Ah. Silly me, I didn't notice the -log and -status options. Thanks Nick.
I have now included those into my super-recon script as well. Problem
solved.
(if you have seen my script already, you may need to hit RELOAD on your
browser to see the new version)
Daniel
Nick Schmansky wrote:
The script looks good. The one thing it needs though is for the right
and left hemi steps to log to separate files, otherwise output to recon-
all.log will be interleaved, making debugging impossible.
On Thu, 2006-03-16 at 12:15 -0500, Daniel Goldenholz wrote:
Ooops. I sent the below with the wrong subject tag. Here it is again:
Daniel Goldenholz wrote:
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
--
Daniel Goldenholz
-----------------------------------------------------
Cell: 617-935-9421 http://people.bu.edu/danielg/
"Mavet v'chaim b'yad halashon"
"Life and death are in the hands of language"
- Proverbs 18:21
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