<html><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /></head><body style='font-size: 10pt; font-family: Verdana,Geneva,sans-serif'>
<p>Hi Klara,</p>
<p>I would recommend to</p>
<p>- update to a newer Gate version (in the old Gate version you could also try following command: /gate/actor/myLETActor/stepHitType random )</p>
<p>- set electron cut to 10 mm</p>
<p>- set max step size limit to 1/10 of scoring grid size in beam direction (after that you may gradually increase it until the effect sets in again).</p>
<p>to convert dcm files, maybe check out gatetools </p>
<p>best,</p>
<p>Andreas</p>
<p id="reply-intro">Am 2022-03-31 14:21, schrieb Klára Badraoui Čuprová:</p>
<blockquote type="cite" style="padding: 0 0.4em; border-left: #1010ff 2px solid; margin: 0">
<div id="replybody1">
<style type="text/css">@font-face
{ font-family: "Cambria Math"; }
@font-face
{ font-family: Calibri; }
@font-face
{ font-family: Verdana; }
#replybody1 p.v1MsoNormal, #replybody1 li.v1MsoNormal, #replybody1 div.v1MsoNormal
{ margin: 0cm; margin-bottom: .0001pt; font-size: 12.0pt; font-family: "Times New Roman",serif; }
#replybody1 a:link, #replybody1 span.v1MsoHyperlink
{ mso-style-priority: 99; color: blue; text-decoration: underline; }
#replybody1 a:visited, #replybody1 span.v1MsoHyperlinkFollowed
{ mso-style-priority: 99; color: purple; text-decoration: underline; }
#replybody1 p
{ mso-style-priority: 99; mso-margin-top-alt: auto; margin-right: 0cm; mso-margin-bottom-alt: auto; margin-left: 0cm; font-size: 12.0pt; font-family: "Times New Roman",serif; }
#replybody1 p.v1v1msonormal, #replybody1 li.v1v1msonormal, #replybody1 div.v1v1msonormal
{ mso-style-name: v1msonormal; mso-margin-top-alt: auto; margin-right: 0cm; mso-margin-bottom-alt: auto; margin-left: 0cm; font-size: 12.0pt; font-family: "Times New Roman",serif; }
#replybody1 p.v1v1xmsonormal, #replybody1 li.v1v1xmsonormal, #replybody1 div.v1v1xmsonormal
{ mso-style-name: v1xmsonormal; mso-margin-top-alt: auto; margin-right: 0cm; mso-margin-bottom-alt: auto; margin-left: 0cm; font-size: 12.0pt; font-family: "Times New Roman",serif; }
#replybody1 p.v1v1msochpdefault, #replybody1 li.v1v1msochpdefault, #replybody1 div.v1v1msochpdefault
{ mso-style-name: v1msochpdefault; mso-margin-top-alt: auto; margin-right: 0cm; mso-margin-bottom-alt: auto; margin-left: 0cm; font-size: 12.0pt; font-family: "Times New Roman",serif; }
#replybody1 span.v1v1msohyperlink
{ mso-style-name: v1msohyperlink; }
#replybody1 span.v1v1msohyperlinkfollowed
{ mso-style-name: v1msohyperlinkfollowed; }
#replybody1 span.v1v1style-mailovzprvy19
{ mso-style-name: v1style-mailovzprvy19; }
#replybody1 span.v1v1style-mailovzprvy20
{ mso-style-name: v1style-mailovzprvy20; }
#replybody1 p.v1v1msonormal1, #replybody1 li.v1v1msonormal1, #replybody1 div.v1v1msonormal1
{ mso-style-name: v1msonormal1; mso-style-priority: 99; margin: 0cm; margin-bottom: .0001pt; font-size: 11.0pt; font-family: "Calibri",sans-serif; mso-fareast-language: EN-US; }
#replybody1 span.v1v1msohyperlink1
{ mso-style-name: v1msohyperlink1; mso-style-priority: 99; color: #0563C1; text-decoration: underline; }
#replybody1 span.v1v1msohyperlinkfollowed1
{ mso-style-name: v1msohyperlinkfollowed1; mso-style-priority: 99; color: #954F72; text-decoration: underline; }
#replybody1 p.v1xmsonormal, #replybody1 li.v1xmsonormal, #replybody1 div.v1xmsonormal
{ mso-style-name: x_msonormal; mso-style-priority: 99; margin: 0cm; margin-bottom: .0001pt; font-size: 12.0pt; font-family: "Times New Roman",serif; }
#replybody1 span.v1StylE-mailovZprvy29
{ mso-style-type: personal; font-family: "Calibri",sans-serif; color: windowtext; }
#replybody1 span.v1StylE-mailovZprvy30
{ mso-style-type: personal; font-family: "Calibri",sans-serif; color: #1F497D; }
#replybody1 span.v1StylE-mailovZprvy32
{ mso-style-type: personal-reply; font-family: "Calibri",sans-serif; color: #1F497D; }
#replybody1 .v1MsoChpDefault
{ mso-style-type: export-only; font-size: 10.0pt; }
@page WordSection1
{ size: 612.0pt 792.0pt; margin: 70.85pt 70.85pt 70.85pt 70.85pt; }
#replybody1 div.v1WordSection1
{ }</style>
<div lang="CS">
<div class="v1WordSection1">
