<html>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p>Dear Kurt, and all,</p>
<p><br>
</p>
<p>Regarding CASToR, as Panagiotis and Konstantinos mentioned, the
software contains several tools to convert a GATE output root file
to a datafile format, which can then be used by CASToR for
reconstruction. They are described in the section 8.2 of the
documentation
(<a class="moz-txt-link-freetext" href="http://www.castor-project.org/sites/default/files/2017-10/CASToR_general_documentation.pdf">http://www.castor-project.org/sites/default/files/2017-10/CASToR_general_documentation.pdf</a>)</p>
<p><br>
</p>
<p>For SPECT reconstruction, the conversion tool requires to divide
the crystal surface in "virtual" pixels (assuming a pixel matrix
was not already defined in the macros), by selecting a number of
transaxial/axial pixels which the singles will be assigned to,
depending on their detected position. It is done through the
command-line options of the conversion tool.<br>
</p>
<p><br>
</p>
<p>Several information about the geometry of the gamma cameras will
be read from the macros files of the simulation (i.e number of
heads, crystal dimensions, number of projections, etc..). These
tools have some limitations, such as they will not recover
information about the collimator from the macro files (parallel
collimator will be set by default). CASToR uses different models
to mimic the effect of different collimators (parallel, cone-beam,
fan-beam, mono or multi convergent, etc..). These models are
described in the section 5.2 of the documentation. The model and
their parameters must be set manually.</p>
<p><br>
</p>
<p>I can share with you some sample shell scripts to use these tools
if you wish.<br>
</p>
<p><br>
</p>
<p>Best regards,</p>
<p>Thibaut<br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
<br>
<div class="moz-cite-prefix">On 01/11/2017 14:11, Panagiotis
Papadimitroulas wrote:<br>
</div>
<blockquote
cite="mid:HE1PR10MB1691D5A1D7B1B4E5A283F855BB5F0@HE1PR10MB1691.EURPRD10.PROD.OUTLOOK.COM"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
<div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif;"
dir="ltr">
<p><br>
</p>
<br>
<p>Dear Kurt,</p>
<p><br>
</p>
<p>As Konstantinos mentioned, there are several tools to apply
reconstruction on the SPECT simulated data.
<br>
</p>
<p>A first step is to extract the projections of your SPECT
imaging acquisition. There is one possibility to save them
directly in projection format through GATE, or to extract them
from your root file.
<br>
</p>
<p>In our group we are extracting the projections from the root
files in order to do the reconstruction, using the QSPECT
tool. If you want we can share with you these .c scripts to
create your own projections from root.
<br>
</p>
<p>Also using the Castor software, I think you can apply
directly the reconstruction using as input the root file.
