i use nohup with recon-all remotely, with: nohup recon-all -s subj -all >& /dev/null &
notice the >& /dev/null, which redirects stdout and stderr to null. i've found this is necessary. note that recon-all output still goes to its log. after launching this way, you can close the terminal, and recon-all will still be running on whereever you launched it. n. On Tue, 2010-12-14 at 21:54 -0500, Scott Burns wrote: > 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 > sbu...@nmr.mgh.harvard.edu > > The information in this e-mail is intended only for the person to whom > it is addressed. If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the > Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error but does not contain patient information, please contact the > sender and properly dispose of the e-mail. > > > > On Tue, Dec 14, 2010 at 9:02 PM, Watson, Christopher > <christopher.wat...@childrens.harvard.edu> wrote: > You can also just run e.g. "nohup recon-all -autorecon-all -s > doe_j &" > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Scott > Burns [sbu...@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 > > sbu...@nmr.mgh.harvard.edu<mailto:sbu...@nmr.mgh.harvard.edu> > > The information in this e-mail is intended only for the person > to whom it is addressed. If you believe this e-mail was sent > to you in error and the e-mail contains patient information, > please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error but does not contain patient information, > please contact the sender and properly dispose of the e-mail. > > > > > On Tue, Dec 14, 2010 at 5:51 PM, Nathan Dankner > <nathan.dank...@vanderbilt.edu<mailto:nathan.dank...@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 > > _______________________________________________ > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
