I corrected the spell errors and changed the command line a bit:
3dDeconvolve -input runall-norm+orig -concat '1D: 0 90 180 270' \
-num_stimts 4 \
-stim_times 1 '1D: 0 18 30 48 62 80 92 108 122 138 152 170' 'BLOCK(2,1)' \
-stim_times 2 '1D: 182 194 216 226 242 258 270 288 302 320 334 350' 'BLOCK(2,1)' \
-stim_times 3 '1D: 362 376 388 404 422 440 452 466 482 494 512 526' 'BLOCK(2,1)' \
-stim_times 4 '1D: 542 560 576 588 602 620 632 648 662 674 690 704' 'BLOCK(2,1)' \
-stim_label 1 A -stim_label 2 B -stim_label 3 C -stim_label 4 D \
-gltsym 'SYM: +A[[2..8]] -B[[9..15]]' -glt_label 1 AvsB \
-gltsym 'SYM: +B[[16..22]] -C[[23..29]]' -glt_label 2 BvsC \
-gltsym 'SYM: +C[[30..36]] -D[[37..43]]' -glt_label 3 CvsD \
-gltsym 'SYM: +D[[44..50]] -A[[51..57]]' -glt_label 4 DvsA \
-fout -tout -bucket runall
PS:I want to use 'SYM: +A[[2..8]] -B[[9..15]] to express such glt matrix as below:
001000000-1000000000000000000000
0001000000-100000000000000000000
00001000000-10000000000000000000
000001000000-1000000000000000000
0000001000000-100000000000000000
00000001000000-10000000000000000
000000001000000-1000000000000000
yet my effort failed.
the system reports:
GLT matrix from 'SYM: +A[[2..8]] -B[[9..15]]':
0 0 0 0 0 0 0 0 1 -1 0 0
ALL Error reports:
++ loading dataset runall-norm+orig
++ current memory malloc-ated = 123362 bytes (about 123 thousand)
*+ WARNING: Input polort=1; Longest run=180.0 s; Recommended minimum polort=2
++ -stim_times using TR=2 s for stimulus timing conversion
++ -stim_times using TR=2 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** NOTE ** Will guess GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times 1 using LOCAL times
*+ WARNING: '-stim_times 1' file '1D: 0 18 30 48 62 80 92 108 122 138 152 170' has 1 rows, but dataset has 4 time blocks
++ ** GUESSED ** -stim_times 2 using LOCAL times
*+ WARNING: '-stim_times 2' file '1D: 182 194 216 226 242 258 270 288 302 320 334 350' has 1 rows, but dataset has 4 time blocks
*+ WARNING: '-stim_times 2' (LOCAL) run#1 has 12 times outside range 0 .. 178 [PSFB syndrome]
*+ WARNING: dataset TR being used is 2 s
*+ WARNING: !! '-stim_times 2' file '1D: 182 194 216 226 242 258 270 288 302 320 334 350' has no good time values
++ ** GUESSED ** -stim_times 3 using LOCAL times
*+ WARNING: '-stim_times 3' file '1D: 362 376 388 404 422 440 452 466 482 494 512 526' has 1 rows, but dataset has 4 time blocks
*+ WARNING: '-stim_times 3' (LOCAL) run#1 has 12 times outside range 0 .. 178 [PSFB syndrome]
*+ WARNING: dataset TR being used is 2 s
*+ WARNING: !! '-stim_times 3' file '1D: 362 376 388 404 422 440 452 466 482 494 512 526' has no good time values
++ ** GUESSED ** -stim_times 4 using LOCAL times
*+ WARNING: '-stim_times 4' file '1D: 542 560 576 588 602 620 632 648 662 674 690 704' has 1 rows, but dataset has 4 time blocks
*+ WARNING: '-stim_times 4' (LOCAL) run#1 has 12 times outside range 0 .. 178 [PSFB syndrome]
*+ WARNING: dataset TR being used is 2 s
*+ WARNING: !! '-stim_times 4' file '1D: 542 560 576 588 602 620 632 648 662 674 690 704' has no good time values
** ERROR: sub-brick index 2 is out of range 0..0
** ERROR: sub-brick index 9 is out of range 0..0
------------------------------------------------------------
GLT matrix from 'SYM: +A[[2..8]] -B[[9..15]]':
0 0 0 0 0 0 0 0 1 -1 0 0
** ERROR: sub-brick index 16 is out of range 0..0
** ERROR: sub-brick index 23 is out of range 0..0
------------------------------------------------------------
GLT matrix from 'SYM: +B[[16..22]] -C[[23..29]]':
0 0 0 0 0 0 0 0 0 1 -1 0
** ERROR: sub-brick index 30 is out of range 0..0
** ERROR: sub-brick index 37 is out of range 0..0
------------------------------------------------------------
GLT matrix from 'SYM: +C[[30..36]] -D[[37..43]]':
0 0 0 0 0 0 0 0 0 0 1 -1
** ERROR: sub-brick index 44 is out of range 0..0
** ERROR: sub-brick index 51 is out of range 0..0
------------------------------------------------------------
GLT matrix from 'SYM: +D[[44..50]] -A[[51..57]]':
0 0 0 0 0 0 0 0 -1 0 0 1
++ Memory required for output bricks = 8192000 bytes (about 8.2 million)
++ Wrote matrix values to file runall.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:
3dREMLfit -matrix runall.xmat.1D -input runall-norm+orig \
-fout -tout -Rbuck runall_REML -Rvar runall_REMLvar -verb
++ N.B.: 3dREMLfit command above written to file runall.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 9 [B#0] is all zeros
*+ WARNING: !! * Column 10 [C#0] is all zeros
*+ WARNING: !! * Column 11 [D#0] is all zeros
*+ WARNING: -------------------------------------------------
++ ----- Signal+Baseline matrix condition [X] (360x12): 2.41509 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=1.70729
* 3 singular values are less than cutoff=1.70729e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
0 0 0 0.292711 1
1 1 1 1 1
1 1.70729
++ ----- Signal-only matrix condition [X] (360x4): 1 ++ VERY GOOD ++
*+ WARNING: !! in Signal-only matrix:
* Largest singular value=1
* 3 singular values are less than cutoff=1e-07
* Implies strong collinearity in the matrix columns!
++ Signal-only matrix singular values:
0 0 0 1
++ ----- Baseline-only matrix condition [X] (360x8): 1 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (360x8): 1 ++ VERY GOOD ++
*+ WARNING: +++++ !! Matrix inverse average error = 0.0208333 ** BEWARE **
*+ WARNING: GLT setup: inversion of C[1/(X'X)]C' fails; trying SVD.
[This happens when some regressor columns are all ]
[zero, or when the GLT has linearly-dependent rows]
[********* EXAMINE YOUR RESULTS WITH CARE ********]
*+ WARNING: GLT setup: inversion of C[1/(X'X)]C' fails; trying SVD.
[This happens when some regressor columns are all ]
[zero, or when the GLT has linearly-dependent rows]
[********* EXAMINE YOUR RESULTS WITH CARE ********]
++ Matrix setup time = 0.02 s
** ERROR: !! 3dDeconvolve: Can't run past 9 matrix warnings without '-GOFORIT 9'
** 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 !!
