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<p>Hi Niccolo,</p>
<p>Thank you for your helpful remarks. The GATE utilities indeed
require some corrections and will be patched soon (current month).
For the moment, please try the code in the zip file enclosed to
this mail which should address point 1) and 2).</p>
<p>For 3), there is no current plan to support aliases. I will look
if it is possible to implement it in the next patch though. <br>
</p>
<p>4) seems looks like a path issue indeed. We'll have a look at it
for the next patch. For the moment, absolute patch should work
fine.</p>
<p>Best regards,</p>
<p>Thibaut<br>
</p>
<p><br>
</p>
<p> </p>
<br>
<div class="moz-cite-prefix">On 14/06/2017 16:21, CASToR wrote:<br>
</div>
<blockquote
cite="mid:616c0a78-6dc7-8578-e834-683ae3a1f55a@castor-project.org"
type="cite">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
Dear Castor users and developers,
<div><br>
</div>
<div>I'm trying to reconstruct the data coming from a scanner I
simulated with gate (MyScanner.mac). </div>
<div>When I use the castor-GATEMacToGeom the conversion goes fine
but I think there is something strange in the converted .geom
file (Myscanner.geom):</div>
<div><br>
</div>
<div>1) The .geom file generated by the utility contains the
following lines</div>
<div>
<p class="gmail-m_-8092076495502286594gmail-p1"><span
class="gmail-m_-8092076495502286594gmail-s1">layers size
depth : 12</span></p>
<p class="gmail-m_-8092076495502286594gmail-p1">layers size
transaxial : 1.6</p>
<p class="gmail-m_-8092076495502286594gmail-p1">layers size
axial : 1.6</p>
</div>
<div><br>
</div>
<div>I think that they should be like this:</div>
<p class="gmail-p1"><span class="gmail-s1">crystals size depth
: 12</span></p>
<p class="gmail-p1"><span class="gmail-s1">crystals size trans
: 1.6</span></p>
<p class="gmail-p1"><span class="gmail-s1">crystals size axial
: 1.6</span></p>
<p class="gmail-p1"><span class="gmail-s1"><br>
</span></p>
<p class="gmail-p1"><span class="gmail-s1">2) <font face="Menlo">In
the .mac file I provided you, the original rsector offset is
61.4 mm from the center of the FOV.</font></span></p>
<p class="gmail-p1"><span class="gmail-s1"> </span></p>
<p class="gmail-p1"><span class="gmail-s1">/gate/rsector/placement/setTranslation
61.4 mm </span></p>
<p class="gmail-p1"><span class="gmail-s1"></span></p>
<p class="gmail-p1"><span
style="font-variant-ligatures:no-common-ligatures;font-family:Menlo">In
the .geom file the scanner radius is reported as</span></p>
<p class="gmail-p1"><span
style="font-variant-ligatures:no-common-ligatures;font-family:Menlo">scanner
radius : 61.4 </span></p>
<div>However, If I understood correctly, the scanner radius should
be </div>
<div>61.4- crystals size depth/2.0. <br>
</div>
<p class="gmail-p1"><span class="gmail-s1"><br>
</span></p>
<p class="gmail-p1"><span class="gmail-s1">3) I noticed that the
utility doesn't support the </span><span
style="font-variant-ligatures:no-common-ligatures;font-family:Menlo">/control/alias
statement of GATE is there any plan to implement it? </span><br>
</p>
<p class="gmail-p1"><br>
</p>
<p class="gmail-p1"><span class="gmail-s1">4) Minor thing: </span></p>
<p class="gmail-p1">When I run the GATERootToCastor utily </p>
<p class="gmail-p1"> </p>
<p class="gmail-p1">./castor-GATERootToCastor -i
~/prova_nick/PointSource_X0_Y0_Z0.root -m
~/MyScanner/MyScanner/example_castor.mac -o ./test-output -s
MyScanner<br>
</p>
<p class="gmail-p1"><span class="gmail-s1"> </span></p>
<p class="gmail-p1">I got this error <br>
</p>
<p class="gmail-p1">0 :
/home/nick/MyScanner/MyScanner/example_castor.mac</p>
<p class="gmail-p1">1 :
/home/nick/MyScanner/MyScanner//home/nick/MyScanner/MyScanner/MyScanner/MyScanner_geometry_castor.mac</p>
<p class="gmail-p1"><span class="gmail-s1">2 :
/home/nick/MyScanner/MyScanner//home/nick/MyScanner/MyScanner/MyScanner/NEMACubePhantom.mac</span></p>
<p class="gmail-p1"><span class="gmail-s1">3 :
/home/nick/MyScanner/MyScanner//home/nick/MyScanner/MyScanner/MyScanner/NEMACubeSource.mac</span></p>
<p class="gmail-p1"><span class="gmail-s1">4 :
/home/nick/MyScanner/MyScanner//home/nick/MyScanner/MyScanner/MyScanner/MyScanner_digitizer.mac</span></p>
<p class="gmail-p1"><span class="gmail-s1">5 :
/home/nick/MyScanner/MyScanner//home/nick/MyScanner/MyScanner/MyScanner/MyScanner_physics_castor.mac</span></p>
<p class="gmail-p1"><span class="gmail-s1">*****
GetGATESystemType() -> Error : Couldn't open mac file
/home/nick/MyScanner/MyScanner//home/nick/MyScanner/MyScanner/MyScanner/MyScanner_geometry_castor.mac
!</span></p>
<p class="gmail-p1"><span class="gmail-s1">*****
castor-GATERootToCastor :: GATE system type not found : </span></p>
<p class="gmail-p1"><span class="gmail-s1">
This script only supports conversion for cylindricalPET
and ecat systems</span></p>
<p class="gmail-p1"><span class="gmail-s1">
The system type is recovered from the lines
'/gate/systems/...'</span></p>
<p class="gmail-p1"><span class="gmail-s1"> </span></p>
<p class="gmail-p1"><span class="gmail-s1">***** Exit function
called. Abort with code 1.</span></p>
<p class="gmail-p1"><span class="gmail-s1">I think that this is
due to the path of the file </span>~/MyScanner/MyScanner/example_castor.mac
begin process in a wrong way.</p>
<p class="gmail-p1"><br>
</p>
<p class="gmail-p1"><span class="gmail-s1">Thank you for your
support and best regards</span></p>
<p class="gmail-p1"><span class="gmail-s1"><br>
</span></p>
<p class="gmail-p1"><span class="gmail-s1">Niccolo' Camarlinghi <br>
</span></p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</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>
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