This is various python code related to data processing and analysis.

deface.py: this performing defacing of an anatomical image using a 
custom mask developed at UT.  you will need to grab the template
and mask from the data directory and then change the paths to those
images in the code

launch.py: this is an experimental front-end for the launch_qsub
function to allow it to be used from the command line.  not well 
tested yet.

launch_qsub.py: code to launch SGE jobs from within python. This is
customized for the TACC system and will require modification to run
on any other system.

run_shell_cmd.py: simple front end to Popen to run shell command
and wait for it to finish

setup_subject.py: a script to perform preprocessing and setup for
a full fMRI study.  this is a recent port of the setup_subject 
script from UCLA, and has not been thoroughly tested yet.
It makes a number of assumptions about the DICOM structure which
are true of GE data but probably will not work without modification
for any other systems.

fsld: this is an R script used by setup_subject.py to perform data
diagnostics, but it could also be used in standalone mode.