<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body>
<p><br>
</p>
<p>Hi Inge,</p>
<p><br>
</p>
<p>The building problem might come from the CMake configuration
file, as these projects have been relocated (now you must enable
CASToR_BUILD_SAMPLE_UTILITIES in cmake to build them). It should
not have caused issues to build the solution though, so I will
have a closer look at it.</p>
<p><br>
</p>
<p>Could you try to rebuild the 3.1 version with
CASToR_BUILD_SAMPLE_UTILITIES enabled ? Alternatively if there are
still some issues, you can use the configuration file from the
previous version in attachements (to replace the one in the castor
directory).</p>
<p><br>
</p>
<p>Let me know if this helps<br>
</p>
<p><br>
</p>
<p>Kind regards,</p>
<p>Thibaut</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 22/09/2020 09:41, Schagt, I.H. van
der wrote:<br>
</div>
<blockquote type="cite"
cite="mid:8036f73676b147818a4fa9bda11ce517@umcutrecht.nl">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<meta name="Generator" content="Microsoft Word 15 (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:"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;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",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
{mso-style-priority:99;
margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
p.MsoNoSpacing, li.MsoNoSpacing, div.MsoNoSpacing
{mso-style-priority:1;
margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.EmailStyle20
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:#1F497D;}
span.EmailStyle21
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:70.85pt 70.85pt 70.85pt 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]-->
<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>Dear Zacharis,</p>
<p><br>
</p>
<p>Thank you for your quick response.</p>
<p><span>As for oDynamicDataManager, in the datafile header a
start time and duration are indeed given, these are 0s and
900s respectively. <span>even though these values are
included, the frame time stop remains 0s when I apply
motion correction without framing.</span></span><br>
</p>
<p><span><span>I tried the new version of Castor (V3.1), but I
have trouble with configuring and building te program. C<span>onfiguring
only creates four projects in the solution (all_build,
<b>castor-recon</b>, install and zero_check) instead of
seven projects (all_build,
<b>castor-recon</b>, install, zero_check, <b>castor-datafileExplorer,
castor-imageDynamicTools and castor-scannerLUTExplorer</b>)
and this causes problems building the solution. </span></span></span></p>
<p><span><span><span><span>As far as configuring and building is
concerned, I did everything the same as with v_3.0.1.
I configured Castor with CMake and tried to build it
in Windows Visual Studio.</span><br>
</span></span></span></p>
<p><span><span><span><span><span>Do you know if the problem with
configuring and building could be with this new
version?</span><br>
</span></span></span></span></p>
<p><span><span><span><span><span><br>
</span></span></span></span></span></p>
<p><span><span><span><span><span>Kind regards,</span></span></span></span></span></p>
<p><span><span><span><span><span>Inge</span></span></span></span></span></p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>Van:</b>
Chalampalakis, Zacharias
<a class="moz-txt-link-rfc2396E" href="mailto:zacharias.chalampalakis@kcl.ac.uk"><zacharias.chalampalakis@kcl.ac.uk></a><br>
<b>Verzonden:</b> maandag 21 september 2020 18:21:32<br>
<b>Aan:</b> Schagt, I.H. van der;
<a class="moz-txt-link-abbreviated" href="mailto:castor-users@lists.castor-project.org">castor-users@lists.castor-project.org</a><br>
<b>Onderwerp:</b> RE: Problems with –im (involuntary patient
motion correction)</font>
<div> </div>
</div>
<div>
<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"
lang="FR">Good afternoon Igne
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"
lang="FR"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thank
you for your email.
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">We
actually just released a new version of CASToR ( V3.1 )
which fixed some bugs related to the handling of motion
timestamps.
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Maybe
you could try with this version , if it is not too
difficult , to check if the behaviour you experience is
related to these bugs ?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">In
the latest version , the
<i>oDynamidDataManager</i> will remove all timestamps that
occur after the end of the last frame.
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Normally
the duration of the frame ( even when not specifying
framing ) is set by the
<b>Start time (s) </b>and <b>Duration (s) </b>entries
in the datafile header. <o:p>
</o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Do
you have these entries in your datafile header?
