<div dir="ltr"><div><div><div>Hi all,<br><br></div>I build again the SimpleITK using the tag v0.8.0 from the git. Making the same experiment, I do not get the same error of serie not found.<br></div>However, I have an issue as problematic since that whatever the serie ID passed as argument, the dicom_names return belong to the first ID serie.<br><br></div>Did anybody got the issue with 0.8.0 build?<br><div><div class="gmail_extra"><br></div><div class="gmail_extra">Cheers,<br><br></div><div class="gmail_extra"><div class="gmail_quote">On 3 November 2014 22:38, Guillaume Lemaître <span dir="ltr"><<a href="mailto:g.lemaitre58@gmail.com" target="_blank">g.lemaitre58@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Dave<br><div><br>I build SimpleITK through anaconda recipe. I check and the versions are: SimpleITK 0.9.0 and ITK 4.6.1<br></div><div>I will downgrade the build to be able to work. Let me know if I can help to fix this issue.<br><br>Cheers,<br></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On 3 November 2014 22:23, David Chen <span dir="ltr"><<a href="mailto:dchen@mail.nih.gov" target="_blank">dchen@mail.nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div>Hi Guillaume</div><div><br></div>What version of SimpleITK are you running?  I tried your script using the current git master, and it doesn’t work for me.  But when I ran it using SimpleITK 0.8.0 it does.  So clearing something has gone wrong that we have to figure out.  For now, try and use 0.8.0.<br><div><font color="#0f61c8"><br></font></div><div><font color="#0f61c8"><br></font></div><div><font color="#0f61c8">Cheers,</font></div><div><font color="#0f61c8">Dave</font></div><div><font color="#0f61c8"><br><br></font><blockquote type="cite"><div style="word-wrap:break-word"><div><b>From: </b>Guillaume Lemaître <<a href="mailto:g.lemaitre58@gmail.com" target="_blank">g.lemaitre58@gmail.com</a>><br><b>Subject: </b><b>[ITK-users] SimpleITK - Reading different DICOM serie</b><br><b>Date: </b>October 31, 2014 at 7:03:36 PM EDT<br><b>To: </b>"<a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a>" <<a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a>><div><div><br><blockquote type="cite"></blockquote><font color="#007316"><br></font>Hi all,<br><font color="#007316"><br></font>I am currently using SimpleITK with python to read directly some DICOM data.<br>My dataset is corresponding to an MRI modality composed of 40 series. Each serie is a 3D volume.<br><font color="#007316"><br></font>I would like to read the serie one-by-one. As a minimal example, I can post the following code:<br><font color="#007316" face="courier new, monospace"><br></font><span style="font-size:x-small;font-family:'courier new',monospace;color:rgb(0,0,255)">reader</span><span style="font-size:x-small;font-family:'courier new',monospace"> = sitk.ImageSeriesReader()</span><br><span style="color:rgb(0,255,0);font-family:'courier new',monospace;font-size:x-small"># For each serie found</span><br><span style="font-family:'courier new',monospace;font-size:x-small;color:rgb(255,0,0)">for</span><span style="font-family:'courier new',monospace;font-size:x-small"> serie </span><span style="font-family:'courier new',monospace;font-size:x-small;color:rgb(255,0,0)">in</span><span style="font-family:'courier new',monospace;font-size:x-small"> </span><span style="font-family:'courier new',monospace;font-size:x-small">reader</span><span style="font-family:'courier new',monospace;font-size:x-small">.GetGDCMSeriesIDs(path_to_data):</span><br><span style="font-family:'courier new',monospace;font-size:x-small">   </span><span style="font-family:'courier new',monospace;font-size:x-small;color:rgb(56,118,29)"> <span style="color:rgb(0,255,0)"># Get the dicom filename corresponding to the current serie</span></span><br><span style="font-family:'courier new',monospace;font-size:x-small">    </span><span style="font-family:'courier new',monospace;font-size:x-small;color:rgb(0,0,255)">dicom_names</span><span style="font-family:'courier new',monospace;font-size:x-small"> = </span><span style="font-family:'courier new',monospace;font-size:x-small">reader</span><span style="font-family:'courier new',monospace;font-size:x-small">.GetGDCMSeriesFileNames(path_to_data, serie)</span><br><span style="font-family:'courier new',monospace;font-size:x-small">    </span><span style="font-family:'courier new',monospace;font-size:x-small">reader</span><span style="font-family:'courier new',monospace;font-size:x-small">.SetFileNames(dicom_names)</span><br><span style="font-family:'courier new',monospace;font-size:x-small">    </span><span style="font-family:'courier new',monospace;font-size:x-small;color:rgb(0,0,255)">image</span><span style="font-family:'courier new',monospace;font-size:x-small"> = </span><span style="font-family:'courier new',monospace;font-size:x-small">reader</span><span style="font-family:'courier new',monospace;font-size:x-small">.Execute()</span><br><font color="#007316"><br></font>I got the following error:<br><font color="#007316"><br></font><span style="font-family:'courier new',monospace;font-size:x-small">WARNING: In /home/lemaitre/anaconda/conda-bld/work/build/ITK/Modules/IO/GDCM/src/itkGDCMSeriesFileNames.cxx, line 138</span><br><span style="font-family:'courier new',monospace;font-size:x-small">GDCMSeriesFileNames (0x3078840): No Series were found</span><br><font color="#007316"><br></font>However, the output of<font size="1"><span style="font-family:courier new,monospace"> reader.GetGDCMSeriesIDs(path_to_data)</span></font> seems ok:<br><span style="font-size:x-small;font-family:'courier new',monospace">('1.2.826.0.1.3680043.2.1125.1.12083572272639445972057901411530444',</span><br><span style="font-size:x-small;font-family:'courier new',monospace"> ............................ 