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Hi Mark,</div>
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Have you had any progress? What GATE version are you using by the way? I did some tests myself, and it seems that voxelized sources are either broken in GATE v9.2 or then the documentation is outdated. The shift that worked previously (at least in 8.2), now
shifts the source in completely different location. In fact, using the original rule, the source seems to be shifted completely out of the scanner FOV in the current version.</div>
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Has the voxelized source example been tested/validated for the current version?</div>
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Regards,
<div>Ville-Veikko Wettenhovi<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Ville-Veikko Wettenhovi <ville-veikko.wettenhovi@uef.fi><br>
<b>Sent:</b> Wednesday, June 29, 2022 10:59<br>
<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23@nhs.net>; gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> Re: Voxelised Source Placement Confusion</font>
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Hi Mark,</div>
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Sorry for the late response. I've not used DICOM images myself with GATE ever so I really can't comment them. One possibility is if you convert the DICOM images into interfile or MetaImage files and then try again. Those have always worked fine in my case.</div>
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Regards,
<div>Ville-Veikko Wettenhovi<br>
</div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23@nhs.net><br>
<b>Sent:</b> Thursday, June 23, 2022 14:55<br>
<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23@nhs.net>; Ville-Veikko Wettenhovi <ville-veikko.wettenhovi@uef.fi>; gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> RE: Voxelised Source Placement Confusion</font>
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<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Hi Ville-Veikko (and everyone else)</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Apologies for the delay in getting this data back, I’ve not had much project time recently. I’ve attached a single slice from each of the PET and CT data,
and as far as I can tell, the data looks correct.</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<div>
<p class="x_x_MsoNormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Mark Baker</span></b></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Principal Clinical Scientist</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Imaging Physics (Ionising)</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span></p>
<p class="x_x_MsoNormal"><i><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">(he, him)</span></i></p>
<p class="x_x_MsoNormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871"> </span></b></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCW Tel: 0151 556 5030
</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCL Tel: 0151 318 8438</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Email:
</span><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">
</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7Ca719963092e24f0f6a7908da550f4442%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637915821314592660%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2h3ThYQDwJ%2FRxjF7%2FgIiRlG9evvjiRfrNJNI3tgsuwQ%3D&reserved=0" originalsrc="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" shash="FBJXaRegtqQ8QHOQCQciTBNyoQaLTfKsZSQMKzWCZaZRFaDeueeN7QVlFDJOsAmTrGFemGzsbiPgkpVMdjXSr0ZG6WEqvWcL0GgPjy649/cHjFiOZ9eF5YZb/9b/pMCiZJoAjD0ZPwQUHE/XCF8fx1u469CZr5ixH4y1tph2kL0="><span style="color:#4472C4">Microsoft
Teams (click here)</span></a></span><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"></span></p>
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<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
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<p class="x_x_MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Gate-users <gate-users-bounces@lists.opengatecollaboration.org>
<b>On Behalf Of </b>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)<br>
<b>Sent:</b> 17 June 2022 09:27<br>
<b>To:</b> Ville-Veikko Wettenhovi <ville-veikko.wettenhovi@uef.fi>; gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> Re: [Gate-users] Voxelised Source Placement Confusion</span></p>
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<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">I think so. I got the information direct from the header files, with both imageJ and Weasis. I’m away from my data at the moment, but when I am back I’ll
attach a sample slice with the header attached, in case I’m being a complete numpty.</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<div>
<p class="x_x_MsoNormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Mark Baker</span></b></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Principal Clinical Scientist (Interim)</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Imaging Physics (Ionising)</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span></p>
<p class="x_x_MsoNormal"><i><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">(he, him)</span></i></p>
<p class="x_x_MsoNormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871"> </span></b></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCW Tel: 0151 556 5030
</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCL Tel: 0151 318 8438</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Email:
</span><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">
</span></p>
<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7Ca719963092e24f0f6a7908da550f4442%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637915821314592660%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=2h3ThYQDwJ%2FRxjF7%2FgIiRlG9evvjiRfrNJNI3tgsuwQ%3D&reserved=0" originalsrc="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" shash="FBJXaRegtqQ8QHOQCQciTBNyoQaLTfKsZSQMKzWCZaZRFaDeueeN7QVlFDJOsAmTrGFemGzsbiPgkpVMdjXSr0ZG6WEqvWcL0GgPjy649/cHjFiOZ9eF5YZb/9b/pMCiZJoAjD0ZPwQUHE/XCF8fx1u469CZr5ixH4y1tph2kL0="><span style="color:#4472C4">Microsoft
Teams (click here)</span></a></span></p>
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<p class="x_x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
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<p class="x_x_MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>
<br>
<b>Sent:</b> 16 June 2022 15:23<br>
<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>>;
<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> Re: Voxelised Source Placement Confusion</span></p>
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<p class="x_x_MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Hi Mark,</span></p>
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<p class="x_x_MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="x_x_MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">The macros seem fine. Are you sure the relevant dimensions and the size of voxels are present and correct in the PET data header file?</span></p>
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<p class="x_x_MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="x_x_MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Regards,
</span></p>
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<p class="x_x_MsoNormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Ville-Veikko Wettenhovi</span></p>
