<html>
<head>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p>Hello James,</p>
<p>Apparently something went wrong when generating the binary
datafile, though I can't tell exactly why from your matlab code.</p>
<p>This error occurs when the binary datafile doesn't have the
expected size. The size is computed from the number of event, and
what mandatory/optional fields are in your data. From your header,
the datafile should contain 1966080 events with normalization and
scatter correction factors. Each event will be composed of
(time(uint32) + event value (FLNTBDATA) + scat factor (FLTNBDATA)
+ norm factor (FLTNBDATA) + 2*ID (2*uint32). As you said, default
FLNTBDATA is 32-bits floats, so this means the code will expect a
datafile with a size equal to 1966080*(6*4bytes) = 47185920 bytes.
(The error message erroneously states the expected size is
39321600 bytes because there is a small typo in your data header
for the normalization field. It should be "Normali<b>z</b>ation
correction flag" instead of "Normali<b>s</b>ation correction
flag", unless it won't enable normalization factors).</p>
<p>Now looking at your binary datafile with an hexa editor, it seems
your conversion stopped after 58354 events (see attached file) for
some reasons. Besides, each event has the correct number of
fields, but it seems that all pixel data and scat factor are
equals to 0.</p>
<p>Hope it helps !</p>
<p>Best regards,</p>
<p>Thibaut</p>
<p><br>
</p>
<p><br>
</p>
<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>
<br>
<div class="moz-cite-prefix">On 02/08/2017 20:18, SCUFFHAM, James
(ROYAL SURREY COUNTY HOSPITAL NHS FOUNDATION TRUST) wrote:<br>
</div>
<blockquote
cite="mid:9475bdb1e33243a0af6928c506e6fb2b@NH-SLPEX096.AD1.NHS.NET"
type="cite">
<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]-->
<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" style="border-collapse:collapse"
border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="width:196.8pt;padding:0cm 5.4pt 0cm 5.4pt"
valign="top" width="262">
<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 style="width:160.4pt;padding:0cm 5.4pt 0cm 5.4pt"
valign="top" width="214">
<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 style="width:178.6pt;padding:0cm 5.4pt 0cm 5.4pt"
valign="top" width="238">
<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 style="width:196.8pt;padding:0cm 5.4pt 0cm 5.4pt"
width="262"><br>
</td>
<td style="width:160.4pt;padding:0cm 5.4pt 0cm 5.4pt"
width="214"><br>
</td>
<td style="width:178.6pt;padding:0cm 5.4pt 0cm 5.4pt"
width="238">
<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
style="font-size:10.0pt;font-family:"Tahoma","sans-serif""
lang="EN-US">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif""
lang="EN-US"> Castor-users
[<a class="moz-txt-link-freetext" href="mailto:castor-users-bounces@lists.castor-project.org">mailto:castor-users-bounces@lists.castor-project.org</a>]
<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> <a class="moz-txt-link-abbreviated" href="mailto:castor-users@lists.castor-project.org">castor-users@lists.castor-project.org</a><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 id="Picture_x0020_1"
src="cid:part1.97A3E863.F4365B23@univ-brest.fr"
alt="Inline image 1" height="190" width="560"><br>
<br>
<br>
<img id="Picture_x0020_2"
src="cid:part2.FE9EB923.3E0849D6@univ-brest.fr"
alt="Inline image 2" height="179" width="560"> <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 moz-do-not-send="true"
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 moz-do-not-send="true" href="mailto:Castor-users@lists.castor-project.org" target="_blank">Castor-users@lists.castor-project.org</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" 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 color="Black" face="Courier New" 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,
<a class="moz-txt-link-freetext" href="https://portal.nhs.net/help/joiningnhsmail">https://portal.nhs.net/help/joiningnhsmail</a><br>
<br>
</font>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Castor-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Castor-users@lists.castor-project.org">Castor-users@lists.castor-project.org</a>
<a class="moz-txt-link-freetext" href="http://lists.castor-project.org/listinfo/castor-users">http://lists.castor-project.org/listinfo/castor-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>