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Hi Mark,
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<div class="">I don’t think I can be of any more help. The only ways I could think of are trying to bypass your problem. You could for example create a string that contains your Gate command as follows:</div>
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<div class="">#!/bin/bash</div>
<div class="">NumberPrimaries=0</div>
<div class="">read -p "Enter your number of primaries: “ NumberPrimaries</div>
<div class="">string="Gate –a [Prims,$NumberPrimaries][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha] mac/main1.mac &”</div>
<div class="">echo “$string"</div>
<div class="">#eval $string</div>
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</div>
<div class="">In case the output string is correct, uncomment the “eval $string” command. </div>
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<div class="">Best regards,</div>
<div class="">David</div>
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<div><br class="">
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<div class="">On 21 Mar2022, at 11:58, BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net" class="">mark.baker23@nhs.net</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi David<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you for your reply. I can’t recall exactly what combinations I have tried, so I have just gone through the options below one by one to confirm. I’m currently
in trouble shoot mode, so my code looks more like this now (concentrating more on just getting one variable (Prims) working for now).<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">Gate –a [Prims,${NumberPrimaries}][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha] mac/main1.mac &<span class="Apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: "Calibri Light", sans-serif; color: rgb(31, 73, 125);" class="">-no
spaces as per the bottom solution on github and your example<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">Gate “–a[Prims,${NumberPrimaries}][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha]” mac/main1.mac &<span class="Apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: "Calibri Light", sans-serif; color: rgb(31, 73, 125);" class="">-as
per the other solution on github, with and without a space between –a and [Prims…]</span><span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">Gate –a “’[Prims,${NumberPrimaries}][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha]’” mac/main1.mac & - as per Helge’s email below. I wasn’t sure
if they were ‘ or ` so I tried both. With ` it ignored Prims and errored on CTData (both with the manually typed path and $CTDataFile)<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: "Calibri Light", sans-serif; color: rgb(31, 73, 125);" class="">The next examples were effectively me just guessing potential solutions:<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">Gate –a ‘[Prims,${NumberPrimaries}][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha]’ mac/main1.mac &<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">Gate –a `[Prims,${NumberPrimaries}][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha]` mac/main1.mac &<span class="Apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: "Calibri Light", sans-serif; color: rgb(31, 73, 125);" class="">-
similar error on CTData</span><span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">Gate –a [Prims,”${NumberPrimaries}”][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha] mac/main1.mac &<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: "Calibri Light", sans-serif; color: rgb(31, 73, 125);" class="">This code works though<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">Gate –a [Prims,1000][CTData,data/dcm/CT/br38f.mha][PETData,data/dcm/PT/nomaskPET.mha] mac/main1.mac &</span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">The code for asking for the primaries is below, and seems to work fine according to the echo (just to confirm, it runs early in the script also, before Gate is
ran)..<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">NumberPrimaries=0<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">read –p “How many primaries per core? “ NumberPrimaries<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">echo “You have chosen $NumberPrimaries primaries to run on each core”<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: "Calibri Light", sans-serif; color: rgb(31, 73, 125);" class="">and the code calling {Prims} in main1.mac is<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class="">/gate/application/setTotalNumberOfPrimaries {Prims}<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: "Courier New"; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<span style="font-size: 11pt; font-family: "Calibri Light", sans-serif; color: rgb(31, 73, 125);" class="">Thank you very much<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Mark Baker<o:p class=""></o:p></span></b></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Principal Clinical Scientist (Interim)<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Imaging Physics (Ionising)<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">The Clatterbridge Cancer Centre NHS Foundation Trust<o:p class=""></o:p></span></div>
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<i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">(he, him)<o:p class=""></o:p></span></i></div>
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<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class=""><o:p class=""> </o:p></span></b></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">CCCW Tel: 0151 556 5030<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">CCCL Tel: 0151 318 8438<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Email:<span class="Apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(68, 114, 196);" class=""><a href="mailto:mark.baker23@nhs.net" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">mark.baker23@nhs.net</span></a></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(68, 114, 196);" class=""><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__teams.microsoft.com_l_chat_0_0-3Fusers-3Dmark.baker23-40nhs.net&d=DwMGaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=lfXR69GFfS7NT-Wp5HZqbtBDrbYoilDdmNEG7fKW7aM&m=jFEsVlJw7a8Jr64ONw_NUE9Tky3pwCzd0IBHRkPnmnc&s=qKBUsL42Jr14sw_jYVs7EDRVEqCebIxSdvDWHP-19RQ&e=" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">Microsoft
