You can make it work with nohup? In the past I've had trouble and my thinking was that because recon-all starts many child processes, the currently continues after the terminal is closed, but any subsequent process can't start. That's why I've been using screen, but YMMV.
Scott Burns Kuperberg Lab Martinos Center, MGH sburns@nmr.mgh.harvard.edu
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On Tue, Dec 14, 2010 at 9:02 PM, Watson, Christopher < Christopher.Watson@childrens.harvard.edu> wrote:
You can also just run e.g. "nohup recon-all -autorecon-all -s doe_j &" ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Scott Burns [ sburns@nmr.mgh.harvard.edu] Sent: Tuesday, December 14, 2010 8:05 PM To: Nathan Dankner Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] running in the background?
This tip comes from Sam at the helpdesk...
At the command prompt, type 'screen' and press enter. This opens the terminal emulation program, aptly named screen. In this new terminal, start your recon as you would normally, whether that's invoking a script of your making or typing in the standard 'recon -all ....'. Once the job starts, either close the terminal window or press Ctrl-A followed by 'd'. This detaches the screen session but safely keeps the reconstruction pipeline going.
When you get back to your desk, type 'screen -r' at the command prompt to reattach to the screen session you created previously. A new terminal will open and will contain all the output from the recon pipeline. Good luck.
Scott Burns Kuperberg Lab Martinos Center, MGH sburns@nmr.mgh.harvard.edumailto:sburns@nmr.mgh.harvard.edu
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On Tue, Dec 14, 2010 at 5:51 PM, Nathan Dankner < nathan.dankner@vanderbilt.edumailto:nathan.dankner@vanderbilt.edu> wrote: Hi All,
I'm running freesurfer on a public station, so I need to sign out when I'm finished with sessions. Has anyone found a suitable way to run freesurfer in the background? I know that I can run matlab in the background here, so if there is a way to run the pipeline through matlab that may work... Thanks,
Nathan
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