<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear all,<div class=""><br class=""></div><div class="">I saw the problem you mention in 1. quite some times and even with GATE examples.</div><div class="">It happens when you execute visualisation commands early in your main.mac</div><div class="">If you move your /control/execute visu.mac right before the application start command it will run fine.</div><div class="">I don’t know what causes this error. I reported an issue on the GitHub:</div><div class=""><a href="https://github.com/OpenGATE/Gate/issues/203" class="">https://github.com/OpenGATE/Gate/issues/203</a></div><div class=""><br class=""></div><div class="">Best regards,</div><div class=""> Maxime Chauvin<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 24 Jan 2019, at 23:14, <a href="mailto:kirova@mskcc.org" class="">kirova@mskcc.org</a> <<a href="mailto:kirova@MSKCC.ORG" class="">kirova@MSKCC.ORG</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Alexandre,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thank you so much for the prompt response!<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><ol start="1" type="1" style="margin-bottom: 0in; margin-top: 0in;" class=""><li class="MsoListParagraph" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">The .mac script runs well on a different installation. It is just a simple geometry with three materials and a histogram defined source.<o:p class=""></o:p></li></ol><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">So we don’t open any files. The error seems to be that during the initialization<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">GateImageT.icc (l.75): tries to open a file different from<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm :<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">“PreInit> /gate/run/initialize<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">…<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">[Core-0] Initialization of actors<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm”<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><ol start="2" type="1" style="margin-bottom: 0in; margin-top: 0in;" class=""><li class="MsoListParagraph" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;">The source-gatev8.1 alias could not run for us after running the installation script. <o:p class=""></o:p></li></ol><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">So we just source gate_enc.sh and that allows us to run Gate.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">That is how we run it on another machine without errors but also without visualization.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> But maybe source-gatev8.1 does more than gate_env.sh and that may fix the above problem ?<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Where is it? I could not find it.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Daniel is an excellent programmer who will be learning GATE and I advised him to request a collaborative account.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks again,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Assen<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt 0.5in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Alexandre CARRÉ [<a href="mailto:xela.errac@gmail.com" style="color: purple; text-decoration: underline;" class="">mailto:xela.errac@gmail.com</a>]<span class="Apple-converted-space"> </span><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Thursday, January 24, 2019 4:26 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Kirov, Assen/Medical Physics <<a href="mailto:kirova@MSKCC.ORG" style="color: purple; text-decoration: underline;" class="">kirova@MSKCC.ORG</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span>gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" style="color: purple; text-decoration: underline;" class="">gate-users@lists.opengatecollaboration.org</a>>; Lafontaine, Daniel/Medical Physics <<a href="mailto:lafontad@mskcc.org" style="color: purple; text-decoration: underline;" class="">lafontad@mskcc.org</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: Re: [Gate-users] Easy Gate Installation<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hello assen,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">1) For the error, I can't tell you where it came from without seeing the script that was run.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">2) source-gatev8.1 is an alias for sourcing environment variables. So you need to execute 'source-gatev8.1' and then 'Gate'.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Alexandre CARRE<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Le jeu. 24 janv. 2019 à 21:07, <<a href="mailto:kirova@mskcc.org" style="color: purple; text-decoration: underline;" class="">kirova@mskcc.org</a>> a écrit :<o:p class=""></o:p></div></div><blockquote style="border-style: none none none solid; border-left-width: 1pt; border-left-color: rgb(204, 204, 204); padding: 0in 0in 0in 6pt; margin-left: 4.8pt; margin-right: 0in;" class=""><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Alexandre and all,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">We just used the script and it is really of great help – thank you very much!<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I had not installed it for a very long time.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Just a couple of comments: <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">1)When trying it we get this error:<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">PreInit> /gate/run/initialize<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">[Core-0] Initialization of geometry<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">[Core-0] Initialization of physics<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">[Physic-0] WARNING: manual physic lists are being deprecated.