<div dir="ltr">This is just a warning, and a quick google search indicates that you can probably ignore it, see, e.g., <a href="https://stackoverflow.com/questions/48392440/git-lfs-clone-vs-git-clone">here</a>. Did it solve your issue?<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Apr 21, 2020 at 4:11 PM Somayeh Asadi <<a href="mailto:somayeh.asadi@polimi.it">somayeh.asadi@polimi.it</a>> wrote:<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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Dear Simon </div>
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I really appreciate your help and your time. I tried to do what you said. Following the instructor in this link"</div>
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<a href="https://github.com/OpenGATE/GateContrib/blob/master/readme.md" rel="noopener noreferrer" style="margin:0px;font-size:15px;background-color:rgb(255,255,255)" target="_blank">readme.md</a><br>
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I have started to download the git, in the terminal I took this message is it matter or not?</div>
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Warning"</div>
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<span>git lfs clone' is deprecated and will not be updated </span><span>with new flags from 'git clone'</span><br>
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<span style="margin:0px;font-size:11pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif"><i>Somayeh Asadi (PhD)</i></span></div>
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<span style="margin:0px;font-size:11pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif"><i>Postdoctoral Researcher </i></span></div>
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<i style="color:rgb(117,123,128);font-family:"Times New Roman",Times,serif;font-size:11pt;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit">Department of Mechanical Engineering</i></div>
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<i style="color:rgb(117,123,128);font-family:"Times New Roman",Times,serif;font-size:11pt;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit">Politecnico di Milano, Italy</i></div>
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<span style="color:rgb(117,123,128);font-family:"Times New Roman",Times,serif;font-size:9pt">Via Giuseppe La Masa,1</span><br>
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<div><span style="color:rgb(117,123,128);font-size:9pt;font-family:"Times New Roman",Times,serif">20156 - Milano - Italy</span><br>
<span style="color:rgb(117,123,128);font-size:9pt;font-family:"Times New Roman",Times,serif">phone: +39 0223998572</span><br>
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<span style="margin:0px;font-size:10pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif">somayeh.asadi@polimi.</span><span style="margin:0px;font-size:10pt;color:rgb(117,123,128)">it</span></div>
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<div id="gmail-m_4977492431790217860divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
<b>Sent:</b> Tuesday, April 21, 2020 3:51 PM<br>
<b>To:</b> Somayeh Asadi <<a href="mailto:somayeh.asadi@polimi.it" target="_blank">somayeh.asadi@polimi.it</a>><br>
<b>Cc:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> Re: [Gate-users] Question about the Thermal Actor and ITK</font>
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<div dir="ltr">I provided the link to <a href="https://github.com/OpenGATE/GateContrib/blob/master/readme.md" target="_blank">
readme.md</a>! It's the first page on the github repository and it's always a good idea to read it first (hence the name). So delete your GateContrib, install git-lfs and clone the repository.<br>
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<div dir="ltr">On Tue, Apr 21, 2020 at 3:45 PM Somayeh Asadi <<a href="mailto:somayeh.asadi@polimi.it" target="_blank">somayeh.asadi@polimi.it</a>> wrote:<br>
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Dear Simon </div>
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Thank you very much for your prompt response and a very good idea. </div>
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When I installed the Gate in the GateContrib-master folder there were different examples for dosimetry, imaging...., It was a ready written program and there was no Readme.txt file inside. </div>
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I think you right but I don't know where I find this file from and install in the related path for Thermal.</div>
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Could you please guide me in this regard.</div>
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I would be so grateful if you provide me with your guidance.  </div>
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Best </div>
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GateContrib-master<br>
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<span style="margin:0px;font-size:11pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif"><i>Somayeh Asadi (PhD)</i></span></div>
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<span style="margin:0px;font-size:11pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif"><i>Postdoctoral Researcher </i></span></div>
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<i style="color:rgb(117,123,128);font-family:"Times New Roman",Times,serif;font-size:11pt;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit">Department of Mechanical Engineering</i></div>
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<i style="color:rgb(117,123,128);font-family:"Times New Roman",Times,serif;font-size:11pt;font-variant-ligatures:inherit;font-variant-caps:inherit;font-weight:inherit">Politecnico di Milano, Italy</i></div>
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<span style="color:rgb(117,123,128);font-family:"Times New Roman",Times,serif;font-size:9pt">Via Giuseppe La Masa,1</span><br>
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<div><span style="color:rgb(117,123,128);font-size:9pt;font-family:"Times New Roman",Times,serif">20156 - Milano - Italy</span><br>