<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Kind
Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Zacharias
Chalampalakis<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><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
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US"> Castor-users
<a class="moz-txt-link-rfc2396E" href="mailto:castor-users-bounces@lists.castor-project.org"><castor-users-bounces@lists.castor-project.org></a>
<b>On Behalf Of </b>Schagt, I.H. van der<br>
<b>Sent:</b> Monday, September 21, 2020 4:33 PM<br>
<b>To:</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> [Castor-users] Problems with –im
(involuntary patient motion correction)<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div id="divtagdefaultwrapper">
<p><span
style="font-family:"Calibri",sans-serif;color:black">Dear
all,<o:p></o:p></span></p>
<p><span
style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p class="MsoNoSpacing"><span
style="font-family:"Calibri",sans-serif;color:black"
lang="EN-US">I am having trouble with motion correction
reconstruction when using the –im option. When I try to
apply motion correction reconstruction I get the error:</span><span
style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNoSpacing" style="margin-left:35.4pt"><i><span
style="font-family:"Calibri",sans-serif;color:black"
lang="EN-US">Error, the 2th motion trigger timestamp:
xxx occurs after the end of the last frame (frame 1,
timestop: 0!</span></i><span
style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-family:"Calibri",sans-serif;color:black"
lang="EN-US">This error occurs in the code in the file
<i>oDynamicDataManager</i> line 413 and arises
incorrectly. When I do –im reconstruction in combination
with 1 frame (so no framing), the time stop value of the
frame remains 0s, it is not read from the data file. As
a result, the time steps of the motion triggers are
greater than the time stop value of the frame (line 407)
and you will eventually get an error. When I manually
adjust this time stop value to the correct value myself,
this error message goes away, but I get incorrect
reconstructed images. I only get black images after
reconstruction where each voxel has NaN as its value.
When I apply the same motion correction where I also
divide the data into, for example, 2 frames (-frm…), I
get correctly reconstructed images.</span><span
style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p style="line-height:106%"><span
style="font-size:11.0pt;line-height:106%;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"
lang="EN-US">Does anyone of you know why the option –im
gives these weird results, or what I maybe do wrong?<br>
I use list-mode PET data with a total duration of 900
seconds. For the motion correction, I used three motion
triggers (and deformations).</span><span
style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p><span
style="font-family:"Calibri",sans-serif;color:black"><o:p> </o:p></span></p>
<p><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"
lang="EN-US">Thanks in advance!</span><span
style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"
lang="EN-US">Inge</span><span
style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<div class="MsoNormal" style="text-align:center"
align="center">
<hr width="100%" size="5" align="center">
</div>
<p><i><span
style="font-size:7.5pt;font-family:"Arial",sans-serif;color:black">De
informatie opgenomen in dit bericht kan vertrouwelijk
zijn en is uitsluitend bestemd voor de geadresseerde.
Indien u dit bericht onterecht ontvangt, wordt u
verzocht de inhoud niet te gebruiken en de afzender
direct te informeren door het bericht te retourneren.
Het Universitair Medisch Centrum Utrecht is een
publiekrechtelijke rechtspersoon in de zin van de W.H.W.
(Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en
staat geregistreerd bij de Kamer van Koophandel voor
Midden-Nederland onder nr. 30244197. </span></i><o:p></o:p></p>
<p><i><span
style="font-size:7.5pt;font-family:"Arial",sans-serif;color:green">Denk
s.v.p aan het milieu voor u deze e-mail afdrukt.
</span></i><o:p></o:p></p>
<div class="MsoNormal" style="text-align:center"
align="center">
<hr width="100%" size="5" align="center">
</div>
<p><i><span
style="font-size:7.5pt;font-family:"Arial",sans-serif;color:black">This
message may contain confidential information and is
intended exclusively for the addressee. If you receive
this message unintentionally, please do not use the
contents but notify the sender immediately by return
e-mail. University Medical Center Utrecht is a legal
person by public law and is registered at the Chamber of
Commerce for Midden-Nederland under no. 30244197.
</span></i><o:p></o:p></p>
<p><i><span
style="font-size:7.5pt;font-family:"Arial",sans-serif;color:green">Please
consider the environment before printing this e-mail.
</span></i><o:p></o:p></p>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-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>
<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)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90</pre>
</body>
</html>