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">Dear Andreas and Gate users, </span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">thank you for your reply, I have Gate version 8.2. I set electron cut in patient 0.1mm and I did not set step size limit.</span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">OK, yes it seems the voxel size is really the problem. Hopefully then, the solution would be </span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">to create voxel phantom with grid 2mmx2mmx2mm. I wrote my own script to convert CT </span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">dicom slices to mhd and raw files, but the voxel size copies the size of the CT (1.2695,1.2695,2). </span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">I would like to ask, is there some program to resample the dicom CT slices (to grid 2mmx2mmx2mm), output can be either dicom or mhd+raw files?</span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">Thank you in advance,</span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">best regards,</span></p>
<p style="margin: 0cm; margin-bottom: .0001pt;"><span style="font-size: 10.0pt;">Klára</span></p>
<p class="v1MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;"> </span></p>
<p class="v1MsoNormal"><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif; color: #1f497d; mso-fareast-language: EN-US;"> </span></p>
<div>
<div style="border: none; border-top: solid #E1E1E1 1.0pt; padding: 3.0pt 0cm 0cm 0cm;">
<p class="v1MsoNormal"><strong><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif;">From:</span></strong><span style="font-size: 11.0pt; font-family: 'Calibri',sans-serif;"> Andreas Resch [mailto:andreas.resch@meduniwien.ac.at] <br /><strong>Sent:</strong> Thursday, March 31, 2022 10:47 AM<br /><strong>To:</strong> Klára Badraoui Čuprová <Klara.BadraouiCuprova@ptc.cz><br /><strong>Cc:</strong> gate-users@lists.opengatecollaboration.org<br /><strong>Subject:</strong> Re: [Gate-users] FW: LET problem in GATE</span></p>
</div>
</div>
<p class="v1MsoNormal"> </p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Dear Klara,</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">interesting! </span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Which Gate version are you using? e- production cuts? Max Step size limit? </span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">" May there be some artefact because of calculation grid and phantom voxel size?" yes, that would be my first guess. Seems like is happening every 2-3 voxels, which can come from having a non constant number of geometric boundaries per scoring unit volume, e.g. if CT is 1.2695 mm spaced and calculation grid 2 mm, in the third calculation voxel there are two geometric boundaries, whereas in the first two are only one each. </span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">best,</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Andreas</span></p>
<p id="v1reply-intro"><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Am 2022-03-31 07:34, schrieb Klára Badraoui Čuprová:</span></p>
<blockquote style="border: none; border-left: solid #1010FF 1.5pt; padding: 0cm 0cm 0cm 5.0pt; margin-left: 0cm; margin-right: 0cm;">
<div id="v1replybody1">
<div>
<div>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Dear,</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">I am medical physicist in Proton Therapy Center in Czech and I am concerned with Monte Carlo simulations in GATE for proton therapy.</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">I calculate dose and LET distributions in patients and in some patients I get strange results for LETdistributions. (Dose distributions are all OK.)</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">In some LET distributions a line pattern appears (I am attaching printscreen). (The patients with such problem are irradiated from main angles (0°,90° or 270°).</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Calculation of LET to water phantom was OK. May there be some artefact because of calculation grid and phantom voxel size? Calculation grid is 2mmx2mmx2mm.</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Voxel phantom of one particular prostatic patient is of size 1.2695mm, 1.2695mm, 2mm. Please, do you have some idea why this happens?</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">I would be very grateful for help.</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Best regards,</span></p>
<p><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;">Klára Badraoui Čuprová</span></p>