<span style="color:rgb(117,123,128);font-size:9pt;font-family:"Times New Roman",Times,serif">phone: +39 0223998572</span><br>
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<span style="margin:0px;font-size:10pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif">somayeh.asadi@polimi.</span><span style="margin:0px;font-size:10pt;color:rgb(117,123,128)">it</span></div>
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<div id="gmail-m_4977492431790217860x_gmail-m_6781419828457145308divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
<b>Sent:</b> Tuesday, April 21, 2020 3:32 PM<br>
<b>To:</b> Somayeh Asadi <<a href="mailto:somayeh.asadi@polimi.it" target="_blank">somayeh.asadi@polimi.it</a>><br>
<b>Cc:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> Re: [Gate-users] Question about the Thermal Actor and ITK</font>
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<div>Hi,</div>
<div>Have you installed git-lfs first (see <a href="https://github.com/OpenGATE/GateContrib/blob/master/readme.md" target="_blank">
readme.md</a>)? Because it looks like it cannot read the file and if <span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline">
<span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline">output/Mobydose-AbsorptionMap.mhd is there, maybe
<span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline">
<span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline">output/Mobydose-AbsorptionMap.raw isn't because you have not installed
 git-lfs.</span></span></span></span></span></span></span></span></div>
<div><span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline">Simon<br>
</span></span></span></span></span></span></span></span></div>
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<div dir="ltr">On Tue, Apr 21, 2020 at 3:25 PM Somayeh Asadi <<a href="mailto:somayeh.asadi@polimi.it" target="_blank">somayeh.asadi@polimi.it</a>> wrote:<br>
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<b><span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline">Dear Gate User</span><br>
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<span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><b>For the ready program related to thermal therapy with the name of thermaltherapy.mac
 in the folder of <span style="background-color:rgb(255,255,255);display:inline">
Imaging/Thermal in the subfolder of GateContrib-master, there is an error that seems to be related to ITK.</span></b></span></span></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><b>the error is:</b></span></span></span></div>
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<span>terminate called after throwing an instance of 'itk::ImageFileReaderException'</span><br>
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<span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"> 
 what():  /home/BuildFiles/ITK/InsightToolkit-5.0.0-Source/Modules/IO/ImageBase/include/itkImageFileReader.hxx:136:</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255);display:inline"> Could not create IO object for reading file output/Mobydose-AbsorptionMap.mhd</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255);display:inline">  Tried to create one of the following:</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255);display:inline">    GDCMImageIO</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255);display:inline">  You probably failed to set a file suffix, or</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255);display:inline">    set the suffix to an unsupported type.</span><br style="background-color:rgb(255,255,255)">
<span style="background-color:rgb(255,255,255);display:inline">Aborted (core dumped)</span><br>
</span></span></span></div>
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<span style="color:rgb(50,49,48);font-size:14.6667px;background-color:rgb(255,255,255);display:inline"><span style="background-color:rgb(255,255,255);display:inline"><br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b>I have downloaded and tried the ITK both the versions of 5.0.1 and 14.2, but after compiling the Gate with them I get the error. </b></div>
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<b>For downloading the ITK, I use this link:</b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b><a href="https://itk.org/download/" target="_blank">https://itk.org/download/</a><br>
</b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b>I have recently check it with the ITK version 4.13.2 but I couldn't download all the related files.</b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b>Has any person had the same problem and experience with the thermal actor?</b></div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<b>Has any person used the ITK version 5 and work with the thermal actor in which he/she didn't get any error?</b></div>
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<b> </b></div>
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<b>Thank you very much for your time and any suggestion. </b></div>
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<span style="margin:0px;font-size:11pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif"><i>Somayeh Asadi (PhD)</i></span></div>
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<span style="color:rgb(117,123,128);font-family:"Times New Roman",Times,serif;font-size:9pt">Via Giuseppe La Masa,1</span><br>
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<span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;color:rgb(117,123,128)"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;color:rgb(117,123,128)"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:11pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-size:10pt;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span><span style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols"></span></p>
<div style="margin:0px;font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols;text-align:start;background-color:rgb(255,255,255)">
<span style="margin:0px;font-size:10pt;color:rgb(117,123,128);font-family:"Times New Roman",Times,serif">somayeh.asadi@polimi.</span><span style="margin:0px;font-size:10pt;color:rgb(117,123,128)">it</span></div>
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