<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=utf-8">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@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;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
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";}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
mso-fareast-language:EN-GB;}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";
mso-fareast-language:EN-GB;}
span.hoenzb
{mso-style-name:hoenzb;}
span.EmailStyle23
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
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-GB" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear CASToR community,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I am appealing for some help getting CASToR to reconstruct some SPECT projection data with scatter correction.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I have attached the Matlab code we’re using to convert SPECT projection data from Interfile into CASToR .cdh/.cdf files. I also attach the result of this code
when we feed it three interfiles (photopeak and upper/lower scatter windows). The code estimates the scatter component (in counts/sec) using the Triple Energy Window method.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">When we run the resulting datafiles through castor-recon.exe, we get the attached error message. As there is a mismatch between the expected and actual sizes,
I suspect the problem relates to the bit depth of the variables as I write them to the .cdf file, or a problem with the header and CASToR not recognising the fact that I’ve included normalisation factors. As we are using the pre-compiled binaries, we haven’t
changed the default FLTNMDATA variable, so I am writing variables of this type as 32-bit floats.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I can’t spot any other issues with the conversion code, but I’m obviously missing something. I would appreciate any help anyone can offer. I have already
had some very helpful email exchanges with Michael Ljungberg in Lund, who has already got this working. But rather than continue to hassle Michael, I thought I would give him a break and appeal to the wider community!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">James.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">James Scuffham, MSc, PhD, MIPEM
<o:p></o:p></span></b></p>
<table class="MsoNormalTable" border="0" cellspacing="0" cellpadding="0" style="border-collapse:collapse">
<tbody>
<tr>
<td width="262" valign="top" style="width:196.8pt;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Deputy Head of Section
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Nuclear Medicine Physics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Royal Surrey County Hospital
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Egerton Road, Guildford, GU2 7XX<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">T: 01483 406708<o:p></o:p></span></p>
</td>
<td width="214" valign="top" style="width:160.4pt;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Associate Tutor
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Department of Physics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">University of Surrey<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US">Guildford, GU2 7XH<o:p></o:p></span></p>
</td>
<td width="238" valign="top" style="width:178.6pt;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
</td>
</tr>
<tr>
<td width="262" style="width:196.8pt;padding:0cm 5.4pt 0cm 5.4pt"></td>
<td width="214" style="width:160.4pt;padding:0cm 5.4pt 0cm 5.4pt"></td>
<td width="238" style="width:178.6pt;padding:0cm 5.4pt 0cm 5.4pt">
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Castor-users [mailto:castor-users-bounces@lists.castor-project.org]
<b>On Behalf Of </b>Kajal Aggarwal<br>
<b>Sent:</b> 02 August 2017 10:10<br>
<b>To:</b> tmerlin<br>
<b>Cc:</b> castor-users@lists.castor-project.org<br>
<b>Subject:</b> Re: [Castor-users] Query related to castor-GateMacToGeom<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hello,<o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Thank you for the detailed explanation. I am having troubles to reconstruct an image for a cylindrical PET system simulated using Gate. I am generating .geom file and .cdh and .cdf files (attached in this email)
for my .mac file and for the output root file. But the image generated has some problem (see the screen-shot below). Please guide me where I am going wrong.
<o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Thank you very much for all your support.<o:p></o:p></p>
</div>
<p class="MsoNormal">Regards,<o:p></o:p></p>
</div>
<p class="MsoNormal">Kajal<o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<img width="560" height="190" id="Picture_x0020_1" src="cid:image002.png@01D30BAF.6C483450" alt="Inline image 1"><br>
<br>
<br>
<img width="560" height="179" id="Picture_x0020_2" src="cid:image004.png@01D30BAF.6C483450" alt="Inline image 2"> <o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Tue, Aug 1, 2017 at 9:00 PM, tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">Thibaut.Merlin@univ-brest.fr</a>> wrote:<o:p></o:p></p>
<div>
<p>Hello Kajal,<o:p></o:p></p>
<p>F.O.V variables are arbitrary computed as <i>scanner_radius(mm)/4</i> for the transaxial component, and the axial dimension (mm) of the rsector/block for the axial component. The transaxial/axial number of voxels are calculated from these values in order
to get (large) isotropic 4mm voxels.<o:p></o:p></p>
<p>The sole purpose of these variables is to be used as default for reconstruction dimensions/voxel sizes when using this scanner, in the case no dimensions have been initialized in command-line options. In practice, they are overwritten by the parameters entered
in command line options (<i>-dim</i> for number of voxels, <i>-fov /-vox</i> for field of view and voxel dimensions initializations ).<o:p></o:p></p>
<p>Best regards,<o:p></o:p></p>
<p>Thibaut<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 01/08/2017 16:54, Kajal Aggarwal wrote:<o:p></o:p></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hello everyone,<o:p></o:p></p>
</div>
<p class="MsoNormal">I am trying to create .geom file from a .mac file for PET scanner system. In the .geom file created, I would like to know how the voxels number transaxial, voxels number axial, field of view transaxial, field of view axial are being calculated.<br>
<br>
<br>
<br clear="all">
<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"><br>
-- <o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">Thanking you.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Yours sincerely,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Kajal Aggarwal<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
</div>
</div>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Castor-users mailing list<o:p></o:p></pre>
<pre><a href="mailto:Castor-users@lists.castor-project.org" target="_blank">Castor-users@lists.castor-project.org</a><o:p></o:p></pre>
<pre><a href="http://lists.castor-project.org/listinfo/castor-users" target="_blank">http://lists.castor-project.org/listinfo/castor-users</a><span class="hoenzb"><span style="color:#888888"><o:p></o:p></span></span></pre>
</blockquote>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span class="hoenzb"><span style="color:#888888"><o:p> </o:p></span></span></p>
<pre><span style="color:#888888">-- </span><o:p></o:p></pre>
<pre><span style="color:#888888">Thibaut MERLIN -- PhD<o:p></o:p></span></pre>
<pre><span style="color:#888888"><o:p> </o:p></span></pre>
<pre><span style="color:#888888">Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)<o:p></o:p></span></pre>
<pre><span style="color:#888888">Bâtiment 1<o:p></o:p></span></pre>
<pre><span style="color:#888888">CHRU Morvan - 2, Av. Foch<o:p></o:p></span></pre>
<pre><span style="color:#888888">29609 Brest CEDEX - FRANCE<o:p></o:p></span></pre>
<pre><span style="color:#888888">Tel: 06.75.12.24.90</span><o:p></o:p></pre>
</div>
</div>
<p class="MsoNormal"><br>
<br clear="all">
<br>
-- <o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal">Thanking you.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Yours sincerely,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Kajal Aggarwal<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<br>
<font face="Courier New" color="Black" size="2"><br>
********************************************************************************************************************<br>
<br>
This message may contain confidential information. If you are not the intended recipient please inform the<br>
sender that you have received the message in error before deleting it.<br>
Please do not disclose, copy or distribute information in this e-mail or take any action in relation to its contents. To do so is strictly prohibited and may be unlawful. Thank you for your co-operation.<br>
<br>
NHSmail is the secure email and directory service available for all NHS staff in England and Scotland. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.<br>
<br>
For more information and to find out how you can switch, https://portal.nhs.net/help/joiningnhsmail<br>
<br>
</font>
</body>
</html>