Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
This server cannot run any X11 for security reasons. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Nov 5, 2014 at 8:11 PM, Chris Watson christopher.wat...@childrens.harvard.edu wrote: Have you tried installing 'xauth' on the server and connecting via 'ssh -X'? That should show all graphical output on the local machine. On 11/05/2014 05:03 PM, Bruce Fischl wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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. ___ 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.
Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
Hi Bruce. I believe Tksurfer, even with renderoffscreen, requires X11. I suppose I could export one slice of T1 data and the same Slice of Aseg data and make a script to superimpose both. Not sure which of the cmd line tools to use for this slice export. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Nov 5, 2014 at 8:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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. ___ 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.
Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
Hi PPJ I think mri_extract will do the trick. cheers Bruce On Thu, 6 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: Hi Bruce. I believe Tksurfer, even with renderoffscreen, requires X11. I suppose I could export one slice of T1 data and the same Slice of Aseg data and make a script to superimpose both. Not sure which of the cmd line tools to use for this slice export. - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 On Wed, Nov 5, 2014 at 8:03 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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. ___ 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.
[Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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.
Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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.
Re: [Freesurfer] Generating T1 + Aseg views without Tkmedit and Freeview
Have you tried installing 'xauth' on the server and connecting via 'ssh -X'? That should show all graphical output on the local machine. On 11/05/2014 05:03 PM, Bruce Fischl wrote: Hi PPJ I'm not sure it is. Tksurfer has an offscreen rendering option : setenv renderoffscreen 1 used to work, and maybe still does, but I don't think we ever implemented it in tkmedit, and I'm not sure about freeview. Ruopeng can answer that part On Wed, 5 Nov 2014, Pedro Paulo de Magalhães Oliveira Junior wrote: I'm sorry if this has been answered before, I have browsed the mailing and found nothing answering this. I need to generate three views of the T1 data superimposed with Aseg data automatically for Quality Control without using FreeView or Tkmedit (the server generating this has no X11) Is it possible to do it with the command line tools? Thanks - Pedro Paulo de Magalhães Oliveira Junior Netfilter SpeedComm Telecom-- www.netfilter.com.br -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441 ___ 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. ___ 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.
