=4.54934
* 1 singular value is less than cutoff=4.54934e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
2.36909e-10 1.72592e-06 0.00145009 0.00246522 0.00535354
0.0196994 0.0257479 0.0964718 0.191477 0.314207
0.382698 0.796788 0.806621 0.930177 0.955658
1.04239 1.09121 1.15697 1.24835 1.59853
1.95337 2.33152 2.57335 2.92617 4.54934
++ ----- Signal-only matrix condition [X] (495x5): 1.01422 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (495x20): 1551.7 ++ OK ++
*+ WARNING: !! in Baseline-only matrix:
* Largest singular value=4.26916
* 1 singular value is less than cutoff=4.26916e-07
* Implies strong collinearity in the matrix columns!
++ Baseline-only matrix singular values:
2.52515e-10 1.77307e-06 0.00147394 0.00252534 0.00562549
0.0198543 0.0277432 0.100008 0.198359 0.360187
0.989907 1.03045 1.0455 1.07183 1.42522
1.93601 2.29273 2.54082 2.68259 4.26916
++ ----- stim_base-only matrix condition [X] (495x6): 7.13277 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (495x14): 1105.72 ++ OK ++
*+ WARNING: !! in polort-only matrix:
* Largest singular value=2.41543
* 1 singular value is less than cutoff=2.41543e-07
* Implies strong collinearity in the matrix columns!
++ polort-only matrix singular values:
2.60533e-10 1.97563e-06 0.00201808 0.300356 0.969759
0.975513 0.982974 0.988926 1 1.03556
1.04727 1.99731 2.28488 2.41543
++ +++++ Matrix inverse average error = 1.50447e-08 ++ VERY GOOD ++
++ Matrix setup time = 5.62 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 = Sep 16 2009
---------------------------------------
** 3dDeconvolve error, failing...
(consider the file 3dDeconvolve.err)




Script:
set subj = 20617

# ================================ regress =================================
# run the regression analysis
3dDeconvolve -input pb04.$subj.r??.scale+orig.HEAD \
-local_times \
-polort 6 \
-num_stimts 11 \
-stim_times_AM1 1 stimuli/20617-1fraf1.txt 'dmBLOCK' \
-stim_label 1 rrfn \
-stim_times_AM1 2 stimuli/20617-1fraf2.txt 'dmBLOCK' \
-stim_label 2 rrfr \
-stim_times_AM1 3 stimuli/20617-1frbf1.txt 'dmBLOCK' \
-stim_label 3 rnfn \
-stim_times_AM1 4 stimuli/20617-1frbf2.txt 'dmBLOCK' \
-stim_label 4 rnfr \
-stim_times_AM1 5 stimuli/20617-1vwait.txt 'dmBLOCK' \
-stim_label 5 baseline \
-stim_file 6 dfile.rall.1D'[0]' -stim_base 6 -stim_label 6 roll \
-stim_file 7 dfile.rall.1D'[1]' -stim_base 7 -stim_label 7 pitch \
-stim_file 8 dfile.rall.1D'[2]' -stim_base 8 -stim_label 8 yaw \
-stim_file 9 dfile.rall.1D'[3]' -stim_base 9 -stim_label 9 dS \
-stim_file 10 dfile.rall.1D'[4]' -stim_base 10 -stim_label 10 dL \
-stim_file 11 dfile.rall.1D'[5]' -stim_base 11 -stim_label 11 dP \
-censor censor.1D \
-iresp 1 iresp_rrfn.$subj \
-iresp 2 iresp_rrfr.$subj \
-iresp 3 iresp_rnfn.$subj \
-iresp 4 iresp_rnfr.$subj \
-iresp 5 iresp_baseline.$subj \
-num_glt 12 \
-gltsym 'SYM: +rrfr -rnfr' \
-glt_label 1 rrfr_rnfr \
-gltsym 'SYM: +rnfr -rrfr' \
-glt_label 2 rnfr_rrfr \
-gltsym 'SYM: +rrfr -rrfn' \
-glt_label 3 rrfr_rrfn \
-gltsym 'SYM: +rrfn -rrfr' \
-glt_label 4 rrfn_rrfr \
-gltsym 'SYM: +rnfr -rnfn' \
-glt_label 5 rnfr_rnfn \
-gltsym 'SYM: +rnfn -rnfr' \
-glt_label 6 rnfn_rnfr \
-gltsym 'SYM: +rrfr +rnfr -rrfn -rnfn' \
-glt_label 7 rrfrrnfr_rrfnrnfn \
-gltsym 'SYM: +rrfr +rrfn -rnfr -rnfn' \
-glt_label 8 rrfrrrfn_rnfrrnfn \
-gltsym 'SYM: +rrfr -baseline' \
-glt_label 9 rrfr_baseline \
-gltsym 'SYM: +rrfn -baseline' \
-glt_label 10 rrfn_baseline \
-gltsym 'SYM: +rrfr +rnfr -2*baseline' \
-glt_label 11 fr_baseline \
-gltsym 'SYM: +rrfn +rnfn -2*baseline' \
-glt_label 12 fn_baseline \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-fitts fitts.$subj \
-errts errts.$subj \
-bucket stats.$subj


