<html><body><div style="color:#000; background-color:#fff; font-family:Courier New, courier, monaco, monospace, sans-serif;font-size:14pt"><div>Hi Tibo,</div><div>I have tried it and I'm afraid it does not work in the format that you are suggesting. I believe since it is saved as zubal-HU2mat.txt, it would need to be set up as a range. Essentially trying to "trick" Gate by replacing Hounsfield Units with the index numbers.</div><div> </div><div> </div><div>Best regards,</div><div>Mike </div> <div class="qtdSeparateBR"> </div><div style="display: block;" class="yahoo_quoted"> <div style="font-family: Courier New, courier, monaco, monospace, sans-serif; font-size: 14pt;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 12pt;"> <div dir="ltr"> On Tuesday, July 8, 2014 1:04 PM, "gate-users-request@lists.opengatecollaboration.org" <gate-users-request@lists.opengatecollaboration.org> wrote: </div> <div class="y_msg_container">Send Gate-users mailing list submissions to <a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> To subscribe or unsubscribe via the World Wide Web, visit <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> or, via email, send a message with subject or body 'help' to <a href="mailto:gate-users-request@lists.opengatecollaboration.org" ymailto="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</a> You can reach the person managing the list at <a href="mailto:gate-users-owner@lists.opengatecollaboration.org" ymailto="mailto:gate-users-owner@lists.opengatecollaboration.org">gate-users-owner@lists.opengatecollaboration.org</a> When replying, please edit your Subject line so it is more specific than "Re: Contents of Gate-users digest..." Today's Topics: 1. Re: Reading in tissues / organs from the Zubal phantom (thibaultmauxion) 2. HTML emails (Stathis Kamperis) 3. File Transfer from vGATE (<a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a>) 4. Re: File Transfer from vGATE (Nicolas Karakatsanis) 5. Re: File Transfer from vGATE (<a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a>) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jul 2014 09:28:03 -0400 From: thibaultmauxion <<a href="mailto:thibault.mauxion@gmail.com" ymailto="mailto:thibault.mauxion@gmail.com">thibault.mauxion@gmail.com</a>> To: "<a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: Re: [Gate-users] Reading in tissues / organs from the Zubal phantom Message-ID: <<a href="mailto:5B42104E-098A-4005-83BE-D31C9B98DD97@gmail.com" ymailto="mailto:5B42104E-098A-4005-83BE-D31C9B98DD97@gmail.com">5B42104E-098A-4005-83BE-D31C9B98DD97@gmail.com</a>> Content-Type: text/plain; charset="iso-8859-1" Hi Mike, if vacuum is 0, skin is 1, etc etc I would use : 0 0 vacum 1 1 skin 2 2 brain etc etc regards Tibo On Jul 7, 2014, at 7:25 PM, Mike Tabriz <<a href="mailto:mtabriz@yahoo.com" ymailto="mailto:mtabriz@yahoo.com">mtabriz@yahoo.com</a>> wrote: > Dear Gate users, > > I am trying to simulate energy distribution originating from different source organs. My final output images appear to be very illogical which makes me suspect there is a problem with the way I set up tissues / organs. > > I am using the Zubal phantom which comes with unique index numbers for each individual tissue / organ. So the way I have associated each organ with their respective index numbers is as follows: > #============= > #zubal-HU2mat.txt > #============= > 0 1 Vacuum > 1 2 Skin > 2 3 Brain > 3 4 SpinalCord > 4 5 Skull > 5 6 Spine > 6 7 RibCage > 7 8 Pelvis > . > . > . > My question is whether this is the right way of reading in the organs and if not whether you could make a suggestion as to how I can correctly identify these tissues so that GATE recognizes them. > > Thank you in advance. > _______________________________________________ > Gate-users mailing list > <a href="mailto:Gate-users@lists.opengatecollaboration.org" ymailto="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> > <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/0f2c7016/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/0f2c7016/attachment-0001.html</a>> ------------------------------ Message: 2 Date: Tue, 8 Jul 2014 17:26:56 +0300 From: Stathis Kamperis <<a href="mailto:ekamperi@gmail.com" ymailto="mailto:ekamperi@gmail.com">ekamperi@gmail.com</a>> To: gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: [Gate-users] HTML emails Message-ID: <CACYCkUtnTPEiFgB_Uwtz16JOjiRL=C4OzenOU4gGCrBJsqP+<a href="mailto:WQ@mail.gmail.com" ymailto="mailto:WQ@mail.gmail.com">WQ@mail.gmail.com</a>> Content-Type: text/plain; charset="utf-8" Hi people, sorry for the kind of offtopic message. It would be awesome if the administrators disabled HTML emails in the mailing list. HTML emails look *very ugly* most of the times and when they are archived by various sites the HTML tags show up. Thank you for considering! -Stathis -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/69909c7c/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/69909c7c/attachment-0001.html</a>> ------------------------------ Message: 3 Date: Tue, 8 Jul 2014 15:30:44 +0000 From: <<a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a>> To: <<a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Cc: <a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a> Subject: [Gate-users] File Transfer from vGATE Message-ID: <<a href="mailto:47F349D2693A7144AA7408C96DC8847E121662A0@exbl1.infotech.hamptonu.edu" ymailto="mailto:47F349D2693A7144AA7408C96DC8847E121662A0@exbl1.infotech.hamptonu.edu">47F349D2693A7144AA7408C96DC8847E121662A0@exbl1.infotech.hamptonu.edu</a>> Content-Type: text/plain; charset="us-ascii" To Whom it May Concern, I've been trying to enable file transfer between my virtual machine running vGATE (linux, Ubutnu) and my host machine running Windows. I have created a shared file in the virtual machine, and then I was attempting to mount this file from within linux. However, the mount command requires root/su, which I do not have. Any suggestions? Thanks in advance. Regards, Lars Ewell The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service. -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/4ae9dad6/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/4ae9dad6/attachment-0001.html</a>> ------------------------------ Message: 4 Date: Tue, 8 Jul 2014 17:44:50 +0200 From: Nicolas Karakatsanis <<a href="mailto:nkaraka2@jhmi.edu" ymailto="mailto:nkaraka2@jhmi.edu">nkaraka2@jhmi.edu</a>> To: "<a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a>" <<a href="mailto:LARS.EWELL@hamptonu.edu" ymailto="mailto:LARS.EWELL@hamptonu.edu">LARS.EWELL@hamptonu.edu</a>> Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: Re: [Gate-users] File Transfer from vGATE Message-ID: <CAPjDHBMrbboLjFpk=aiNkSmiX+<a href="mailto:NCcY0b_92ZGGJ0wz1g9emTmA@mail.gmail.com" ymailto="mailto:NCcY0b_92ZGGJ0wz1g9emTmA@mail.gmail.com">NCcY0b_92ZGGJ0wz1g9emTmA@mail.gmail.com</a>> Content-Type: text/plain; charset="utf-8" Dear Lars, try the password "virtual" Regards Nicolas Nicolas A. Karakatsanis, PhD Electrical and Computer Engineer | Postdoctoral Research Associate PET Instrumentation and Neuroimaging Laboratory Division of Nuclear Medicine | Geneva University Hospital Faculty of Medicine | University of Geneva Site Cluse - Roseraie, Rue Gabrielle-Perret-Gentil 4, CH-1211, Geneva 14, Switzerland Tomographic Image Reconstruction and Analysis Lab Division of Nuclear Medicine | Johns Hopkins Hospital School of Medicine | Johns Hopkins University 601 N Caroline St, JHOC Room 3263 Baltimore, MD, USA, 21287 On Tue, Jul 8, 2014 at 5:30 PM, <a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a> < <a href="mailto:LARS.EWELL@hamptonu.edu" ymailto="mailto:LARS.EWELL@hamptonu.edu">LARS.EWELL@hamptonu.edu</a>> wrote: > To Whom it May Concern, > > > > I?ve been trying to enable file transfer between my virtual machine > running vGATE (linux, Ubutnu) and my host machine running Windows. > > > > I have created a shared file in