Wait a second... before anyone starts attempting to debug this, I might have found the solution, I just can't try it out right now. I followed the python traceback call to here: [bugs.python.org] and I am indeed using Python 2.7.2. I'm going to update my python to 2.7.3 and report back ASAP.

This is what I get when I kill the script:

File "/Applications/afni/align_epi_anat.py", line 3042, in <module>
ps.align_anat2epi(e, a, ps.epi_wt, ps.AlOpt, suff, mcost)
File "/Applications/afni/align_epi_anat.py", line 1852, in align_anat2epi
com.run()
File "/Applications/afni/afni_base.py", line 385, in run
self.status, self.so, self.se = shell_exec2(self.trimcom, self.capture)
File "/Applications/afni/afni_base.py", line 767, in shell_exec2
status = pipe.wait() #Wait till it is over and store returncode
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1291, in wait
pid, sts = _eintr_retry_call(os.waitpid, self.pid, 0)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 478, in _eintr_retry_call



Edited 1 time(s). Last edit at 11/23/2012 07:00PM by jdviviano.