Teams (click here)</span></a></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><o:p class=""> </o:p></span></div>
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<b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>David Leibold
<<a href="mailto:D.Leibold@tudelft.nl" class="">D.Leibold@tudelft.nl</a>><span class="Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>21 March 2022 10:22<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net" class="">mark.baker23@nhs.net</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" class="">gate-users@lists.opengatecollaboration.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Gate-users] Using parameters for mac files<o:p class=""></o:p></span></div>
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Hi Mark,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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do you mind posting the variants you tried and that didn’t work?<o:p class=""></o:p></div>
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In your example, I would use the following command in my bash script:<o:p class=""></o:p></div>
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<span style="font-family: Consolas;" class="">Gate -a [CTData,${CTDataFile}][NoOfPrimaries,${NumberPrimaries}][PETData,${PTDataFile}] mac/main1.mac &</span><o:p class=""></o:p></div>
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That always works for me (the only difference is that my bash script starts the main.mac from the same directory, but you mentioned that this works when putting in the values manually, so it’s unlikely to cause the issue I guess). As mentioned in that second
link of yours, this doesn't use any spaces within or between the square brackets.<o:p class=""></o:p></div>
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Let us know whether that helps.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Best regards,<o:p class=""></o:p></div>
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David<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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On 21 Mar2022, at 11:03, BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net" style="color: purple; text-decoration: underline;" class="">mark.baker23@nhs.net</a>> wrote:<o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi all</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Well it turns out that I was a little premature in my celebration. Whilst my script works perfectly if I manually put in the values I want but if the values is
in the form of a $variable then I alias errors. I’ve tried various combinations of “” `` and ‘’ to no avail unfortunately. In addition to this email chain, I also found this github post<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_OpenGATE_Gate_issues_69&d=DwMGaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=lfXR69GFfS7NT-Wp5HZqbtBDrbYoilDdmNEG7fKW7aM&m=JXkYrD_N3zHhNT53wVMyxPpl-Vu7G4qlA8lefFcef9A&s=0q-TW5D7-_virjlOyAZt3gCt4gst7HGeKexff8I6Nlw&e=" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">https://github.com/OpenGATE/Gate/issues/69</span></a><span class="apple-converted-space"> </span>and
a similar mailbase post (<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.opengatecollaboration.org_pipermail_gate-2Dusers_2015-2DMarch_008227.html&d=DwMGaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=lfXR69GFfS7NT-Wp5HZqbtBDrbYoilDdmNEG7fKW7aM&m=JXkYrD_N3zHhNT53wVMyxPpl-Vu7G4qlA8lefFcef9A&s=mJQ0a9zm2AD3Aj5uNENEbWGAZ6_aYNgX_riUAeuJcpg&e=" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">http://lists.opengatecollaboration.org/pipermail/gate-users/2015-March/008227.html</span></a>)
about the issue but the solution didn’t work me either. I’m on VGate9.0 if that makes a difference, as both of those posts are possibly a version or two earlier based on their date.</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">I know little about bash scripts, but I believe the variable is being stored correctly as it works with echo and displays what I expect.</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Does anyone have any suggestions or alternatives that I can explore?</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you very much</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Mark Baker</span></b><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Principal Clinical Scientist (Interim)</span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Imaging Physics (Ionising)</span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">The Clatterbridge Cancer Centre NHS Foundation Trust</span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">(he, him)</span></i><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class=""> </span></b><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">CCCW Tel: 0151 556 5030</span><o:p class=""></o:p></div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">CCCL Tel: 0151 318 8438</span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Email:<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(68, 114, 196);" class=""><a href="mailto:mark.baker23@nhs.net" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">mark.baker23@nhs.net</span></a></span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(68, 114, 196);" class=""><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__teams.microsoft.com_l_chat_0_0-3Fusers-3Dmark.baker23-40nhs.net&d=DwMGaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=lfXR69GFfS7NT-Wp5HZqbtBDrbYoilDdmNEG7fKW7aM&m=JXkYrD_N3zHhNT53wVMyxPpl-Vu7G4qlA8lefFcef9A&s=jcYxmFfI9EQDmwEWN9bPm0xKwKHlfnGIwAtpSUG-XQE&e=" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">Microsoft
Teams (click here)</span></a></span><o:p class=""></o:p></div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Gate-users
<<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">gate-users-bounces@lists.opengatecollaboration.org</span></a>><span class="apple-converted-space"> </span><b class="">On
