Hello,

The code looks the same to me (except for putting spaces in the label names, which might not be a good idea).

But if you are missing F-stats in the standalone version, I must suspect the your $NUM_CPUS variable is not actually set, and when 3dDeconvolve is run, it sees instead "-jobs -fout", and the -fout option does not make it to the program.

You can check this by running "3dinfo stats.3dDeconvolve..." and looking at the actual command.


In any case, you do not have to write your own 3dDeconvolve command. Copy and edit the original afni_proc.py command script, and add:

-write_3dD_script SCRIPTNAME
-write_3dD_prefix WITH_NEW_GLTs
... and add your new -gltsym options ...

That will generate "SCRIPTNAME" with a 3dDeonvolve command to be run in the already existing results directory, and it will create output files with your specified prefix. You might try that even if you get your current script to work.

- rick