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<p class="MsoNormal"><span style="color:#1F497D">Hi Mark,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">I am not sure if you want to simulate absorbed dose (because you mention you use a F18 PET image as source input) or whether you would like to simulate a F18 PET image of a patient/phantom. Anyways, that doesn’t
matter. In can only share my experience with dose simulations using voxelized input:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">In my dosimetry simulations, I have usually used the mhd format and ensured beforehand that the CT and source are registered by loading them in an imaging viewing software (I am a big fan of ‘amide’, but 3DSlicer
is also popular), but also by comparing the mhd header files. With that, I don’t have to bother about any translation or offset between CT and source image later.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Next, the voxelized source has to be shifted by half of it’s size in x,y,z.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Here an example from one of my simulations: my image matrix is 256x256x1000. My voxel size is 0.145x0.145x0.145 mm^3. That makes a total image size of 37.12 37.12 145 mm^3. That means the command line for my
source is:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"># Source has always to be shifted to -1/2 of its total length in x,y,z<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">/gate/source/YOURSOURCE/setPosition -18.56 -18.56 -72.5 mm<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<span style="font-family:"Calibri",sans-serif;color:#1F497D">Lastly, here is a snippet from the GATE manual:<br>
</span><span style="font-size:19.0pt;font-family:"Georgia",serif;color:#3E4349;font-weight:normal"><a href="https://opengate.readthedocs.io/en/latest/voxelized_source_and_phantom.html#id20"><span style="color:#004B6B">7.3.2. Position</span></a><o:p></o:p></span></h3>
<p style="line-height:16.8pt;background:white;hyphens: auto;font-variant-ligatures: normal;font-variant-caps: normal;orphans: 2;widows: 2;-webkit-text-stroke-width: 0px;text-decoration-thickness: initial;text-decoration-style: initial;text-decoration-color: initial;word-spacing:0px">
<span style="font-size:13.0pt;font-family:"Georgia",serif;color:#3E4349">By default the activity image is placed in the “first quarter”, i.e. the image is placed starting at 0 0 0 mm (x, y, z). This is different from the placing of volumes in Geant4 and GATE
where volumes are centered on their geometrical center. In order to align the activity image with a phantom volume, a translation is needed which in the simplest case (where the activity image has the same size and position as the volume) is a translation
of half the size of the volume in the negative direction.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Hope that helps you for the source positioning. Unfortunately, I have not enough experience with the GATE visualization to help you there.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Julia<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="mso-fareast-language:EN-CA">From:</span></b><span lang="EN-US" style="mso-fareast-language:EN-CA"> 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> April 7, 2022 7:18 AM<br>
<b>To:</b> gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> [Gate-users] Position Voxel PET Source on top of DICOM CT<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p><span style="color:black">This email came from an </span><b><span style="color:red">EXTERNAL SENDER.</span>
</b><span style="color:black">If you think this message is suspicious, please do not open any attached files or links, and forward it as an attachment to
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<p class="MsoNormal"><span lang="EN-GB" style="font-size:12.0pt;font-family:"Times New Roman",serif;mso-fareast-language:EN-CA"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span lang="EN-GB">Hi all<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I’m really struggling with my current macro, in which I am aiming to position a F18 PET image as a voxelised source on top of a CT image. I have two sets of data at the moment, a patient image and a NEMA phantom image.
With the NEMA phantom image, when observing the geometry using OGL, my trajectories appear to come from what I think is too far a negative z-direction (assuming the axis from the visualisation is pointing in a positive direction) i.e. almost the edge of the
world and definitely outside of the CT phantom image. With the patient image, the source distribution does overlay the CT information, but it is flipped such that the head is in the pelvis region and vice versa.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">My best guess is that the orientation or offset of either setup is incorrect. The CT dataset originally started as set as 0 translation in all directions, with no rotation axis or angle, and the source position set as
negative half of the PET image size (e.g. -400 -400 -170 mm) – this is what I understand as to how the images should be arranged. However, I have tried all sorts of combinations of rotations, translations and source positions (including some wild numbers just
to see if they make any impact) but they don’t change what I’m seeing. I get the same effect whether the images are DCM or MHD (albeit converted from DCM to MHD using ImageJ).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I’ve attached all three relevant macs to this email. To actually run Gate, I use a script to pass variables into 8 instances of Gate in order to utilise the 8 cores on the machine. Only main1.mac contains instructions
to open the visualisation (as main2-8 are exact copies, there is no need to duplicate resource demand).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">I’m sure I am just missing something really obvious, but I’d appreciate if anyone could help me out.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Additionally, whether this is related or not, but when I first open the terminal and run my macro, I can almost guarantee that the process will hang on deleting the visualisation manager the first time it is run. I can
CTRL-C and then re-run the exact same script, and it proceeds fine. It only started doing this pretty recently, and I’m not sure what I have done differently to cause this. It might possibly be linked, or might be a total red herring.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Thank you<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">Mark Baker<o:p></o:p></span></b></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">Principal Clinical Scientist<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">Imaging Physics (Ionising)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">The Clatterbridge Cancer Centre NHS Foundation Trust<o:p></o:p></span></p>
<p class="MsoNormal"><i><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">(he, him)<o:p></o:p></span></i></p>
<p class="MsoNormal"><b><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">CCCW Tel: 0151 556 5030
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">CCCL Tel: 0151 318 8438<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">Email:
</span><span lang="EN-GB" style="color:#4472C4;mso-fareast-language:EN-GB"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#4472C4;mso-fareast-language:EN-GB"><a href="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net"><span style="color:#4472C4">Microsoft Teams (click here)</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-GB"> <span style="color:#006871"><o:p></o:p></span></span></p>
<p class="MsoNormal"><i><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">Honorary Lecturer, Dept. of Physics<o:p></o:p></span></i></p>
<p class="MsoNormal"><i><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB">University of Liverpool<o:p></o:p></span></i></p>
<p class="MsoNormal"><span lang="EN-GB" style="color:#006871;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-GB"><img border="0" width="624" height="163" style="width:6.5in;height:1.7013in" id="Picture_x0020_3" src="cid:image001.jpg@01D84A5F.936D44F0" alt="CCC email footer April 2021"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
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