# if 3dDeconvolve fails, terminate the script
if ( $status != 0 ) then
echo '---------------------------------------'
echo '** 3dDeconvolve error, failing...'
echo ' (consider the file 3dDeconvolve.err)'
exit
endif


# create an all_runs dataset to match the fitts, errts, etc.
3dTcat -prefix all_runs.$subj pb04.$subj.r??.scale+orig.HEAD

# ============================ blur estimation =============================
# compute blur estimates
touch blur_est.$subj.1D # start with empty file

# -- estimate blur for each run in errts --
touch blur.errts.1D

set b0 = 0 # first index for current run
set b1 = -1 # will be last index for current run
foreach reps ( 362 341 348 )
@ b1 += $reps # last index for current run
3dFWHMx -detrend -mask full_mask.$subj+orig \
errts.$subj+orig"[$b0..$b1]" >> blur.errts.1D
@ b0 += $reps # first index for next run
end

# compute average blur and append
set blurs = ( `3dTstat -mean -prefix - blur.errts.1D\'` )
echo average errts blurs: $blurs
echo "$blurs # errts blur estimates" >> blur_est.$subj.1D


# =========================== gen_epi_review.py ============================
# generate a review script for the unprocessed EPI data
gen_epi_review.py -script @epi_review.$subj \
-dsets pb00.$subj.r??.tcat+orig.HEAD

# ================================ cleanup =================================

# remove temporary rm.* files
\rm -f rm.*

# return to parent directory
cd ..




# ==========================================================================
# script generated by the command:
#
# afni_proc.py -subj_id 20617 -script afni_proc_py_script -dsets \
# OutBrick_r1+orig.HEAD OutBrick_r2+orig.HEAD OutBrick_r3+orig.HEAD \
# -tcat_remove_first_trs 0 -volreg_align_to last -blur_size 6 \
# -regress_basis dmBLOCK -regress_stim_times 20617-1fraf1.txt \
# 20617-1fraf2.txt 20617-1frbf1.txt 20617-1frbf2.txt 20617-1vwait.txt \
# -regress_stim_labels rrfn rrfr rnfn rnfr baseline \
# -regress_est_blur_errts -regress_errts_prefix errts -regress_opts_3dD \
# -num_glt 12 -gltsym 'SYM: +rrfr -rnfr' -glt_label 1 rrfr_rnfr -gltsym \
# 'SYM: +rnfr -rrfr' -glt_label 2 rnfr_rrfr -gltsym 'SYM: +rrfr -rrfn' \
# -glt_label 3 rrfr_rrfn -gltsym 'SYM: +rrfn -rrfr' -glt_label 4 \
# rrfn_rrfr -gltsym 'SYM: +rnfr -rnfn' -glt_label 5 rnfr_rnfn -gltsym \
# 'SYM: +rnfn -rnfr' -glt_label 6 rnfn_rnfr -gltsym 'SYM: +rrfr +rnfr \
# -rrfn -rnfn' -glt_label 7 rrfrrnfr_rrfnrnfn -gltsym 'SYM: +rrfr +rrfn \
# -rnfr -rnfn' -glt_label 8 rrfrrrfn_rnfrrnfn -gltsym 'SYM: +rrfr \
# -baseline' -glt_label 9 rrfr_baseline -gltsym 'SYM: +rrfn -baseline' \
# -glt_label 10 rrfn_baseline -gltsym 'SYM: +rrfr +rnfr -2*baseline' \
# -glt_label 11 fr_baseline -gltsym 'SYM: +rrfn +rnfn -2*baseline' \
# -glt_label 12 fn_baseline