the virtual machine, and then I was > attempting to mount this file from within linux. However, the mount > command requires root/su, which I do not have. > > > > Any suggestions? > > > > Thanks in advance. > > > > Regards, > > > > Lars Ewell > The information contained in this message is intended only for the > recipient, and may otherwise be privileged and confidential. If the reader > of this message is not the intended recipient, or an employee or agent > responsible for delivering this message to the intended recipient, please > be aware that any dissemination or copying of this communication is > strictly prohibited. If you have received this communication in error, > please immediately notify us by replying to the message and deleting it > from your computer. This footnote also confirms that this email has been > scanned for all viruses by the Hampton University Center for Information > Technology Enterprise Systems service. > -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/706c2dba/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140708/706c2dba/attachment-0001.html</a>> ------------------------------ Message: 5 Date: Tue, 8 Jul 2014 17:02:05 +0000 From: <<a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a>> To: <<a href="mailto:nkaraka2@jhmi.edu" ymailto="mailto:nkaraka2@jhmi.edu">nkaraka2@jhmi.edu</a>> Cc: <a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> Subject: Re: [Gate-users] File Transfer from vGATE Message-ID: <<a href="mailto:47F349D2693A7144AA7408C96DC8847E121662F8@exbl1.infotech.hamptonu.edu" ymailto="mailto:47F349D2693A7144AA7408C96DC8847E121662F8@exbl1.infotech.hamptonu.edu">47F349D2693A7144AA7408C96DC8847E121662F8@exbl1.infotech.hamptonu.edu</a>> Content-Type: text/plain; charset="utf-8" Nicolas, Thanks for the suggestion. Unfortunately, it did not work. That password gets me logged in, but it did not give me su/root. Thanks again. Regards, Lars From: Nicolas Karakatsanis [mailto:<a href="mailto:nkaraka2@jhmi.edu" ymailto="mailto:nkaraka2@jhmi.edu">nkaraka2@jhmi.edu</a>] Sent: Tuesday, July 08, 2014 11:45 AM To: EWELL LARS Cc: <a href="mailto:gate-users@lists.opengatecollaboration.org" ymailto="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> Subject: Re: [Gate-users] File Transfer from vGATE Dear Lars, try the password "virtual" Regards Nicolas Nicolas A. Karakatsanis, PhD Electrical and Computer Engineer | Postdoctoral Research Associate PET Instrumentation and Neuroimaging Laboratory Division of Nuclear Medicine | Geneva University Hospital Faculty of Medicine | University of Geneva Site Cluse - Roseraie, Rue Gabrielle-Perret-Gentil 4, CH-1211, Geneva 14, Switzerland Tomographic Image Reconstruction and Analysis Lab Division of Nuclear Medicine | Johns Hopkins Hospital School of Medicine | Johns Hopkins University 601 N Caroline St, JHOC Room 3263 Baltimore, MD, USA, 21287 On Tue, Jul 8, 2014 at 5:30 PM, <a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a><mailto:<a href="mailto:LARS.EWELL@HAMPTONU.EDU" ymailto="mailto:LARS.EWELL@HAMPTONU.EDU">LARS.EWELL@HAMPTONU.EDU</a>> <<a href="mailto:LARS.EWELL@hamptonu.edu" ymailto="mailto:LARS.EWELL@hamptonu.edu">LARS.EWELL@hamptonu.edu</a><mailto:<a href="mailto:LARS.EWELL@hamptonu.edu" ymailto="mailto:LARS.EWELL@hamptonu.edu">LARS.EWELL@hamptonu.edu</a>>> wrote: To Whom it May Concern, I?ve been trying to enable file transfer between my virtual machine running vGATE (linux, Ubutnu) and my host machine running Windows. I have created a shared file in the virtual machine, and then I was attempting to mount this file from within linux. However, the mount command requires root/su, which I do not have. Any suggestions? Thanks in advance. Regards, Lars Ewell The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service. The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service. -------------- next part -------------- An HTML attachment was scrubbed... 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