<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.EmailStyle18
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.EmailStyle19
{mso-style-type:personal;
font-family:"Tahoma",sans-serif;
color:#200498;
font-weight:normal;
font-style:normal;
text-decoration:none none;}
span.EmailStyle20
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:#1F497D;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:"Tahoma",sans-serif;
color:#200498;
font-weight:normal;
font-style:normal;
text-decoration:none none;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:70.85pt 70.85pt 56.7pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Great! Have a great day.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Mahdjoub<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Russ, Tom [mailto:Tom.Russ@medma.uni-heidelberg.de]
<br>
<b>Sent:</b> Thursday, August 22, 2019 9:12 AM<br>
<b>To:</b> Mahdjoub Hamdi <mahdjoub.hamdi@hotmail.fr><br>
<b>Subject:</b> AW: Output imageCT<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Mahdjoub,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">thank you so much for your fast reply.<o:p></o:p></p>
<p class="MsoNormal">With your help I could read in the data!<o:p></o:p></p>
<p class="MsoNormal">Thank you so much, I was missing the ‘float32’, instead, I just typed ‘float’.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I wish you a beautiful Thursday!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Tom<o:p></o:p></p>
<p class="MsoNormal"><span style="color:black">=============================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Tom Russ, M.Sc.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Project Group ‚Image Guided Interventions‘<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Computer Assisted Clinical Medicine<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Medical Faculty Mannheim<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Ruprecht-Karls-Universität Heidelberg<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Theodor-Kutzer-Ufer 1 - 3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">68167 Mannheim<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Tel. +49 621 383-6552<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">E-Mail:</span><span lang="DE" style="color:#1F497D">
<a href="mailto:Tom.Russ@MedMa.Uni-Heidelberg.de"><span style="color:blue">Tom.Russ@MedMa.Uni-Heidelberg.de</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:#1F497D"><a href="http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/"><span style="color:blue">http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span lang="DE">Von:</span></b><span lang="DE"> Mahdjoub Hamdi <<a href="mailto:mahdjoub.hamdi@hotmail.fr">mahdjoub.hamdi@hotmail.fr</a>>
<br>
<b>Gesendet:</b> Donnerstag, 22. August 2019 16:03<br>
<b>An:</b> Russ, Tom <<a href="mailto:Tom.Russ@medma.uni-heidelberg.de">Tom.Russ@medma.uni-heidelberg.de</a>>;
<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>
<b>Betreff:</b> RE: Output imageCT<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Hi Tom,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">The CTscanner output (*.dat) are raw data files coded as float (32 bits) and here is a way you can read it using matlab:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">fid = fopen(‘CTscannerProjection.dat’,’r’);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">p = fread(fid,’float32’) ;<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">fclose(fid);<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">p1 = reshape(p,[N M]); % N,M are the sizes of your detector panel (in number of pixels)
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">You can read them also using ImageJ software by navigating to: File->Import->raw then select your *.dat file, a new window will appear, go to Image type and scroll down to 32-bit
Real, and specify the image width and height (in pixels), check Little-endian byte order case and clique OK
</span><span style="font-family:Wingdings;color:#200498">J</span><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">I hope it helps
</span><span style="font-family:Wingdings;color:#200498">J</span><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Mahdjoub,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Postdoc research Associate,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Washington University in St. Louis,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Phone number: +1 314 362 8315<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Campus box: 8225<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498">Stl, MO, USA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Tahoma",sans-serif;color:#200498"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b>From:</b> Gate-users [<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org">mailto:gate-users-bounces@lists.opengatecollaboration.org</a>]
<b>On Behalf Of </b>Russ, Tom<br>
<b>Sent:</b> Thursday, August 22, 2019 8:23 AM<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> [Gate-users] Output imageCT<o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="DE">Dear Gate-community,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal">at the moment, I am starting with simulations of simple cone-beam CT images.<o:p></o:p></p>
<p class="MsoNormal">For starters, I am running the example in the GateContrib folder, classic mode.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The problem I am having is regarding the output ‘imageCT’.<o:p></o:p></p>
<p class="MsoNormal">I am assuming (more like hoping) that this output can provide me with direct CT projections, i.e. a matrix (with the size of the number of pixels) with the number of Singles in each pixel.<o:p></o:p></p>
<p class="MsoNormal">Is that correct or a misconception?<o:p></o:p></p>
<p class="MsoNormal">Because when I am trying to import the resulting ‘.dat’-file into MATLAB it is giving me a matrix with far more elements than pixels in my detector.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you very much in advance for your help!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Tom<o:p></o:p></p>
<p class="MsoNormal"><span style="color:black">=============================================<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:black">Tom Russ, M.Sc.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Projektgruppe „Image Guided Interventions“<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Computerunterstützte Klinische Medizin<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Medizinische Fakultät Mannheim<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Ruprecht-Karls-Universität Heidelberg<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Theodor-Kutzer-Ufer 1 - 3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">68167 Mannheim<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">Tel. +49 621 383-6552<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="color:black">E-Mail:</span><span lang="DE">
<a href="mailto:Tom.Russ@MedMa.Uni-Heidelberg.de"><span style="color:blue">Tom.Russ@MedMa.Uni-Heidelberg.de</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><a href="http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/"><span style="color:blue">http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
</div>
</body>
</html>