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 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.