<br>
</p>
<p>Thus I would recommend you to run your simulations, saving
your output in .root format.</p>
<p><br>
</p>
<p>Kind regards,<br>
Panagiotis</p>
<p><br>
</p>
<div>
<p><br>
</p>
<pre class="moz-signature" cols="72">--
Panagiotis Papadimitroulas
Project Director, PhD
BET Solutions
116 Alexandras Av.
11472 Athens
Greece
Tel: +30 2130290586
Fax: +30 2130290587
Web: <a class="moz-txt-link-abbreviated" href="http://www.betsolutions.gr">www.betsolutions.gr</a>
e-mail: <a class="moz-txt-link-abbreviated" href="mailto:panpap@betsolutions.gr">panpap@betsolutions.gr</a></pre>
</div>
<br>
<div style="color: rgb(0, 0, 0);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
color="#000000" face="Calibri, sans-serif"><b>From:</b>
Gate-users
<a class="moz-txt-link-rfc2396E" href="mailto:gate-users-bounces@lists.opengatecollaboration.org"><gate-users-bounces@lists.opengatecollaboration.org></a>
on behalf of Konstantinos P. Chatzipapas, MSc
<a class="moz-txt-link-rfc2396E" href="mailto:konhat88@yahoo.gr"><konhat88@yahoo.gr></a><br>
<b>Sent:</b> Wednesday, November 1, 2017 2:40 PM<br>
<b>To:</b> Kurt V;
<a class="moz-txt-link-abbreviated" href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> [Gate-users] How do you perform Image
Reconstruction for a SPECT based Imaging procedure?</font>
<div> </div>
</div>
<div>
<div style="color:#000; background-color:#fff;
font-family:Helvetica Neue,Helvetica,Arial,Lucida
Grande,sans-serif; font-size:16px">
<div id="yui_3_16_0_ym19_1_1509532683142_22980"><span
id="yui_3_16_0_ym19_1_1509532683142_22981">Hello,</span></div>
<div id="yui_3_16_0_ym19_1_1509532683142_22982"><span
id="yui_3_16_0_ym19_1_1509532683142_22983"><br
id="yui_3_16_0_ym19_1_1509532683142_22984">
</span></div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1509532683142_22985"><span
id="yui_3_16_0_ym19_1_1509532683142_22986">For image
reconstruction, as free softwares, I know a few. You
can try QSPECT
(<a class="moz-txt-link-freetext" href="http://www.bme.teiath.gr/ni/EnglishVersion/Downloads_files/Downloads.html">http://www.bme.teiath.gr/ni/EnglishVersion/Downloads_files/Downloads.html</a>),
CASToR (<a class="moz-txt-link-freetext" href="http://www.castor-project.org/">http://www.castor-project.org/</a>) or STIR
(<a class="moz-txt-link-freetext" href="http://stir.sourceforge.net/">http://stir.sourceforge.net/</a>)</span></div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1509532683142_22987"><span
id="yui_3_16_0_ym19_1_1509532683142_22988"><br
id="yui_3_16_0_ym19_1_1509532683142_22989">
</span></div>
<div dir="ltr" id="yui_3_16_0_ym19_1_1509532683142_22990"><span
id="yui_3_16_0_ym19_1_1509532683142_22991">Regards,</span></div>
<span id="yui_3_16_0_ym19_1_1509532683142_22992">Konstantinos</span>
<div id="yui_3_16_0_ym19_1_1509532683142_23091"> </div>
<div class="signature"
id="yui_3_16_0_ym19_1_1509532683142_23060">
<div id="yui_3_16_0_ym19_1_1509532683142_23090"
style="color:rgb(0,0,0); font-family:Arial;
font-size:16px; font-style:normal; font-weight:normal;
letter-spacing:normal; orphans:2; text-indent:0px;
text-transform:none; white-space:normal; widows:2;
word-spacing:0px">
<span id="yui_3_16_0_ym19_1_1509532683142_23089"
style="font-style:italic">-----------------------------------------------------</span></div>
<span id="yui_3_16_0_ym19_1_1509532683142_23088"
style="color:rgb(0,0,0); font-family:Arial;
font-size:16px; font-weight:normal;
letter-spacing:normal; orphans:2; text-indent:0px;
text-transform:none; white-space:normal; widows:2;
word-spacing:0px; font-style:italic"> Konstantinos
Chatzipapas<br>
Medical Physicist, </span><span
id="yui_3_16_0_ym19_1_1509532683142_23105"
style="color:rgb(0,0,0); font-family:Arial;
font-size:16px; font-weight:normal;
letter-spacing:normal; orphans:2; text-indent:0px;
text-transform:none; white-space:normal; widows:2;
word-spacing:0px; font-style:italic">MSc<br>
</span>
<div id="yui_3_16_0_ym19_1_1509532683142_23062"
style="color:rgb(0,0,0); font-family:Arial;
font-size:16px; font-style:normal; font-weight:normal;
