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<p>Dear Alessandro,</p>
<p>Thank you for the feedback. <br>
</p>
<p>In histogram mode, the converter fills an histogram with all the
events recorded in the simulation. The histogram does not depend
on any geometry and blindly assumes all crystal combinations are
available, so that is why you end up with a very large file with a
lot of nil events. This could actually be improved by checking
first if the line is available depending on the transaxial angle
restriction in the geom file, but this is not implemented.</p>
<p>This does not usually lead to such artifacts as in your first
reconstruction, I believe this could be due to the octagonal
geometry. I will have a closer look at that. <br>
</p>
<p>I would however expect that removing all the zero-events from the
histogram could lead to artifacts, as in histogram mode the lines
of response in the histogram are used to generate the sensitivity
image. This doesn't appear in your second reconstructed image, but
that might be object/system dependent.</p>
<p>Normalization artifacts are also more or less visible depending
on the object. I believe they would be more visible with the
simulation of a large object with uniform activity. <br>
</p>
<p>Best regards,<br>
Thibaut<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 18/12/2020 10:08, Alessandro Pilleri
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAM3r8o-GZ-KOp+KTxgSLWSkULnpOMwKU3cwfe9y0RTPhodKg8g@mail.gmail.com">
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<div dir="ltr">
<div>Dear All,<br>
</div>
<div>with the intent to include the normalization coefficients I
was looking at the data file created by
castor-GATERootToCastor and I saw that It contains an odd
number of events (LORs), in which an event is identified by a
pair crystal1-crystal2. The scanner (with a coincidence scheme
of 1vs3) has ~9.7 million LORs but the entries in the data
file are more than 25 million. This event includes LOR
identified for example by crystals belonging to the same
module, even adjacent crystals, that are clearly not in
coincidence. The "amount" value for these events is equal to
zero. If I remove all the zero-amount events from the data
file and create a new histogram, the reconstruction shows no
artefacts, even without the application of the normalization
correction. I attach the images, left with all the events,
right after removing the zero-amount LORs.<br>
</div>
<div><br>
</div>
<div>Is this normal behaviour?</div>
<div><br>
</div>
<div>Best</div>
<div>Alessandro<br>
</div>
<div>
<div>
<div><br>
</div>
<div><br>
</div>
<div><img src="cid:part1.6020A452.AD1A6AA2@univ-brest.fr"
alt="image.png" class="" width="565" height="275"><br>
<br>
</div>
<div><br>
</div>
<div><br>
</div>
<br>
<div><br>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Dec 16, 2020 at 1:31
PM Alessandro Pilleri <<a href="mailto:a.pilleri@gmail.com"
moz-do-not-send="true">a.pilleri@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr"><br>
<div class="gmail_quote">
<div dir="ltr">
<div>Dear Simon,</div>
<div>thank you for your answer. <br>
</div>
<div><br>
</div>
<div>I used the GateRoot converter to create the data
file in histogram mode and to automatically generate
the geometry (-geo parameter). It automatically added
the 135 deg min angle difference in the .geom file. <br>
</div>
<div>I thought the min angle difference was applied in
the loop over the data, so I tried to change it in the
.geom file. By the way, now I created two different
data files changing the digitizer option in the gate
macfile to change the coincidence scheme and the
sensitivity images do look different.</div>
<div><br>
</div>
<div>For the application of the normalization
coefficients, in histogram mode, do I have to manually
modify the datafile to change the normalization
coefficients of the events from 1 to the appropriate
coefficient? <br>
</div>
<div><br>
</div>
<div>Alessandro<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Dec 16, 2020
at 11:42 AM STUTE Simon <<a
href="mailto:simon.stute@chu-nantes.fr"
target="_blank" moz-do-not-send="true">simon.stute@chu-nantes.fr</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div dir="ltr"
style="font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255);font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi Alessandro,</p>
<p><br>
</p>
<p>The artifacts are totally normal if you do not
apply a normalization correction, especially with
low number of detector panels.</p>
<p><br>
</p>
<p>As for the min angle difference, did you let
CASToR compute the sensitivity image in both cases
(135 and 180) ? Are they different ?</p>
<p>The min angle difference is not apply in the loop
over the data, so it should be applied by yourself
when building the datafile.</p>
<p>Also, how did you build the geometry of your
scanner, from your own LUT file or using the GATE
converter ?</p>
<p><br>
</p>
<p>By the way, your emails successfully reached the
mailing list.</p>
<p><br>
</p>
<p>Best</p>
<p>Simon<br>
</p>
<p><br>
</p>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block;width:98%">
<div
id="gmail-m_-5668255377793089237m_-5657436389587298817gmail-m_-7038651256240700032gmail-m_8150782361906084038gmail-m_1628418551026549971divRplyFwdMsg"
dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>De
:</b> Castor-users <<a
href="mailto:castor-users-bounces@lists.castor-project.org"
target="_blank" moz-do-not-send="true">castor-users-bounces@lists.castor-project.org</a>>
de la part de Alessandro Pilleri <<a
href="mailto:a.pilleri@gmail.com"
target="_blank" moz-do-not-send="true">a.pilleri@gmail.com</a>><br>
<b>Envoyé :</b> mardi 15 décembre 2020 16:37<br>
<b>À :</b> <a
href="mailto:castor-users@lists.castor-project.org"
target="_blank" moz-do-not-send="true">castor-users@lists.castor-project.org</a><br>
<b>Objet :</b> [Castor-users] artifacts in the
reconstruction</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Dear castor-users,</div>
<div>I give an update to my previous email.</div>
<div>I tried to change the min angle
difference in the geometry file from 135
(meaning a coincidence schema 1vs3) to 180
(meaning a coincidence schema 1vs1) and the
two reconstructions provided exactly the
same results.
<br>
</div>
<div><br>
</div>
<div>Could the artifact be related to some
kind of bug (or a misuse by my side) related
to the "min angle difference"?</div>
<div><br>
</div>
<div>Thank you</div>
<div>Alessandro<br>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</blockquote>
</div>
<br>
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<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>
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