AFNI Message Board

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

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

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

History of AFNI updates  

|
April 01, 2013 09:39AM
Good morning AFNI experts - thanks in advance for some more help.

I have been running afni_proc.py for preprocessing of resting state analysis. Two of my subjects are coming back with this error, and I am not sure how to interpret it.

*+ WARNING: !! in Signal+Baseline matrix:
* Largest singular value=2.51095
* 9 singular values are less than cutoff=2.51095e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: !! in Baseline-only matrix:
* Largest singular value=2.51095
* 9 singular values are less than cutoff=2.51095e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: !! in stim_base-only matrix:
* Largest singular value=2.28363
* 5 singular values are less than cutoff=2.28363e-07
* Implies strong collinearity in the matrix columns!
*+ WARNING: +++++ !! Matrix inverse average error = 0.013769 ** BEWARE **
** ERROR: !! 3dDeconvolve: Can't run past 4 matrix warnings without '-GOFORIT 4'
** 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 !!


the afni_proc settings (in case needed) are:
afni_proc.py -subj_id $name \
-dsets $name/rest1+orig.HEAD $name/rest2+orig.HEAD \
-copy_anat $name/anat+orig \
-blocks despike tshift align tlrc volreg mask regress \
-tcat_remove_first_trs 6 \
-volreg_align_e2a \
-volreg_tlrc_warp \
-mask_segment_anat yes \
-regress_censor_motion 0.2 \
-regress_censor_outliers 0.1 \
-regress_bandpass 0.0083 0.15 \
-regress_apply_mot_types demean deriv \
-regress_ROI brain WM CSF \
-regress_run_clustsim no \
-regress_est_blur_errts \
-out_dir $name/rest_results \

Thanks!
Subject Author Posted

3dDeconvolve/afni_proc error

Noah April 01, 2013 09:39AM

Re: 3dDeconvolve/afni_proc error

rick reynolds April 01, 2013 10:45AM