letter-spacing:normal; orphans:2; text-indent:0px;
text-transform:none; white-space:normal; widows:2;
word-spacing:0px">
<div id="yui_3_16_0_ym19_1_1509532683142_23061"><span
id="yui_3_16_0_ym19_1_1509532683142_23087"
style="font-style:italic"> <span
id="yui_3_16_0_ym19_1_1509532683142_23086"
style="font-weight:bold">University of Patras</span></span></div>
<div id="yui_3_16_0_ym19_1_1509532683142_23064">
<div id="yui_3_16_0_ym19_1_1509532683142_23063"><span
style="font-style:italic"><br>
</span></div>
<div id="yui_3_16_0_ym19_1_1509532683142_23085"><span
id="yui_3_16_0_ym19_1_1509532683142_23084"
style="font-style:italic"><span class="Apple-tab-span" style="white-space:pre"></span>
web page:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true" rel="nofollow"
target="_blank"
href="http://www.physicsmag.com/"
id="yui_3_16_0_ym19_1_1509532683142_23083">Physics
Magazine</a></span></div>
</div>
</div>
</div>
<div class="qtdSeparateBR"><br>
<br>
</div>
<div class="yahoo_quoted" style="display:block">
<div style="font-family:Helvetica
Neue,Helvetica,Arial,Lucida Grande,sans-serif;
font-size:16px">
<div style="font-family:HelveticaNeue,Helvetica
Neue,Helvetica,Arial,Lucida Grande,sans-serif;
font-size:16px">
<div dir="ltr"><font face="Arial" size="2">Στις 9:14
μ.μ. Δευτέρα, 30 Οκτωβρίου 2017, ο/η Kurt V
<a class="moz-txt-link-rfc2396E" href="mailto:kurtv1@hotmail.com"><kurtv1@hotmail.com></a> έγραψε:<br>
</font></div>
<br>
<br>
<div class="y_msg_container">
<div id="yiv9312372316">
<div>
<div class="yiv9312372316WordSection1">
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt">I am new to
image reconstruction using GATE, I was
wondering if anyone could provide me
with details on how to best perform
image reconstruction using a SPECT based
imaging procedure?</span></div>
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<ul style="margin-top:0cm" type="disc">
<li
class="yiv9312372316MsoListParagraphCxSpFirst"
style="margin-left:0cm"><span
style="font-size:14.0pt;
line-height:106%">What is the best
way?</span></li>
<li
class="yiv9312372316MsoListParagraphCxSpMiddle"
style="margin-left:0cm"><span
style="font-size:14.0pt;
line-height:106%">Can this somehow be
done with an ECAT7 workflow?</span></li>
<li
class="yiv9312372316MsoListParagraphCxSpMiddle"
style="margin-left:0cm"><span
style="font-size:14.0pt;
line-height:106%">Is it better to go
from ASCII to another software?</span></li>
<li
class="yiv9312372316MsoListParagraphCxSpMiddle"
style="margin-left:0cm"><span
style="font-size:14.0pt;
line-height:106%">Interfile to another
software?</span></li>
<li
class="yiv9312372316MsoListParagraphCxSpLast"
style="margin-left:0cm"><span
style="font-size:14.0pt;
line-height:106%">Is there another
software efficient workflow that
anyone knows of?</span></li>
</ul>
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt">If anyone has
any words of wisdom for me, all advice
would be greatly appreciated.</span></div>
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt"> </span></div>
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt">Thank you very
much,
</span></div>
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt">Sincerely,</span></div>
<div class="yiv9312372316MsoNormal"><span
style="font-size:14.0pt">Kurt W. Van
Delinder</span></div>
<div class="yiv9312372316MsoNormal"> </div>
<div class="yiv9312372316MsoNormal"> </div>
</div>
</div>
</div>
_______________________________________________<br>
Gate-users mailing list<br>
<a moz-do-not-send="true"
href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br>
<a moz-do-not-send="true"
href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users"
target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Gate-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a>
<a class="moz-txt-link-freetext" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Thibaut MERLIN -- PhD
Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Bâtiment 1
CHRU Morvan - 2, Av. Foch
29609 Brest CEDEX - FRANCE
Tel: 06.75.12.24.90</pre>
</body>
</html>