<div dir="ltr"><div dir="ltr"><div dir="ltr"><div>Hello Assen,</div><div><br></div><div>To better understand the problem :</div><div>What is your Linux distribution ?</div><div>Did you get any error during the installation ?</div><div>When you have Gate is it version 8.1 or a previous installed version?</div><div><br></div><div>Best regards,</div><div><br></div><div>Alexandre <br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le jeu. 24 janv. 2019 à 23:14, <<a href="mailto:kirova@mskcc.org">kirova@mskcc.org</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal">Hi Alexandre,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you so much for the prompt response!<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<ol style="margin-top:0in" start="1" type="1">
<li class="gmail-m_6525962700361660019MsoListParagraph" style="margin-left:0in">The .mac script runs well on a different installation. It is just a simple geometry with three materials and a histogram defined source.<u></u><u></u></li></ol>
<p class="MsoNormal">So we don’t open any files. The error seems to be that during the initialization<u></u><u></u></p>
<p class="MsoNormal">GateImageT.icc (l.75): tries to open a file different from <u></u>
<u></u></p>
<p class="MsoNormal">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm : <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">“PreInit> /gate/run/initialize<u></u><u></u></p>
<p class="MsoNormal">…<u></u><u></u></p>
<p class="MsoNormal">[Core-0] Initialization of actors<u></u><u></u></p>
<p class="MsoNormal">GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
<u></u><u></u></p>
<p class="MsoNormal">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm”<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<ol style="margin-top:0in" start="2" type="1">
<li class="gmail-m_6525962700361660019MsoListParagraph" style="margin-left:0in">The source-gatev8.1 alias could not run for us after running the installation script.
<u></u><u></u></li></ol>
<p class="gmail-m_6525962700361660019MsoListParagraph">So we just source gate_enc.sh and that allows us to run Gate.<u></u><u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph">That is how we run it on another machine without errors but also without visualization.
<u></u><u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph"> But maybe source-gatev8.1 does more than gate_env.sh and that may fix the above problem ?<u></u><u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph">Where is it? I could not find it.<u></u><u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph"><u></u> <u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph">Daniel is an excellent programmer who will be learning GATE and I advised him to request a collaborative account.<u></u><u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph"><u></u> <u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph">Thanks again,<u></u><u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph">Assen<u></u><u></u></p>
<p class="gmail-m_6525962700361660019MsoListParagraph"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b>From:</b> Alexandre CARRÉ [mailto:<a href="mailto:xela.errac@gmail.com" target="_blank">xela.errac@gmail.com</a>] <br>
<b>Sent:</b> Thursday, January 24, 2019 4:26 PM<br>
<b>To:</b> Kirov, Assen/Medical Physics <<a href="mailto:kirova@MSKCC.ORG" target="_blank">kirova@MSKCC.ORG</a>><br>
<b>Cc:</b> gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>>; Lafontaine, Daniel/Medical Physics <<a href="mailto:lafontad@mskcc.org" target="_blank">lafontad@mskcc.org</a>><br>
<b>Subject:</b> [EXTERNAL] Re: Re: [Gate-users] Easy Gate Installation<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Hello assen,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal">1) For the error, I can't tell you where it came from without seeing the script that was run.<u></u><u></u></p>
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<div>
<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<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'.<u></u><u></u></p>
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<div>
<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal">Alexandre CARRE<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
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</div>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
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<div>
<p class="MsoNormal">Le jeu. 24 janv. 2019 à 21:07, <<a href="mailto:kirova@mskcc.org" target="_blank">kirova@mskcc.org</a>> a écrit :<u></u><u></u></p>
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<p class="MsoNormal">Hi Alexandre and all,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">We just used the script and it is really of great help – thank you very much!<u></u><u></u></p>
<p class="MsoNormal">I had not installed it for a very long time.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Just a couple of comments:
<u></u><u></u></p>
<p class="MsoNormal">1)When trying it we get this error:<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">PreInit> /gate/run/initialize<u></u><u></u></p>
<p class="MsoNormal">[Core-0] Initialization of geometry<u></u><u></u></p>
<p class="MsoNormal">[Core-0] Initialization of physics<u></u><u></u></p>
<p class="MsoNormal">[Physic-0] WARNING: manual physic lists are being deprecated.<u></u><u></u></p>
<p class="MsoNormal">Please, use physic list builder mechanism instead. Related documentation can be found at:<u></u><u></u></p>
<p class="MsoNormal"><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><u></u><u></u></p>
<p class="MsoNormal">[Core-0] Initialization of actors<u></u><u></u></p>
<p class="MsoNormal">GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
<u></u><u></u></p>
<p class="MsoNormal">.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Do you have any clues what may be wrong?<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">2)On the github explanation before running Gate,<u></u><u></u></p>
<p class="MsoNormal">I guess you mean to source gate_env.sh<u></u><u></u></p>
<p class="MsoNormal">you have something else there.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">I am copying to this message our new colleague Daniel Lafontaine,<u></u><u></u></p>
<p class="MsoNormal">who will join the collaboration soon.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thanks again,<u></u><u></u></p>
<p class="MsoNormal">Assen<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">--
<u></u><u></u></p>
<p class="MsoNormal">Assen S. Kirov, Ph.D., DABR
<u></u><u></u></p>
<p class="MsoNormal">Associate Attending Physicist
<u></u><u></u></p>
<p class="MsoNormal">Department of Medical Physics<u></u><u></u></p>
<p class="MsoNormal">room S-1119G
<u></u><u></u></p>
<p class="MsoNormal">tel: (212) 639-7126
<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal"><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<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
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<div>
<div>
<p class="MsoNormal">Great to hear that ! I'm glad that you like it.<u></u><u></u></p>
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<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Best regards,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Have a nice week.<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal">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 :<u></u><u></u></p>
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<p class="MsoNormal">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,<u></u><u></u></p>
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