Behalf Of<span class="apple-converted-space"> </span></b>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)<br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>17 March 2022 14:03<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>Helge Pettersen <<a href="mailto:helge.e.s.pettersen@gmail.com" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">helge.e.s.pettersen@gmail.com</span></a>>;
Schneider Tim <<a href="mailto:Tim.Schneider@curie.fr" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">Tim.Schneider@curie.fr</span></a>><br class="">
<b class="">Cc:</b><span class="apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">gate-users@lists.opengatecollaboration.org</span></a><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [Gate-users] [BULK ?] Using parameters for mac files</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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.</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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.</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thank you</span><o:p class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Mark Baker</span></b><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Principal Clinical Scientist (Interim)</span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Imaging Physics (Ionising)</span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">The Clatterbridge Cancer Centre NHS Foundation Trust</span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<i class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">(he, him)</span></i><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<b class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class=""> </span></b><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">CCCW Tel: 0151 556 5030</span><o:p class=""></o:p></div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">CCCL Tel: 0151 318 8438</span><o:p class=""></o:p></div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(0, 104, 113);" class="">Email:<span class="apple-converted-space"> </span></span><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(68, 114, 196);" class=""><a href="mailto:mark.baker23@nhs.net" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">mark.baker23@nhs.net</span></a></span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(68, 114, 196);" class=""><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__teams.microsoft.com_l_chat_0_0-3Fusers-3Dmark.baker23-40nhs.net&d=DwMGaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=lfXR69GFfS7NT-Wp5HZqbtBDrbYoilDdmNEG7fKW7aM&m=JXkYrD_N3zHhNT53wVMyxPpl-Vu7G4qlA8lefFcef9A&s=jcYxmFfI9EQDmwEWN9bPm0xKwKHlfnGIwAtpSUG-XQE&e=" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">Microsoft
Teams (click here)</span></a></span><o:p class=""></o:p></div>
</div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: "Times New Roman", serif;" class="">
<b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">Helge
Pettersen <<a href="mailto:helge.e.s.pettersen@gmail.com" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">helge.e.s.pettersen@gmail.com</span></a>><span class="apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>17 March 2022 13:37<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>Schneider Tim <<a href="mailto:Tim.Schneider@curie.fr" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">Tim.Schneider@curie.fr</span></a>><br class="">
<b class="">Cc:</b><span class="apple-converted-space"> </span>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">mark.baker23@nhs.net</span></a>>;<span class="apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">gate-users@lists.opengatecollaboration.org</span></a><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [Gate-users] [BULK ?] Using parameters for mac files</span><o:p class=""></o:p></div>
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Hi,<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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I don't know if this is the issue, but I usually have to escape the parameter list when I use bash $variables. See example below:<o:p class=""></o:p></div>
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<span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class=""> </span><o:p class=""></o:p></div>
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<span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">Gate -a<span class="apple-converted-space"> </span><span class="gmail-pl-pds">"</span><span class="gmail-pl-s">'[phantom,</span><span class="gmail-pl-smi">$phantom</span><span class="gmail-pl-s">]
[spotx,</span><span class="gmail-pl-smi">$x</span><span class="gmail-pl-s">]</span></span><o:p class=""></o:p></div>
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<span class="gmail-pl-s"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">[spoty,</span></span><span class="gmail-pl-smi"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">$y</span></span><span class="gmail-pl-s"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">]
[theta,</span></span><span class="gmail-pl-smi"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">$theta</span></span><span class="gmail-pl-s"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">]
[axisx,</span></span><span class="gmail-pl-smi"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">$axis_x</span></span><span class="gmail-pl-s"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">]
[axisy,</span></span><span class="gmail-pl-smi"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">$axis_y</span></span><span class="gmail-pl-s"><span style="font-size: 9pt; font-family: Consolas; color: rgb(36, 41, 47);" class="">]</span></span><o:p class=""></o:p></div>
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Good luck,<o:p class=""></o:p></div>
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Helge Egil Seime Pettersen, PhD<br class="">
Particle Therapy / Imaging / Proton CT<br class="">
Department of Oncology and Medical Physics<br class="">
Haukeland University Hospital<br class="">
Bergen, Norway<o:p class=""></o:p></div>
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On Thu, Mar 17, 2022 at 2:15 PM Schneider Tim <<a href="mailto:Tim.Schneider@curie.fr" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">Tim.Schneider@curie.fr</span></a>> wrote:<o:p class=""></o:p></div>
