Dear gurus,
I am attempting to run a 3dDeconvolve and am having trouble with warnings concerning my matrix files.
It's a block design and I have 5 1D files. The originals have 1s and 0s and I applied the HRF using waver. When I use GOFORIT, the results don't look right, suggesting the warnings are relevant. And by "look right" I mean I have no significant activation during stimulus versus quiet/blank/baseline blocks.
I've attached two 1D files since existing b.b posting suggested it could be related to the 1D files being colinear/similar. I don't think this is the case, though.
Here is the command line I ran followed by the output:
3dDeconvolve -input train_reg_blur6mm_scaled_detrended_resample3+orig
-polort 16 -num_stimts 5
-stim_file 1 ../WAVi.1D -stim_label 1 i
-stim_file 2 ../WAVe.1D -stim_label 2 e
-stim_file 3 ../WAVidp.1D -stim_label 3 iDP
-stim_file 4 ../WAVedp.1D -stim_label 4 eDP
-stim_file 5 ../WAVTr.1D -stim_label 5 Tr
-tout -fout -bucket MORLt
-num_glt 2
-glt_label 1 e_i -gltsym 'SYM: +e -i'
-glt_label 2 eDP_iDP -gltsym 'SYM: +eDP -iDP'>output
++ 3dDeconvolve: AFNI version=AFNI_2008_02_01_1144 (Apr 18 2008) [32-bit]
++ Authored by: B. Douglas Ward, et al.
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./train_reg_blur6mm_scaled_detrended_resample3+orig.BRIK,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:./train_reg_blur6mm_scaled_detrended_resample3+orig.BRIK is 0.500068 degrees from plumb.
++ current memory malloc-ated = 119245 bytes (about 119 thousand)
++ loading dataset train_reg_blur6mm_scaled_detrended_resample3+orig
++ current memory malloc-ated = 119245 bytes (about 119 thousand)
++ Input polort=16; Longest run=974.0 s; Recommended minimum polort=7 ++ OK ++
++ Memory required for output bricks = 17820176 bytes (about 18 million)
++ Wrote matrix values to file MORLt.xmat.1D
++ ----- Signal+Baseline matrix condition [X] (487x22): 7.65687 ++ VERY GOOD ++
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=3.29653
* 1 singular value is less than cutoff=3.29653e-07
* Implies strong collinearity in the matrix columns!
++ Signal+Baseline matrix singular values:
1.57305e-14 0.0562283 0.267356 0.41982 0.565775
0.934174 0.941098 0.949921 0.952988 0.957765
0.966555 0.970758 0.976441 0.978037 0.987907
0.992919 1.1349 1.21128 1.24825 1.28809
1.9032 3.29653
++ ----- Signal-only matrix condition [X] (487x5): 2.20809 ++ VERY GOOD ++
*+ WARNING: !! in Signal-only matrix:
* Largest singular value=2.40075
* 1 singular value is less than cutoff=2.40075e-07
* Implies strong collinearity in the matrix columns!
++ Signal-only matrix singular values:
1.49877e-14 0.492397 0.630927 1.47592 2.40075
++ ----- Baseline-only matrix condition [X] (487x17): 1.17179 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (487x17): 1.17179 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 0.000134783 ++ OK ++
++ Matrix setup time = 0.08 s
** ERROR: !! 3dDeconvolve: Can't run past 2 matrix warnings without '-GOFORIT 2'
** 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 !!
Any help is appreciated!!
One suspicion I have is that I don't have enough "0" or baseline TRs. Could that be the case? Note the long period of 0 at the end...
Thank you,
Marc
