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Hello Elia,<br>
<br>
My feeling is the image is converted to short integer. I suppose you
use clitkImageConvert to convert dicom to mha, could you try with
the option -t ushort please ?<br>
The black area you can see are the values >= 32767 (the short
max).<br>
<br>
Thomas<span style="color: rgb(23, 23, 23); font-family: "Segoe
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<br>
<div class="moz-cite-prefix">On 07/09/2021 16:30, Lombardo, Elia
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:b910b361d7d94661932d84c9719ce888@MITMB4.helios.med.uni-muenchen.de">
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<p class="MsoNormal"><span lang="IT">Dear vv team,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="IT"><o:p> </o:p></span></p>
<p class="MsoNormal">Me and my colleagues are using vv to
preprocess PET Dicom images for a project.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When opening some of the Dicom images in vv
we see many ‘black islands’, i.e. areas with large negative
values (top row in the image below). We then turn the negative
values to positive values for the island areas, convert dicom
to mha and get a reasonably well looking image (bottom row).<o:p></o:p></p>
<p class="MsoNormal"><img style="width:6.369in;height:4.7797in"
id="Picture_x0020_3"
src="cid:part1.B3646B81.EE4322A9@creatis.insa-lyon.fr"
class="" width="611" height="459"><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">However, we checked the exact data value in
a few points of interest and compared it with the PET values
displayed when opening the original dicom in a Raystation TPS
and saw some discrepancies (e.g. in Raystation we get a value
of 34000 while in the corrected mha opened in vv we have
31000).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is this issue known?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks in advance for your help!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal"><b><span style="color:#595959" lang="IT">Elia
Lombardo, M.Sc.<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span
style="font-size:9.0pt;color:#595959" lang="DE">Medizinische
Physik / Medical Physics<span style="letter-spacing:.6pt"><o:p></o:p></span></span></b></p>
<p class="MsoNormal"><span style="font-size:4.0pt;color:#595959"
lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959"
lang="DE">LMU Klinikum
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959"
lang="DE">Klinik und Poliklinik für Strahlentherapie und
Radioonkologie<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:4.0pt;color:#595959"
lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959"
lang="DE">Campus Großhadern | Marchioninistraße 15 |
81377 München<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:#595959"
lang="DE">Tel. 089 4400-73757<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;color:black"
lang="DE"><a href="mailto:Elia.Lombardo@med.uni-muenchen.de"
moz-do-not-send="true"><span style="color:blue">Elia.Lombardo@med.uni-muenchen.de</span></a></span><span
style="font-size:9.0pt;color:#595959" lang="DE"> |
</span><u><span style="font-size:9.0pt;color:blue" lang="DE"><a
href="http://www.lmu-klinikum.de/strahlentherapie-und-radioonkologie"
moz-do-not-send="true"><span style="color:blue">www.lmu-klinikum.de/strahlentherapie-und-radioonkologie</span></a></span></u><span
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<p class="MsoNormal"><span
style="font-size:8.0pt;font-family:"LMU
CompatilFact";color:#595959" lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;color:#595959"
lang="DE">Das Klinikum der Universität München ist eine
Anstalt des öffentlichen Rechts (AöR)<o:p></o:p></span></p>
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style="font-size:4.0pt;font-family:"LMU
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src="cid:part4.CA5E565F.04EBDB82@creatis.insa-lyon.fr"
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style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:13.5pt;font-family:Webdings;color:green"
lang="DE">PS:</span><span style="font-family:"LMU
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