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Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

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The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Signy
December 18, 2008 11:21AM
I am unsure what I am doing wrong in the following script.
My study has 5 runs and 5 trial types. Any help would be amazing!

3dDeconvolve \
-input scaled_allruns+orig \
-mask mask+orig \
-concat runs.1D \
-polort 1 \
-censor 'idealA.1D[5]' \
-num_stimts 5 \
-stim_file 1 'idealA.1D[0]' -stim_label 1 A \
-stim_file 2 'idealA.1D[1]' -stim_label 2 Se \
-stim_file 3 'idealA.1D[2]' -stim_label 3 Sp \
-stim_file 4 'idealA.1D[3]' -stim_label 4 Ph \
-stim_file 5 'idealA.1D[4]' -stim_label 5 BA \
-stim_minlag 1 0 -stim_maxlag 1 6 \
-stim_minlag 2 0 -stim_maxlag 2 6 \
-stim_minlag 3 0 -stim_maxlag 3 6 \
-stim_minlag 4 0 -stim_maxlag 4 6 \
-stim_minlag 5 0 -stim_maxlag 5 6 \
-num_glt 5 \
-glt 1 AutovsBase.glt -glt_label 1 AutovBase \
-glt 1 SemvsBase.glt -glt_label 2 SemvBase \
-glt 1 SpavsBase.glt -glt_label 3 SpavBase \
-glt 1 PhovsBase.glt -glt_label 4 PhovBase \
-glt 1 BaselinevsBase.glt -glt_label 5 BaselinevsBase \
-iresp 1 irf_A.irf \
-iresp 2 irf_Se.irf \
-iresp 3 irf_Sp.irf \
-iresp 4 irf_Ph.irf \
-iresp 5 irf_BA.irf \
-fitts Fdecon_fit.fit \
-errts residual_error.fit \
-fout -tout -rout -bucket Fdecon_session


Here is the error message I received:

*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as ./scaled_allruns+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.
*+ WARNING: Input polort=1; Longest run=730.0 s; Recommended minimum polort=5
*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=7.37634
* 1 singular value is less than cutoff=7.37634e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: +++++ !! Matrix inverse average error = 0.00493827 ** BEWARE **
** 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 !!
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Subject Author Posted

3Ddeconvolve

Signy December 18, 2008 11:21AM

Re: 3Ddeconvolve

rick reynolds December 18, 2008 01:11PM