How to understand the result of AFNI 3dDeconvolve with .1D file?

Hi experts,

I have a .1D file generated from 3dmaskave. I want to examine its activation with the stimuli. So I used 3dDeconvolve command. Here is my code:

3dDeconvolve -force_TR 2.4 \
             -input epi01_CAL_to_MT_L.1D\' epi02_CAL_to_MT_L.1D\'     \
             -jobs 4                                            \
             -polort A                                           \
             -censor motion1_PA4_censor.1D             \
             -num_stimts 3                                                        \
             -local_times                                                         \
             -stim_times 1 ConA.txt 'TWOGAM(5.1849,1.4339,0.0446,1.0352,665.5736,10)'               \
             -stim_label 1 ConA                                            \
             -stim_times 2 ConB.txt 'TWOGAM(5.1849,1.4339,0.0446,1.0352,665.5736,10)'                     \
             -stim_label 2 ConB                                                  \
             -stim_times 3 ConC.txt 'TWOGAM(5.1849,1.4339,0.0446,1.0352,665.5736,8)'                       \
             -stim_label 3 ConC                                                   \
             -gltsym 'SYM: ConA + ConB'                                   \
             -glt_label 1 C+R                                                     \
             -gltsym 'SYM: ConA - ConB'                                   \
             -glt_label 2 C-R                                                     \
             -gltsym 'SYM: ConA - ConC'                                    \
             -glt_label 3 C-Re                                                    \
             -fout -tout -bout -x1D X.xmat.1D -xjpeg X.jpg                              \
             -x1D_uncensored X.nocensor.xmat.1D                                   \
             -errts errts                                          \
             -bucket stats > stats_details

Then I got the result:


However, it is difficult to understand the meaning of each row. From the output in shell, I found “Number of parameters: 13 [10 baseline ; 3 signal]”. So I guess each row may represent the co-efficient of each parameters. But

  1. Why there are 10 baseline? What are they?
  2. Where are the beta values of the 3 “stim_label”? Does the last 3 rows correspond to the 3 stim?
  3. When I deleted “-fout” or “-tout”, why the result did not change? The result of -gltsym also seems not to work, because when I added or deleted -gltsym, the result also does not change.

Thank you for your help!

Best regards,


For reference, this has been resolved in a thread on the AFNI message board with Roger and Gang.

To summarize:

In order to get t/f-stats displayed, the (1D-format) input needs to have at least 2 voxels.

  1. The 10 baseline parameters are from 2 runs of trend fitting.
  2. The baseline parameters come first (note that parameters 0 and 5 are basically 100, as they are the contant baseline terms for each run).
  3. Since there are no t/f-stats output, the -fout and -tout options do not matter. But with a 2+ voxel input, they are shown. GLTs are not shown with this simple format, either.


  • rick