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  

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January 04, 2023 05:13PM
Oh, and from spacing out the command, I think I see the issue: "-ortvec .." takes 2 parameters after it, not 1. From the 3dDeconvolve help:
-ortvec fff lll      This option lets you input a rectangular array    
                     of 1 or more baseline vectors from file 'fff',    
                     which will get the label 'lll'.  Functionally,    
                     it is the same as using '-stim_file' on each      
                     column of 'fff' separately (plus '-stim_base').   
                     This method is just a faster and simpler way to   
                     include a lot of baseline regressors in one step. 
          -->>**N.B.: This file is NOT included in the '-num_stimts'   
                      count that you provide.                          
               *N.B.: These regression matrix columns appear LAST      
                      in the matrix, after everything else.            
               *N.B.: You can use column '[..]' and/or row '{..}'      
                      selectors on the filename 'fff' to pick out      
                      a subset of the numbers in that file.            
               *N.B.: The q-th column of 'fff' will get a label        
                      like 'lll[q]' in the 3dDeconvolve results.       
               *N.B.: This option is known as the 'Inati Option'.      
               *N.B.: Unlike the original 'Inati' (who is unique), it  
                      is allowed to have more than one '-ortvec' option.
               *N.B.: Program 1dBport is one place to generate a file  
                      for use with '-ortvec'; 1deval might be another.
So, if you changed:
-ortvec          /mnt/analysis/sub-${subject}/func/confound_test.1D      \
... to:
-ortvec          /mnt/analysis/sub-${subject}/func/confound_test.1D  ORT_LABEL    \
... does that sort that error message out?

Note some of the other points in the other reply might still apply and be useful to address, too.

--pt
Subject Author Posted

3D Convolve with variable block durations based on response timing of the participant

Abipolar January 04, 2023 02:58PM

Re: 3D Convolve with variable block durations based on response timing of the participant

ptaylor January 04, 2023 05:05PM

Re: 3D Convolve with variable block durations based on response timing of the participant

ptaylor January 04, 2023 05:13PM

Re: 3D Convolve with variable block durations based on response timing of the participant

rick reynolds January 04, 2023 06:38PM