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Hi Mark,<o:p class=""></o:p></div>
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When I run macros with parameters, I call them like this:<o:p class=""></o:p></div>
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Gate -a [param,value] mac/macro.mac<o:p class=""></o:p></div>
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Not sure if your way of doing it is correct as well, but the above always worked for me.<o:p class=""></o:p></div>
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Cheers,<o:p class=""></o:p></div>
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Tim<o:p class=""></o:p></div>
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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" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">mark.baker23@nhs.net</span></a>>:<o:p class=""></o:p></p>
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Hi all<o:p class=""></o:p></div>
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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 class=""></o:p></div>
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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 class=""></o:p></div>
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In the main1.mac, I have changed the geometry to<o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">/gate/world/daughters/name patientCT</span><o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">/gate/world/daughters/insert ImageNestedParametrisedVolume</span><o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">/gate/patientCT/geometry/setImage {CTData}</span><o:p class=""></o:p></div>
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The main1.mac calls sourceF18.mac as its source, which contains the link to the PET data. The relevant part is<o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">/gate/source/addSource patientPET voxel</span><o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">/gate/source/patientPET/imageReader/readFile {PETData}</span><o:p class=""></o:p></div>
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I also change the number of primaries on the fly, so I set that to the following in main1.mac<o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">/gate/application/setTotalNumberOfPrimaries {NoOfPrimaries}</span><o:p class=""></o:p></div>
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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 class=""></o:p></div>
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I call Gate using the following<o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">Gate mac/main1.mac [CTData,$CTDataFile] [NoOfPrimaries,$NumberPrimaries] [PETData,$PTDataFile] &</span><o:p class=""></o:p></div>
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where the user could select the following information, for example,<o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">$CTDataFile is data/dcm/CT/br38f.mha</span><o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">$PTDataFile is data/dcm/PT/brainmaskPET.mha</span><o:p class=""></o:p></div>
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<span style="font-family: "Courier New";" class="">$NumberPrimaries is 1000</span><o:p class=""></o:p></div>
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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 class="apple-converted-space"> </span><span style="font-family: "Courier New";" class="">Gate mac/main1.mac &</span><span class="apple-converted-space"> </span> it
works perfectly, so presumably I am doing something wrong with passing the parameters through.<o:p class=""></o:p></div>
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I’d appreciate it if anyone had any thoughts on this?<o:p class=""></o:p></div>
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Thank you<o:p class=""></o:p></div>
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<b class=""><span style="color: rgb(0, 104, 113);" class="">Mark Baker</span></b><o:p class=""></o:p></div>
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<span style="color: rgb(0, 104, 113);" class="">Principal Clinical Scientist (Interim)</span><o:p class=""></o:p></div>
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<span style="color: rgb(0, 104, 113);" class="">Imaging Physics (Ionising)</span><o:p class=""></o:p></div>
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<span style="color: rgb(0, 104, 113);" class="">The Clatterbridge Cancer Centre NHS Foundation Trust</span><o:p class=""></o:p></div>
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<i class=""><span style="color: rgb(0, 104, 113);" class="">(he, him)</span></i><o:p class=""></o:p></div>
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<span style="color: rgb(0, 104, 113);" class="">CCCW Tel: 0151 556 5030</span><o:p class=""></o:p></div>
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<span style="color: rgb(0, 104, 113);" class="">CCCL Tel: 0151 318 8438</span><o:p class=""></o:p></div>
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<span style="color: rgb(0, 104, 113);" class="">Email:<span class="apple-converted-space"> </span></span><span style="color: rgb(68, 114, 196);" class=""><a href="mailto:mark.baker23@nhs.net" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">mark.baker23@nhs.net</span></a></span><o:p class=""></o:p></div>
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<span style="color: rgb(68, 114, 196);" class=""><a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__teams.microsoft.com_l_chat_0_0-3Fusers-3Dmark.baker23-40nhs.net&d=DwMGaQ&c=XYzUhXBD2cD-CornpT4QE19xOJBbRy-TBPLK0X9U2o8&r=lfXR69GFfS7NT-Wp5HZqbtBDrbYoilDdmNEG7fKW7aM&m=JXkYrD_N3zHhNT53wVMyxPpl-Vu7G4qlA8lefFcef9A&s=jcYxmFfI9EQDmwEWN9bPm0xKwKHlfnGIwAtpSUG-XQE&e=" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(68, 114, 196);" class="">Microsoft
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<i class=""><span style="color: rgb(0, 104, 113);" class="">Honorary Lecturer, Dept. of Physics</span></i><o:p class=""></o:p></div>
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<i class=""><span style="color: rgb(0, 104, 113);" class="">University of Liverpool</span></i><o:p class=""></o:p></div>
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