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<p class="MsoNormal">Hi Alexandre,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you so much for the prompt response!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1">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></o:p></li></ol>
<p class="MsoNormal">So we don’t open any files. The error seems to be that during the initialization<o:p></o:p></p>
<p class="MsoNormal">GateImageT.icc (l.75): tries to open a file different from <o:p>
</o:p></p>
<p class="MsoNormal">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm : <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">“PreInit> /gate/run/initialize<o:p></o:p></p>
<p class="MsoNormal">…<o:p></o:p></p>
<p class="MsoNormal">[Core-0] Initialization of actors<o:p></o:p></p>
<p class="MsoNormal">GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
<o:p></o:p></p>
<p class="MsoNormal">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm”<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<ol style="margin-top:0in" start="2" type="1">
<li class="MsoListParagraph" style="margin-left:0in;mso-list:l0 level1 lfo1">The source-gatev8.1 alias could not run for us after running the installation script.
<o:p></o:p></li></ol>
<p class="MsoListParagraph">So we just source gate_enc.sh and that allows us to run Gate.<o:p></o:p></p>
<p class="MsoListParagraph">That is how we run it on another machine without errors but also without visualization.
<o:p></o:p></p>
<p class="MsoListParagraph"> But maybe source-gatev8.1 does more than gate_env.sh and that may fix the above problem ?<o:p></o:p></p>
<p class="MsoListParagraph">Where is it? I could not find it.<o:p></o:p></p>
<p class="MsoListParagraph"><o:p> </o:p></p>
<p class="MsoListParagraph">Daniel is an excellent programmer who will be learning GATE and I advised him to request a collaborative account.<o:p></o:p></p>
<p class="MsoListParagraph"><o:p> </o:p></p>
<p class="MsoListParagraph">Thanks again,<o:p></o:p></p>
<p class="MsoListParagraph">Assen<o:p></o:p></p>
<p class="MsoListParagraph"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b>From:</b> Alexandre CARRÉ [mailto:xela.errac@gmail.com] <br>
<b>Sent:</b> Thursday, January 24, 2019 4:26 PM<br>
<b>To:</b> Kirov, Assen/Medical Physics <kirova@MSKCC.ORG><br>
<b>Cc:</b> gate-users <gate-users@lists.opengatecollaboration.org>; Lafontaine, Daniel/Medical Physics <lafontad@mskcc.org><br>
<b>Subject:</b> [EXTERNAL] Re: Re: [Gate-users] Easy Gate Installation<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello assen,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">1) For the error, I can't tell you where it came from without seeing the script that was run.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">2) source-gatev8.1 is an alias for sourcing environment variables. So you need to execute 'source-gatev8.1' and then 'Gate'.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Alexandre CARRE<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Le jeu. 24 janv. 2019 à 21:07, <<a href="mailto:kirova@mskcc.org">kirova@mskcc.org</a>> a écrit :<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi Alexandre and all,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">We just used the script and it is really of great help – thank you very much!<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I had not installed it for a very long time.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Just a couple of comments:
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">1)When trying it we get this error:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">PreInit> /gate/run/initialize<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">[Core-0] Initialization of geometry<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">[Core-0] Initialization of physics<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">[Physic-0] WARNING: manual physic lists are being deprecated.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Please, use physic list builder mechanism instead. Related documentation can be found at:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics" target="_blank">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">[Core-0] Initialization of actors<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Do you have any clues what may be wrong?<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">2)On the github explanation before running Gate,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I guess you mean to source gate_env.sh<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">you have something else there.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am copying to this message our new colleague Daniel Lafontaine,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">who will join the collaboration soon.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks again,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Assen<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">--
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Assen S. Kirov, Ph.D., DABR
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Associate Attending Physicist
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Department of Medical Physics<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">room S-1119G
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">tel: (212) 639-7126
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>From:</b> Gate-users [mailto:<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>]
<b>On Behalf Of </b>Alexandre CARRÉ<br>
<b>Sent:</b> Monday, November 26, 2018 5:50 AM<br>
<b>To:</b> <a href="mailto:joao.marcos@coimbra.lip.pt" target="_blank">joao.marcos@coimbra.lip.pt</a>; gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> [EXTERNAL] Re: [Gate-users] Easy Gate Installation<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Great to hear that ! I'm glad that you like it.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Best regards,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Have a nice week.<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Le lun. 26 nov. 2018 à 11:17, João Marcos <<a href="mailto:joao.marcos@coimbra.lip.pt" target="_blank">joao.marcos@coimbra.lip.pt</a>> a écrit :<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Alexandre,<br>
<br>
<br>
I will definitely use your script. Thank you very much for make it<br>
available for all.<br>
I have just installed the docker version of Gate.<br>
<br>
Have a nice week.<br>
Regards,<br>
João Marcos<br>
<br>
<br>
On Sun, 25 Nov 2018 11:20:33 +0100, Alexandre CARRÉ<br>
<<a href="mailto:xela.errac@gmail.com" target="_blank">xela.errac@gmail.com</a>><br>
wrote:<br>
> Hello GATE community,<br>
> <br>
> I have developed a small script that allows you to install GATE in a<br>
simple<br>
> way. In addition, new users often have difficulty installing GATE, which<br>
> can help them.<br>
> I hope this tool will be useful.<br>
> <br>
> It is available at the following address:<br>
> <a href="https://github.com/Alxaline/Easy-GATE-Installation" target="_blank">https://github.com/Alxaline/Easy-GATE-Installation</a><br>
> <br>
> Best regards,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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"><span style="font-size:7.5pt;font-family:"Gadugi",sans-serif;color:white">ᐧ</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-size:10.5pt;color:red"><br>
<br>
*** Only open attachments or links from trusted senders. Report phishing to <a href="mailto:infosec@mskcc.org" target="_blank">
infosec@mskcc.org</a> ***</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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Please note that this e-mail and any files transmitted from<br/>
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