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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank you very much Tim and Helge, that is working now. I won’t tell you how embarrassingly long I spent trying to fix what was effectively
just the wrong order.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I have a few other small bugs to iron out, such as it thinks the extension is missing from the PET data etc. now, but it is at least
triggering Gate to open.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank you<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Mark Baker<o:p></o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Principal Clinical Scientist (Interim)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">Imaging Physics (Ionising)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust<o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">(he, him)<o:p></o:p></span></i></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">CCCW Tel: 0151 556 5030
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#006871">CCCL Tel: 0151 318 8438<o:p></o:p></span></p>
<p class="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">
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#4472C4"><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></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="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"> Helge Pettersen <helge.e.s.pettersen@gmail.com>
<br>
<b>Sent:</b> 17 March 2022 13:37<br>
<b>To:</b> Schneider Tim <Tim.Schneider@curie.fr><br>
<b>Cc:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23@nhs.net>; gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> Re: [Gate-users] [BULK ?] Using parameters for mac files<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I don't know if this is the issue, but I usually have to escape the parameter list when I use bash $variables. See example below:<o:p></o:p></p>
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<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F"><o:p> </o:p></span></p>
<p class="MsoNormal" style="line-height:15.0pt"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">Gate -a
<span class="gmail-pl-pds">"</span><span class="gmail-pl-s">'[phantom,</span><span class="gmail-pl-smi">$phantom</span><span class="gmail-pl-s">] [spotx,</span><span class="gmail-pl-smi">$x</span><span class="gmail-pl-s">]<o:p></o:p></span></span></p>
<p class="MsoNormal" style="line-height:15.0pt"><span class="gmail-pl-s"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">[spoty,</span></span><span class="gmail-pl-smi"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">$y</span></span><span class="gmail-pl-s"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">]
[theta,</span></span><span class="gmail-pl-smi"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">$theta</span></span><span class="gmail-pl-s"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">] [axisx,</span></span><span class="gmail-pl-smi"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">$axis_x</span></span><span class="gmail-pl-s"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">]
[axisy,</span></span><span class="gmail-pl-smi"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">$axis_y</span></span><span class="gmail-pl-s"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">]<o:p></o:p></span></span></p>
<p class="MsoNormal" style="line-height:15.0pt"><span class="gmail-pl-s"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">[rotation,90]'</span></span><span class="gmail-pl-pds"><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">"</span></span><span style="font-size:9.0pt;font-family:Consolas;color:#24292F">
Main_phantom.mac<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#24292F"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Segoe UI",sans-serif;color:#24292F"><o:p> </o:p></span></p>
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Good luck,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Helge Egil Seime Pettersen, PhD<br>
Particle Therapy / Imaging / Proton CT<br>
Department of Oncology and Medical Physics<br>
Haukeland University Hospital<br>
Bergen, Norway<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Thu, Mar 17, 2022 at 2:15 PM Schneider Tim <<a href="mailto:Tim.Schneider@curie.fr">Tim.Schneider@curie.fr</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi Mark,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">When I run macros with parameters, I call them like this:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Gate -a [param,value] mac/macro.mac<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Not sure if your way of doing it is correct as well, but the above always worked for me.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers,<o:p></o:p></p>
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<p class="MsoNormal">Tim<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-bottom:12.0pt">Am 17/03/2022 um 13:11 schrieb BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net" target="_blank">mark.baker23@nhs.net</a>>:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif"></span> <o:p>
</o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi all<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I am trying to run some parameters into my Gate simulation, but it doesn’t seem to be working and Gate sticks at the PreInit stage (although the CPU does ramp up to 100%). I am
running multiple instances of Gate (up to 8 simultanouely), so it is laborious to go into each of the macs every time I want to change a parameter, so I was hoping this would help. My project is hoping to calculate dose distributions from PET scans using CT
scans as the geometry. Previously it was working fine until I tried to add the parameters.
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The relevant parts of my code are below (there is obviously a lot more so I’ve attached the files also in case anyone wants to look deeper, some bits commented out during the debugging)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">In the main1.mac, I have changed the geometry to<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">/gate/world/daughters/name patientCT</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">/gate/world/daughters/insert ImageNestedParametrisedVolume</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">/gate/patientCT/geometry/setImage {CTData}</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">The main1.mac calls sourceF18.mac as its source, which contains the link to the PET data. The relevant part is<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">/gate/source/addSource patientPET voxel</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">/gate/source/patientPET/imageReader/readFile {PETData}</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I also change the number of primaries on the fly, so I set that to the following in main1.mac<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">/gate/application/setTotalNumberOfPrimaries {NoOfPrimaries}</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I’ve a got a script to run the multiple instances of Gate, alongside a lot of housework for moving files and merging them etc. I have checked the input to the parameters, and as
far as I can tell, they are fine.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I call Gate using the following<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">Gate mac/main1.mac [CTData,$CTDataFile] [NoOfPrimaries,$NumberPrimaries] [PETData,$PTDataFile] &</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New""> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">where the user could select the following information, for example,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">$CTDataFile is data/dcm/CT/br38f.mha
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">$PTDataFile is data/dcm/PT/brainmaskPET.mha</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New"">$NumberPrimaries is 1000</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">If I go back to my main1.mac etc. and manually change the parameters to the data above and change my run.sh script to
<span style="font-family:"Courier New"">Gate mac/main1.mac &</span> it works perfectly, so presumably I am doing something wrong with passing the parameters through.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I’d appreciate it if anyone had any thoughts on this?
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:#006871">Mark Baker</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">Principal Clinical Scientist (Interim)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">Imaging Physics (Ionising)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span style="color:#006871">(he, him)</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="color:#006871"> </span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">CCCW Tel: 0151 556 5030
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">CCCL Tel: 0151 318 8438</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871">Email:
</span><span style="color:#4472C4"><a href="mailto:mark.baker23@nhs.net" target="_blank"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span style="color:#006871">
</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#4472C4"><a href="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" target="_blank"><span style="color:#4472C4">Microsoft Teams (click here)</span></a></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span style="color:#006871">Honorary Lecturer, Dept. of Physics</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span style="color:#006871">University of Liverpool</span></i><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#006871"> </span><o:p></o:p></p>
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