<p class="v1v1msonormal"><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"> </span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"> </span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.5pt; font-family: 'Verdana',sans-serif; color: black;">Ing. Klára Badraoui Čuprová, PhD.</span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.5pt; font-family: 'Verdana',sans-serif; color: black;">Medical physicist</span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.5pt; font-family: 'Verdana',sans-serif; color: black;"><img id="v1v1x_obrázek_x0020_1" src="cid:1648821693624705bd3bbdc022433900@meduniwien.ac.at" alt="Popis: Popis: Popis: Popis: Popis: cid:1F7383A9-79F3-4EF6-AB2D-742C8E1A5D06" width="108" height="43" /></span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.5pt; font-family: 'Verdana',sans-serif; color: black;"> </span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.0pt; font-family: 'Arial',sans-serif; color: black;">Proton Therapy Center Czech s.r.o., Křenova 11, CZ–162 00 Praha 6</span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.0pt; font-family: 'Arial',sans-serif; color: black;">Zapsáno v OR u MS Praha, odd. C, 84153, IČ 26466791, DIČ CZ26466791</span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1v1xmsonormal"><span style="font-size: 10.0pt; font-family: 'Arial',sans-serif; color: black;">telefon +420 222 998 941 </span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif; color: #1f497d;"><a href="mailto:info@ptc.cz" rel="noreferrer"><span style="font-family: 'Arial',sans-serif;">info@ptc.cz</span></a></span><span style="font-size: 10.0pt; font-family: 'Arial',sans-serif; color: black;">, </span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif; color: #1f497d;"><a href="https://_neklikaci-odkaz_/_podezrely-odkaz_/https:/_neklikaci-odkaz_/http:/www.ptc.cz/" target="_blank" rel="noopener noreferrer"><span style="font-family: 'Arial',sans-serif;">www.ptc.cz</span></a></span><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1v1msonormal"><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"> </span></p>
</div>
<p class="v1MsoNormal" style="margin-bottom: 12.0pt;"><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"> </span></p>
<p class="v1v1msonormal"><em><span style="font-size: 8.0pt; font-family: 'Verdana',sans-serif; color: #002060;">UPOZORNĚNÍ: Pokud jste obdrželi e-mailovou zprávu od Proton Therapy Center, jsou tato zpráva i veškeré přílohy zaslané společně s ní určeny výhradně pro potřeby adresáta a mohou obsahovat zákonem chráněné a důvěrné informace. Pokud nejste zamýšleným příjemcem zprávy nebo zaměstnancem či zástupcem odpovědným za doručení zprávy zamýšlenému příjemci, upozorňujeme Vás tímto, že jakékoliv šíření, distribuce, kopírování nebo jiné použití této zprávy či jejích příloh je přísně zakázáno. Pokud jste tuto zprávu obdrželi omylem, neprodleně o tom, prosím, informujte odesílatele odpovědí na tuto zprávu a poté tuto zprávu vymažte ze svého počítače.</span></em><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
<p class="v1MsoNormal"><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"> </span></p>
<p class="v1v1msonormal"><em><span style="font-size: 8.0pt; font-family: 'Verdana',sans-serif; color: #002060;">WARNING: If you received this e-mail message from Proton Therapy Center, please note that this message and all attachments sent with it are intended solely for the needs of the addressee and may contain proprietary and confidential information. If you are not the intended recipient, or an employee or agent responsible for delivering the messageto the intended recipient, please note that that any dissemination, distribution, copying or other use of this message or its attachments is strictly prohibited. If you have received this message in error, please notify the sender of this message and then delete this message from your computer.</span></em><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"></span></p>
</div>
</div>
<p class="v1MsoNormal"><span style="font-size: 10.0pt; font-family: 'Verdana',sans-serif;"> </span></p>
<div>
<p class="v1MsoNormal"><span style="font-size: 10.0pt; font-family: 'Courier New';">_______________________________________________<br />Gate-users mailing list<br /><a href="mailto:Gate-users@lists.opengatecollaboration.org" rel="noreferrer">Gate-users@lists.opengatecollaboration.org</a><br /><a href="https://_neklikaci-odkaz_/http:/lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank" rel="noopener noreferrer">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></span></p>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</body></html>