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Please, use physic list builder mechanism instead. Related documentation can be found at:<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics" target="_blank" style="color: purple; text-decoration: underline;" class="">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics</a><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">[Core-0] Initialization of actors<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Do you have any clues what may be wrong?<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">2)On the github explanation before running Gate,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I guess you mean to source gate_env.sh<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">you have something else there.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am copying to this message our new colleague Daniel Lafontaine,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">who will join the collaboration soon.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks again,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Assen<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">--<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Assen S. Kirov, Ph.D., DABR<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Associate Attending Physicist<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Department of Medical Physics<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">room S-1119G<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">tel: (212) 639-7126<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Gate-users [mailto:<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank" style="color: purple; text-decoration: underline;" class="">gate-users-bounces@lists.opengatecollaboration.org</a>]<span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Alexandre CARRÉ<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, November 26, 2018 5:50 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:joao.marcos@coimbra.lip.pt" target="_blank" style="color: purple; text-decoration: underline;" class="">joao.marcos@coimbra.lip.pt</a>; gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank" style="color: purple; text-decoration: underline;" class="">gate-users@lists.opengatecollaboration.org</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>[EXTERNAL] Re: [Gate-users] Easy Gate Installation<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div class=""><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Great to hear that ! I'm glad that you like it.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best regards,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Have a nice week.<o:p class=""></o:p></div></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <o:p class=""></o:p></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Le lun. 26 nov. 2018 à 11:17, João Marcos <<a href="mailto:joao.marcos@coimbra.lip.pt" target="_blank" style="color: purple; text-decoration: underline;" class="">joao.marcos@coimbra.lip.pt</a>> a écrit :<o:p class=""></o:p></div></div><blockquote style="border-style: none none none solid; border-left-width: 1pt; padding: 0in 0in 0in 6pt; margin: 5pt 0in 5pt 4.8pt; border-color: currentcolor currentcolor currentcolor rgb(204, 204, 204);" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Alexandre,<br class=""><br class=""><br class="">I will definitely use your script. Thank you very much for make it<br class="">available for all.<br class="">I have just installed the docker version of Gate.<br class=""><br class="">Have a nice week.<br class="">Regards,<br class="">João Marcos<br class=""><br class=""><br class="">On Sun, 25 Nov 2018 11:20:33 +0100, Alexandre CARRÉ<br class=""><<a href="mailto:xela.errac@gmail.com" target="_blank" style="color: purple; text-decoration: underline;" class="">xela.errac@gmail.com</a>><br class="">wrote:<br class="">> Hello GATE community,<br class="">><span class="Apple-converted-space"> </span><br class="">> I have developed a small script that allows you to install GATE in a<br class="">simple<br class="">> way. In addition, new users often have difficulty installing GATE, which<br class="">> can help them.<br class="">> I hope this tool will be useful.<br class="">><span class="Apple-converted-space"> </span><br class="">> It is available at the following address:<br class="">><span class="Apple-converted-space"> </span><a href="https://github.com/Alxaline/Easy-GATE-Installation" target="_blank" style="color: purple; text-decoration: underline;" class="">https://github.com/Alxaline/Easy-GATE-Installation</a><br class="">><span class="Apple-converted-space"> </span><br class="">> Best regards,<o:p class=""></o:p></div></blockquote></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><img border="0" id="gmail-m_-5417195366417198456_x005f_x0000_i1025" src="https://mailfoogae.appspot.com/t?sender=aeGVsYS5lcnJhY0BnbWFpbC5jb20%3D&type=zerocontent&guid=d86a98a5-f06b-400e-b65c-241b544ea853" class=""><span style="font-size: 7.5pt; font-family: Gadugi, sans-serif; color: white;" class="">ᐧ</span><o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10.5pt; color: red;" class=""><br class=""><br class="">*** Only open attachments or links from trusted senders. 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If the reader of<br class="">this message is not the intended recipient, or an employee or agent<br class="">responsible for delivering this message to the intended recipient,<br class="">you are hereby notified that any reading, dissemination, distribution,<br class="">copying, or other use of this communication or any of its attachments<br class="">is strictly prohibited. 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