<div dir="ltr"><div dir="ltr"><div>Hi Assen,</div><div><br></div><div>glad to see you here again!! Hope everything is fine for you and your family.<br></div><div>I have the same error message:<br></div><div><p class="MsoNormal"><b><br></b></p><p class="MsoNormal"><b>[Core-0] Initialization of actors</b></p>
<p class="MsoNormal"><b>GateImageT.icc (l.75): Unknown image file extension. Supported extensions are :
</b></p>
<p class="MsoNormal"><b>.vox, .hdr, .img, .mhd, .mha, .h33, .i33, .dcm</b></p><p class="MsoNormal"><b><br></b></p><p class="MsoNormal">I have no solution and I spent a lot of time to try to understand what happens. Please find hereafter some elements but (again) no solution: <br></p><p class="MsoNormal"><br></p><p class="MsoNormal">- This error only occurs with Gate8.1 (Geant4.10.4) (no error with Gate8.0/G4.10.3.2)</p><p class="MsoNormal">- This error (seems to) occurs when an actor is defined. No error if the command allownooutput is used.</p><p class="MsoNormal">- This error is not systematic and not reproducible. You have to run 10 times a macro to check if you have or not the problem.</p><p class="MsoNormal">- I think but I am not quite sure that this error has absolutely no cause in GateImageT.icc</p><p class="MsoNormal">- I use Gate8.0 now and I am waiting for Gate8.2 (some weeks) to check if this error is still there<br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Sorry, but this message won't help you much. <br></p><p class="MsoNormal">Best regards<br></p><p class="MsoNormal"><br></p><p class="MsoNormal">Luc SIMON</p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p><p class="MsoNormal"><b></b></p></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le lun. 28 janv. 2019 à 20:06, <<a href="mailto:kirova@mskcc.org" target="_blank">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">
<div lang="EN-US">
<div class="gmail-m_8908269083090616704gmail-m_2791061189160588649WordSection1">
<p class="MsoNormal">Hi Alexandre and Maxime,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you very much for responding. Actually disabling vis also give the error.<u></u><u></u></p>
<p class="MsoNormal">Dan will answer your questions in more details, but the Ubuntu version I think was the one required.<u></u><u></u></p>
<p class="MsoNormal">There were some errors in mid installation, but it said successfully installed at the end and both on the other an on this computer we have v8.1.<u></u><u></u></p>
<p class="MsoNormal">Dan will check few more things and will come back to you.<u></u><u></u></p>
<p class="MsoNormal"><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"><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> Sunday, January 27, 2019 12:25 PM<br>
<b>To:</b> Kirov, Assen/Medical Physics <<a href="mailto:kirova@MSKCC.ORG" target="_blank">kirova@MSKCC.ORG</a>>; 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>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Hello Assen,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">To better understand the problem :<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">What is your Linux distribution ?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Did you get any error during the installation ?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">When you have Gate is it version 8.1 or a previous installed version?<u></u><u></u></p>
</div>
<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">Alexandre <u></u><u></u></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<div>
<p class="MsoNormal">Le jeu. 24 janv. 2019 à 23:14, <<a href="mailto:kirova@mskcc.org" target="_blank">kirova@mskcc.org</a>> a écrit :<u></u><u></u></p>
</div>
<blockquote style="border-color:currentcolor currentcolor currentcolor rgb(204,204,204);border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<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 start="1" type="1">
<li class="MsoNormal" 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 start="2" type="1">
<li class="MsoNormal" 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_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph">So we just source gate_enc.sh and that allows us to run Gate.<u></u><u></u></p>
<p class="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph">That is how we run it on another machine without errors but also without visualization.
<u></u><u></u></p>
<p class="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph"> 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_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph">Where is it? I could not find it.<u></u><u></u></p>
<p class="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph"> <u></u><u></u></p>
<p class="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph">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_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph"> <u></u><u></u></p>
<p class="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph">Thanks again,<u></u><u></u></p>
<p class="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph">Assen<u></u><u></u></p>
<p class="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m6525962700361660019msolistparagraph"> <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>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Hello assen,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<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>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<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>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Alexandre CARRE<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
</div>
</div>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<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>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<div>
<div>
<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>
<div>
<div>
<div>
<p class="MsoNormal">Great to hear that ! I'm glad that you like it.<u></u><u></u></p>
</div>
<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>
</div>
<blockquote style="border-style:none none none solid;border-width:medium medium medium 1pt;padding:0in 0in 0in 6pt;margin:5pt 0in 5pt 4.8pt;border-color:currentcolor currentcolor currentcolor rgb(204,204,204)">
<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>
</blockquote>
</div>
</div>
<div>
<p class="MsoNormal"><img id="gmail-m_8908269083090616704gmail-m_2791061189160588649gmail-m_6525962700361660019gmail-m_-5417195366417198456_x005f_x0000_i1025" src="https://mailfoogae.appspot.com/t?sender=aeGVsYS5lcnJhY0BnbWFpbC5jb20%3D&type=zerocontent&guid=d86a98a5-f06b-400e-b65c-241b544ea853" border="0"><span style="font-size:7.5pt;font-family:"Gadugi",sans-serif;color:white">ᐧ</span><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><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><u></u><u></u></p>
</div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
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Please note that this e-mail and any files transmitted from<br>
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Please note that this e-mail and any files transmitted from<br>
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<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" rel="noreferrer" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail-m_8908269083090616704gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>___________________<br><br>SIMON Luc, Physicien Médical, PhD<br>Département d'Ingénierie et de Physique Médicale - IUCT-Oncopole - Toulouse, FRANCE</div><div>INSERM UMR 1037 (CRCT) - Equipe 15 - Toulouse, FRANCE</div></div></div></div></div>