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<p class="x_x_MsoNormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black">From:</span></b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black"> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION
TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>><br>
<b>Sent:</b> Thursday, June 16, 2022 17:08<br>
<b>To:</b> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>;
<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> RE: Voxelised Source Placement Confusion</span> </p>
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<p class="x_x_MsoNormal"> </p>
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<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Hi Ville-Veikko</span></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you for your reply. The relevants macs are attached to this email. I have 8 mains in total (one for each core) which are identical apart from the
first one has visualisation. The current offset was just something I was trying but I can’t seem to get any of the numbers to truly work.</span></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you</span></p>
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<p class="x_x_xmsonormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Mark Baker</span></b></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Principal Clinical Scientist</span></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Imaging Physics (Ionising)</span></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span></p>
<p class="x_x_xmsonormal"><i><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">(he, him)</span></i></p>
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<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCW Tel: 0151 556 5030
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<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCL Tel: 0151 318 8438</span></p>
<p class="x_x_xmsonormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Email:
</span><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">
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<p class="x_x_xmsonormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>
<br>
<b>Sent:</b> 16 June 2022 14:46<br>
<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>>;
<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> Re: Voxelised Source Placement Confusion</span></p>
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<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Hi Mark,</span></p>
</div>
<div>
<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<div>
<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Moving the voxelized source by half of each dimension should indeed work and has worked in the cases where I've used voxelized source. Could you share
the part of the macro where you define and move the voxelized source? </span></p>
</div>
<div>
<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<div>
<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Another way to determine the positioning could be to form the "ground truth" image of the trues, i.e. an image where the coincidences are accumulated
based on their source locations. Then compare that image to the attenuation image from the attenuation map actor (both with the same dimensions).</span></p>
</div>
<div>
<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<div>
<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Regards,
</span></p>
<div>
<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black">Ville-Veikko Wettenhovi</span></p>
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<p class="x_x_xmsonormal" style="background:white"><span style="font-family:"Calibri",sans-serif; color:black"> </span></p>
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<p class="x_x_xmsonormal"><b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black">From:</span></b><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black"> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org">gate-users-bounces@lists.opengatecollaboration.org</a>>
on behalf of BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>><br>
<b>Sent:</b> Thursday, June 16, 2022 16:27<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> [Gate-users] Voxelised Source Placement Confusion</span> </p>
<div>
<p class="x_x_xmsonormal"> </p>
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<div>
<div>
<p class="x_x_xxmsonormal">Hi all</p>
<p class="x_x_xxmsonormal"> </p>
<p class="x_x_xxmsonormal">I raised this query a while (or one similar) but unfortunately, I’ve not managed to get back around to my project for a while. In short, I can’t get good alignment between my CT and PET images. My understanding is that the voxelised
PET source image should be offset by half of its size to account for it being placed in the corner of the world instead of the centre where the CT image is place. My world is 1 1 2 m and my CT data is 780 780 693 mm (512x512x213 matrix). My PET data is 814.568
814.568 639 mm (200x200x213 matrix).</p>
<p class="x_x_xxmsonormal"> </p>
<p class="x_x_xxmsonormal">I think I was a bit confused at first, and was moving the PET source by half of its own size but then I re-read the ReadTheDocs and I think it is suggesting that I actually need to move the PET image by half of the world size (setPosition
-500 -500 -1000 mm) but this results in a large offset. I’ve tried various combinations of half the size of the world, half the size of the PET data etc. and I think I’m just going around in circles now. Logically, I feel like the solution is that I move half
of the world size at first to move the corner of the PET data into the centre of the world, then back by half of the PET image to put the centre of the PET in the centre of the world, but it is still offset. Any suggestions, as I’m tearing my hair out a little
now.</p>
<p class="x_x_xxmsonormal"> </p>
<p class="x_x_xxmsonormal"> </p>
<p class="x_x_xxmsonormal">Additionally, in order to test where the positioning is correct, I’m relying on the generation of secondary electrons within the water phantom in my image and looking at the NbofHits file produced. This works fine when the difference
is obvious between the two, but I wonder if there is a better way to see the isocentre in order to 100% confirm it is correct? The reason I use secondary electrons is that positrons and gammas flood the image making it impossible to see the underlying CT data,
plus I expect the secondary electrons to largely be created in the water and not air.</p>
<p class="x_x_xxmsonormal"> </p>
<p class="x_x_xxmsonormal">Thank you in advance!</p>
<p class="x_x_xxmsonormal"> </p>
<p class="x_x_xxmsonormal"><b><span style="color:#006871">Mark Baker</span></b></p>
<p class="x_x_xxmsonormal"><span style="color:#006871">Principal Clinical Scientist</span></p>
<p class="x_x_xxmsonormal"><span style="color:#006871">Imaging Physics (Ionising)</span></p>
<p class="x_x_xxmsonormal"><span style="color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span></p>
<p class="x_x_xxmsonormal"><i><span style="color:#006871">(he, him)</span></i></p>
<p class="x_x_xxmsonormal"><b><span style="color:#006871"> </span></b></p>
<p class="x_x_xxmsonormal"><span style="color:#006871">CCCW Tel: 0151 556 5030 </span>
</p>
<p class="x_x_xxmsonormal"><span style="color:#006871">CCCL Tel: 0151 318 8438</span></p>
<p class="x_x_xxmsonormal"><span style="color:#006871">Email: </span><span style="color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="color:#006871">
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