<div dir="ltr">Thanks, Emilie for pointing out the exact problem. There is a problem with the header file brain_phantom.h33. I don't know whether I have corrupted the file or it came corrupted. I bypassed it by using amide to read brain_phantom.i33 and setting its dimension, then export the data as interfile. Now everything works fine. <div><br></div><div>Thanks a lot for the help. </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 2, 2020 at 12:10 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu">zliu36@stanford.edu</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"><div dir="ltr">Thanks, Emilie for your quick reply. <div>I am using amide as the viewer. I also doubted the correctness of header file brain_phantom.h33 (especially the dimensions). But all these files cames with the installation of GATE v8. Meanwhile, brain_phantom.h33 is a binary file, I don't know how to convert it into ASCII file to read its content inside. Could you please give me any further help? Have you got the example work with its own data? </div><div><br></div><div>Thanks a lot</div><div>Zhengzhi <br><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 2, 2020 at 11:44 AM Emilie Gaudin <<a href="mailto:Emilie.Odette.Gaudin@usherbrooke.ca" target="_blank">Emilie.Odette.Gaudin@usherbrooke.ca</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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Hi,<br>
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Seems you have a problem in the header of your image not in your GATE code. <br>
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Either the path or the format is wrong <br>
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Try to debug this first with an image reader application such as imageJ or amide.
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Emilie <br>
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<span id="gmail-m_4072375441654538808gmail-m_3396383300776456296OutlookSignature">
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Get <a href="https://aka.ms/ghei36" target="_blank">Outlook for Android</a></div>
</span><br>
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<hr style="display:inline-block;width:98%">
<div id="gmail-m_4072375441654538808gmail-m_3396383300776456296divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>><br>
<b>Sent:</b> Monday, March 2, 2020 2:40:12 PM<br>
<b>To:</b> Emilie Gaudin <Emilie.Odette.Gaudin@USherbrooke.ca><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: Voxelized source and phantom in benchImageNavigators</font>
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<div dir="ltr">Dear Emilie,
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<div>Thank you very much for your help. You are right that <b>interfileReader</b> is deprecated now, and using
<b>imageReader</b> would partially solve the problem in the <a href="https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGate%2Ftree%2Fdevelop%2Fbenchmarks%2FbenchImageNavigators%2Fpet&data=02%7C01%7CEmilie.Odette.Gaudin%40usherbrooke.ca%7C68d48b2e48cc41b1c4cc08d7bee19fe7%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637187748578955552&sdata=ujIvdsBZkOnPYFUlI7uec1hnn8aW1X0nw2czwNjnipM%3D&reserved=0" target="_blank">
example</a> (Gate/benchmarks/benchImagenvators/pet). However, even after switching to imageReader, I still couldn't get the example work. It failed opening brain_phantom.i33 for reading. Could you please have a look at the attached voxlizedSource.mac and error
message to locate my mistake? </div>
<div><br>
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<div>However, when I used brain_phantom.hmd in the voxlizedSource.mac, then everything worked fine. I attached a 3D rending of the brain_phantom.i33, it does not look like a brain phantom source, does it? </div>
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<div>Greatly appreciate your help.</div>
<div>Sincerely,</div>
<div>Zhengzhi </div>
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<div dir="ltr">On Wed, Feb 26, 2020 at 4:58 PM Emilie Gaudin <<a href="mailto:Emilie.Odette.Gaudin@usherbrooke.ca" target="_blank">Emilie.Odette.Gaudin@usherbrooke.ca</a>> wrote:<br>
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Dear Zhengzhi ,</div>
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You are right saying the documentation about voxelized phantom is deprecated, especially for image insertion.<br>
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Here is some working code for a typical phantom. Be careful of the path in your code and in your image header and everything should be fine.</div>
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However, I cannot answer for the visu.<br>
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Cheers,</div>
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Emilie</div>
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<span>/gate/source/addSource voxel voxel<br>
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<div>/gate/source/voxel/reader/insert image<br>
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<div>/gate/source/voxel/imageReader/translator/insert range<br>
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<div>/gate/source/voxel/imageReader/rangeTranslator/readTable {path-to-activity-dat-from-this-mac}<br>
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<div>/gate/source/voxel/imageReader/rangeTranslator/describe 1<br>
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<div># The default position of the voxellized source is in the 1^{st}<br>
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<div># quarter. So the voxellized source has to be shifted over half its<br>
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<div># dimension (dimension = dimImgXYZ * dimVoxXYZ)in the negative direction on each axis<br>
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<div>/gate/source/voxel/setPosition -90 -90 -90 mm<br>
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<div>/gate/source/voxel/imageReader/readFile {path-to-header-from-this-mac}<br>
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<div>/gate/source/voxel/gps/particle e+<br>
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<div>/gate/source/voxel/gps/energytype Fluor18<br>
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<div>/gate/source/voxel/setForcedUnstableFlag true<br>
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<div>/gate/source/voxel/setForcedHalfLife 6586.2 s<br>
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<div>/gate/source/voxel/gps/angtype iso<br>
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<div>/gate/source/voxel/dump 1<br>
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<span>/gate/source/list</span></div>
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<div id="gmail-m_4072375441654538808gmail-m_3396383300776456296x_gmail-m_8009988095786798507appendonsend"></div>
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<div id="gmail-m_4072375441654538808gmail-m_3396383300776456296x_gmail-m_8009988095786798507divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
de la part de Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>><br>
<b>Envoyé :</b> 26 février 2020 18:59<br>
<b>À :</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>>;
<a href="mailto:lomahu@gmail.com" target="_blank">lomahu@gmail.com</a> <<a href="mailto:lomahu@gmail.com" target="_blank">lomahu@gmail.com</a>>; 강한규 <<a href="mailto:lovehangulp@naver.com" target="_blank">lovehangulp@naver.com</a>><br>
<b>Objet :</b> [Gate-users] Voxelized source and phantom in benchImageNavigators</font>
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<div dir="ltr">Dear Han Gyu, Howard, and Gate users,
<div><br>
<div>(I noticed from the previous emails that you two are using voxelized source and phantom, thus I send this email to you. )</div>
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<div>I tried to import voxelized source and phantom in PET GATE simulation by following the <a href="https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGate%2Ftree%2Fdevelop%2Fbenchmarks%2FbenchImageNavigators%2Fpet&data=02%7C01%7CEmilie.Odette.Gaudin%40usherbrooke.ca%7C68d48b2e48cc41b1c4cc08d7bee19fe7%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637187748578965547&sdata=zKu09jeaeGNaE230HanKyYi1nh92EMc3QVUnY1uUSZY%3D&reserved=0" target="_blank">benchImageNavigators</a>
example provided in GATE 8.2 package. However, I can't even get example code work. I have two problems with the example code: <br>
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<ol>
<li>Visualization issue: the qt viewer would automatically close and leaves me no time to visually check the voxelized source or voxelized phantom;</li><li>Running issue: the example can't run and keep throwing the warning message as shown in the attached screenshot, and no actual output is generated but an empty root file. </li></ol>
<div>I believe importing PET/CT image has become very mature in GATE simulation. Could anyone give any help with running this example code? </div>
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<div><br>
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<div>I am very appreciative of your help. </div>
<div>Sincerely,</div>
<div><br>
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<div>Zhengzhi </div>
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