Hi, Brady-
For any FMRI processing, using afni_proc.py will reeeeaaaalllly help you: you can do all the detailed specifying of processing steps and options that you want, and afni_proc.py will take care of lots of annoying details for you (i.e., concatenating transforms, building 3dDeconvolve commands, etc.). Processing in this way is very understandable, compact, sharable, and tailorable-- you have a compact command distilling your processing, and this generates your several hundred++ line script for you.
To answer your question fo processing *without* afni_proc.py-- firstly, again, I strongly recommend you consider processing with it. But note that afni_proc.py generates *a script* for you, that gets executed to do the processing. If you want to emulate some features that afni_proc.py does, you can use the script as an educational tool-- note that Rick has made the generated script commented (!) and organized block sections, so it is very readable.
As to plotting "a voxel's activity against the design" -- I'm not sure what that means. You don't want to plot the betas? Note also that when you plot the betas, if you have used the "scale" block in afni_proc.py (or just scaled your data with AFNI), then you can set the colorbar scale to something meaningful. Very strong betas in task experiments are about 2-3% BOLD percent signal change. You can threshold with the stat value, as you wish (p=0.001, for example, and AFNI can do the calculation between stat and p-value internally for you, taking into account DOFs, etc.).
--pt
Edited 1 time(s). Last edit at 01/18/2019 02:51PM by ptaylor.
