Thanks, this is very helpful On Tue, Dec 14, 2010 at 9:12 PM, Watson, Christopher < christopher.wat...@childrens.harvard.edu> wrote:
> I should have clarified. I use nohup when I ssh into my workstation from > elsewhere. I haven't tried it in which I would have to log out from the > machine running recon-all. > ________________________________________ > From: Scott Burns [sbu...@nmr.mgh.harvard.edu] > Sent: Tuesday, December 14, 2010 9:54 PM > To: Watson, Christopher > Cc: Nathan Dankner; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] running in the background? > > 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<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 9:02 PM, Watson, Christopher < > christopher.wat...@childrens.harvard.edu<mailto: > 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<mailto: > freesurfer-boun...@nmr.mgh.harvard.edu> [ > freesurfer-boun...@nmr.mgh.harvard.edu<mailto: > freesurfer-boun...@nmr.mgh.harvard.edu>] On Behalf Of Scott Burns [ > sbu...@nmr.mgh.harvard.edu<mailto:sbu...@nmr.mgh.harvard.edu>] > Sent: Tuesday, December 14, 2010 8:05 PM > To: Nathan Dankner > Cc: freesurfer@nmr.mgh.harvard.edu<mailto: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><mailto: > 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 > ><mailto: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 > ><mailto: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.
