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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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Get <a href="https://aka.ms/ghei36">Outlook for Android</a></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Zhengzhi Liu <zliu36@stanford.edu><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> gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><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" originalsrc="https://github.com/OpenGATE/Gate/tree/develop/benchmarks/benchImageNavigators/pet" shash="Y2MbuudBZu5BeM3k86m3nQIaRTV6GWhHRB/D0EeTLBEh10Zdlaiwa4A1R4kee8sS9t73TtosIixzsOpL3fpCHLidyoof4weECDGWRVNfXE+Uukmcv6vaSCYuPUGof2wDr6jgY2T/lBWngbmUAkgyIRcvn7PwqHlDpnQvzUveXXM=">
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>
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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" class="x_gmail_attr">On Wed, Feb 26, 2020 at 4:58 PM Emilie Gaudin <<a href="mailto:Emilie.Odette.Gaudin@usherbrooke.ca">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="x_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" originalsrc="https://github.com/OpenGATE/Gate/tree/develop/benchmarks/benchImageNavigators/pet" shash="CiTg69RuhJTJr6pj0WjrBbNfEXjPkUkHkCcQU2cFgqqkDatItt5+MAZWOu2Ab+Qp2eBhu6hJPrvyNBr0q7/tLxdV5ib54BlI3cJvjQJH4rDk1F2vcdJYhftEy4mxwqIcgxxwWXj42EFEghC9Dq3yW9aXK8Ym2qaHhNzKjQanFO4=" 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>I am very appreciative of your help. </div>
<div>Sincerely,</div>
<div><br>
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<div>Zhengzhi </div>
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