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<p class="MsoNormal"><span lang="FR" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Good afternoon Igne
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="FR" 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">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>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Castor-users <castor-users-bounces@lists.castor-project.org>
<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> castor-users@lists.castor-project.org<br>
<b>Subject:</b> [Castor-users] Problems with –im (involuntary patient motion correction)<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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 lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">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 lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">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 lang="EN-US" style="font-family:"Calibri",sans-serif;color:black">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 lang="EN-US" style="font-size:11.0pt;line-height:106%;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language: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 lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">Thanks in advance!</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
<p><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:black;mso-fareast-language:EN-US">Inge</span><span style="font-family:"Calibri",sans-serif;color:black"><o:p></o:p></span></p>
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