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
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.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.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
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.
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
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.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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
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
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.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
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.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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.
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 [sburns@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 sburns@nmr.mgh.harvard.edumailto:sburns@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.Watson@childrens.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Scott Burns [sburns@nmr.mgh.harvard.edumailto:sburns@nmr.mgh.harvard.edu] Sent: Tuesday, December 14, 2010 8:05 PM To: Nathan Dankner Cc: freesurfer@nmr.mgh.harvard.edumailto: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<mailto:sburns@nmr.mgh.harvard.edumailto:sburns@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.dankner@vanderbilt.edumailto:nathan.dankner@vanderbilt.edu<mailto: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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edumailto: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.
Thanks, this is very helpful
On Tue, Dec 14, 2010 at 9:12 PM, Watson, Christopher < Christopher.Watson@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 [sburns@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 sburns@nmr.mgh.harvard.edumailto:sburns@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.Watson@childrens.harvard.edumailto: 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.edumailto: freesurfer-bounces@nmr.mgh.harvard.edu [ freesurfer-bounces@nmr.mgh.harvard.edumailto: freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Scott Burns [ sburns@nmr.mgh.harvard.edumailto:sburns@nmr.mgh.harvard.edu] Sent: Tuesday, December 14, 2010 8:05 PM To: Nathan Dankner Cc: freesurfer@nmr.mgh.harvard.edumailto: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<mailto: sburns@nmr.mgh.harvard.edumailto:sburns@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.dankner@vanderbilt.edu<mailto:nathan.dankner@vanderbilt.edu
<mailto:nathan.dankner@vanderbilt.edu<mailto:
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
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.
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 sburns@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.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.edu<mailto:sburns@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.dankner@vanderbilt.edu<mailto: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 _______________________________________________ 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@nmr.mgh.harvard.edu
-
Nathan Dankner -
Nick Schmansky -
Scott Burns -
Watson, Christopher