Hello,
The most comprehensive example of this is
AFNI_demos/AFNI_pamenc, which we have presented during the more recent bootcamps as part of the
CD/AFNI_demos.tgz package. That contains a complete set of scripts for running FreeSurfer, @SSwarper, afni_proc.py and group analysis (3dttest++, including cases of -ETAC and -ClustSim).
There is a more recent example of processing scripts called
APMULTI_Demo1_rest, which can be installed by simply running:
@Install_APMULTI_Demo1_rest
But while demonstrating options for processing multi-echo rest data, it does not contain anything to loop over subjects.
Both of those packages contain scripts for running on one's desktop, or on an HPC system with swarming.
The scripts in APMULTI_Demo1_rest are what we currently base new analyses on, though again, to keep them simple, they do not loop over subjects.
The AFNI_pamenc scripts do loop over subjects, but they are not quite as nice as the APMULTI scripts.
In any case, please take a look and feel free to ask any questions about them.
- rick
