Freesurfers
I was hoping someone else would do this, but well, it seems that no one did. So I went ahead and made this myself. Amusingly, I don't NEED to reconstruct any brains right now, so I don't have anything to test this out with. Please someone try it, and let me know if it is helpful.
What I did was write a script that runs each and every part of the recon-all -all stream, one command at a time. (based on the NEW version 3 stream). Each one is loaded with -waitfor and -notify so that the dependency structure is intact. However, ALL of the commands start running in the background! If you have a 2 more processor system, then recon-all should complete in about HALF the time as it usually does, since all the hemisphere specific stuff can be done in parallel. At the completion of each hemipshere, it will email you.
I included a command for each minute step so that people can easily fiddle with options and commands and so forth.
Obviously, if you run recon-all -autoreon1, then you can then run my script (after deleting the step1-??.done lines). If you run recon-all -autorecon2, then you can run my script (after deleting the step1-??.done and step2-??.done lines) And so forth.
To see the script, go here: http://www.nmr.mgh.harvard.edu/~daniel click on fMRI scripts click on super-recon
Enjoy, and PLEASE email me if you use this. If there are corrections I can easily post them. Daniel