how to run 1st level general linear tests without re-preprocessing the entire data

AFNI Message Board
1

Hello,

I was wondering if there is a quick way to run the first level/single subject general linear tests without having to preprocess anew the subject. Let say that I realize after preprocessing that I forgot a specific contrast, is it possible to make the adjustment without repreprocessing everything. I have a pretty slow computer and would like to be a bit more efficient. If there is a page for this, a link will be great!

Thank you.
Ilaria

2

Hi Ilaria,

Add the options -write_3dD_script and -write_3dD_prefix to your current afni_proc.py command, e.g.,

-write_3dD_script run.3dd.PICKLES -write_3dD_prefix stats.PICKLES

Running that would create a new 3dDeconvolve command (in run.3dd.PICKLES) that could be run from the results directory, and which would create output datasets with the prefix stats.PICKLES. It would assume all of the other processing had already happened, and would therefore work with your current data.

So you can modify that same afni_proc.py command with the new PICKLES contrasts, and they would be added to run.3dd.PICKLES script.

Does that seem reasonable?

  • rick
3

Great thanks. I’ll add that to my afni_proc.py!!
Ilaria