I am running a resting state analysis with afni_proc.py . I would like to do one analysis without global signal regression and another analysis with global signal regression. Is there any way to make this work without having to repeat all the steps twice? Can I specify that in the command option that generates the script file?
Thanks a lot in advance,
Yes, I expect so. The options -write_3dD_script and -write_3dD_prefix
can be added to an existing afni_proc.py command to generate scripts
for just the linear regression, but assuming the rest of the preprocessing
steps. If the AP command is modified slightly to be for resting state,
hopefully the required file names would still be unchanged.
Give it a try. Note that the resulting 3dDeconvolve script is intended to
be run from the results directory, and that it uses a $prefix variable to
separate output from the new script.