<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Dear Kris,</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature"><span style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">It depends on how you want to make a geometry structure. As you know, in GATE, in the cylindricalPET scanner, the geometrical volumes containing crystal are grouped in matrices, themselves assembled in submodules and modules ( if you want, you can define submodules) and the Rsectors composed of modules are repeated on a cylindrical surface to build up the whole system. So I answer you by an example, I define a biograph6 PET, it is a cylindricalPET system composed of 12 rsectors, 3 modules (repeated along z axis) 4 modules ( repeated along Y axis that it equals to : 3 submodules repeated in Y axis( one submodule has 3 modules in z axis= 3*1) and 13*13 crystals.( 39 crystal in z axis).</span><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">So in STIR header file and in stir_master ( template_for_ROOTscanner. hs):</div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">Num- block _per bucket in transaxial(y) = 4 and num- block _per bucket in axis(z) = 3 </div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">Num_crystal _per block in y= 13</div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">Num_crystal _per block in z= 13</div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">Num_crystal _per singles unit in z and Y = 13</div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">Thus ,bucket= rsector, module =block</div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">Or you can define it like this:</div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;"><div>Num- block _per bucket in transaxial(y) = 1, and num- block _per bucket in axis(z) = 1</div><div>Num_crystal _per block in y= 39( 41 in a real scanner)</div><div>Num_crystal _per block in z= 52( 56 in a real scanner)</div><div>Num_crystal _per singles unit in z =39 and in Y = 52, so in this structure, the bucket equals to block = rsector=1.</div></div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">2 models has a same answering. But when I convert a root file to sinogram by gate_pet_2_stir , it makes this header file:</div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;"><div>Num- block _per bucket in transaxial(y) = 1 and num- block _per bucket in axis(z) = 3 </div><div>Num_crystal _per block in y= 13</div><div>Num_crystal _per block in z= 13</div><div>Num_crystal _per singles unit in z and Y = 13.</div></div><div style="color: rgb(69, 69, 69); text-decoration: -webkit-letterpress;">And about deadtime, for choosing DTVloume, its corresponding system level.</div><div id="AppleMailSignature"><br></div><div id="AppleMailSignature">Cheers,</div><div id="AppleMailSignature"><br></div>Hanieh</div><div id="AppleMailSignature">Envoyé de mon iPhone</div><div><br>Le 27 juin 2017 à 20:17, MOREL Christian <<a href="mailto:morel@cppm.in2p3.fr">morel@cppm.in2p3.fr</a>> a écrit :<br><br></div><blockquote type="cite"><div><meta http-equiv="Content-Type" content="text/html charset=us-ascii">Dear Kris,<div class=""><br class=""></div><div class="">Normally, RSector as defined in the LMF library (see below) can also be repeated along the scanner axis.</div><div class=""><br class=""></div><div class="">Kind regards, Christian Morel</div><div class=""><br class=""></div><div class=""></div></div></blockquote><blockquote type="cite"><div><LMF_geometry.pdf></div></blockquote><blockquote type="cite"><div><meta http-equiv="Content-Type" content="text/html charset=utf-8"><div class=""></div><div class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">Le 27 juin 2017 à 15:52, Thielemans, Kris <<a href="mailto:k.thielemans@ucl.ac.uk" class="">k.thielemans@ucl.ac.uk</a>> a écrit :</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi all<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">As you know, Nikos put code into our development version of STIR to read ROOT files (it needs an additional text file to specify some scanner info). This should handle CylindricalPET and ECAT output. We’re checking this now and have identified 2 “issues”<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="https://github.com/UCL/STIR/issues/80" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://github.com/UCL/STIR/issues/80</a><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><a href="https://github.com/UCL/STIR/issues/79" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://github.com/UCL/STIR/issues/79</a><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">The main problem is that CylindricalPET has 1 extra level of hierarchy:<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">CylindricalPET: RSector, Module, Submodule, Crystal<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">STIR: bucket, block, crystal<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">We’re debating how to map the CylindricalPET case to STIR. However to make a sensible decision, can someone please clarify what the consequences are of the cylindricalPET hierarchy? I realise you can use this do specify geometry (via the repeaters). Does it also have anything to do with dead-time processing?<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Also, can RSector to repetition along the scanner axis as well, or only rotation?<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Of course, feel free to add comments to the Issues above. If not, I’ll summarise this email thread and put it on github as well.<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Please reply to both<span class="Apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">gate-users@lists.opengatecollaboration.org</a><span class="Apple-converted-space"> </span>and<span class="Apple-converted-space"> </span><a href="mailto:stir-devel@lists.sourceforge.net" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">stir-devel@lists.sourceforge.net</a><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Many thanks<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="" class="">Kris Thielemans<br class="">Reader in Medical Imaging Physics at University College London,<br class="">Institute of Nuclear Medicine, UCL Hospital, Tower 5,<br class="">235 Euston Road, London NW1 2BU, UK<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Gate-users mailing list</span><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:Gate-users@lists.opengatecollaboration.org" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Gate-users@lists.opengatecollaboration.org</a><br style="font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 14px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></div></blockquote></div><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">__________________<br class="">Christian MOREL, PhD<br class="">Professeur des universités<br class="">Centre de Physique des Particules de Marseille (CPPM)<br class="">Aix-Marseille Université et CNRS/IN2P3<br class="">163, Av. de Luminy, Case 902, 13288 Marseille, France<br class=""><br class="">tel: +33 (0)4 91 82 76 73<br class="">fax: +33 (0)4 91 82 72 99<br class="">mobile: +33 (0)6 16 44 20 16<br class="">email: <a href="mailto:morel@cppm.in2p3.fr" class="">morel@cppm.in2p3.fr</a><br class="">url: <a href="http://imXgam.in2p3.fr" class="">http://imXgam.in2p3.fr</a></div></div>
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