40 lines ...........................</span><br><span style="font-size:x-small;font-family:'courier new',monospace"> '1.2.826.0.1.3680043.2.1125.1.98804240625293208256969403455867278')</span><br><font color="#007316"><br></font>So my question is the following. What is the right way to passing the serieID to the <font size="1"><span style="font-family:courier new,monospace">GetGDCMSeriesFileNames</span><span style="font-family:courier new,monospace">()</span></font> function.<br><font color="#007316"><br></font>Thanks in advance,<br><font color="#007316"><br></font>Best regards,<br>-- <br><table style="font-family:'Times New Roman';width:638px" border="0" cellpadding="0"><tbody><tr style="height:37.5pt"><td style="width:228px;height:37.5pt;padding:0.75pt" align="left" valign="top"><b><span style="font-family:Arial,Helvetica;font-size:8pt">LEMAÎTRE Guillaume</span><span style="font-size:8pt;font-family:Helvetica"><br></span><font size="1"><span style="font-family:Arial">PhD Candiate<br>MSc Erasmus Mundus ViBOT (Vision-roBOTic)<br></span></font><span style="font-size:7.5pt;font-family:Arial" lang="EN-GB">MSc Business Innovation and Technology Management<br></span></b><span style="font-size:7.5pt;font-family:Arial" lang="EN-GB"><b><br></b><font color="#0DB02B"><a href="mailto:g.lemaitre58@gmail.com" target="_blank">g.lemaitre58@gmail.com</a><br><br></font></span><div><br></div></td><td style="width:400px;height:37.5pt;padding:0.75pt" align="left" valign="top"><span style="font-size:8pt"><b><span style="font-family:Arial,Helvetica">ViCOROB - Computer Vision and Robotic Team</span></b></span><span style="font-size:7.5pt;font-family:Arial"><br>Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona<br>Tel. <a href="tel:%2B34%20972%2041%2098%2012" value="+34972419812" target="_blank">+34 972 41 98 12</a> - Fax. <a href="tel:%2B34%20972%2041%2082%2059" value="+34972418259" target="_blank">+34 972 41 82 59</a> </span><br><span lang="EN-GB"><a href="http://vicorob.udg.es/" style="font-family:Arial;font-size:7.5pt" target="_blank">http://vicorob.udg.es/</a><br><b><font face="Arial, Helvetica"><span style="font-size:11px">LE2I - Le Creusot</span></font><br></b><font face="Arial" size="1">IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot<br>Tel. <a href="tel:%2B33%203%2085%2073%2010%2090" value="+33385731090" target="_blank">+33 3 85 73 10 90</a></font><span style="font-family:Arial;font-size:x-small"> - Fax. <a href="tel:%2B33%203%2085%2073%2010%2097" value="+33385731097" target="_blank">+33 3 85 73 10 97</a></span><span style="font-family:Arial;font-size:x-small"> </span><span style="font-family:Arial;font-size:x-small"><br></span><span style="font-family:Arial;font-size:7.5pt" lang="EN-GB"><a href="http://le2i.cnrs.fr/" target="_blank">http://le2i.cnrs.fr</a></span></span></td></tr></tbody></table><img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103962984/config/le2i.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103388011/config/vico.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103887254/config/ub.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103809482/config/udg.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340104225210/config/vibot.png"><br><a href="https://sites.google.com/site/glemaitre58/" target="_blank">https://sites.google.com/site/glemaitre58/</a><br>Vice - Chairman of A.S.C. Fours UFOLEP<br>Chairman of A.S.C. Fours FFC<br>Webmaster of <a href="http://ascfours.free.fr/" target="_blank">http://ascfours.free.fr</a><br><blockquote type="cite"></blockquote>_____________________________________<br><blockquote type="cite"></blockquote>Powered by <a href="http://www.kitware.com/" target="_blank">www.kitware.com</a><br><blockquote type="cite"></blockquote><font color="#007316"><br></font><blockquote type="cite"></blockquote>Visit other Kitware open-source projects at<br><blockquote type="cite"></blockquote><a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br><blockquote type="cite"></blockquote><font color="#007316"><br></font><blockquote type="cite"></blockquote>Kitware offers ITK Training Courses, for more information visit:<br><blockquote type="cite"></blockquote><a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br><blockquote type="cite"></blockquote><font color="#007316"><br></font><blockquote type="cite"></blockquote>Please keep messages on-topic and check the ITK FAQ at:<br><blockquote type="cite"></blockquote><a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br><blockquote type="cite"></blockquote><font color="#007316"><br></font><blockquote type="cite"></blockquote>Follow this link to subscribe/unsubscribe:<br><a href="http://public.kitware.com/mailman/listinfo/insight-users" target="_blank">http://public.kitware.com/mailman/listinfo/insight-users</a><br></div></div></div></div></blockquote></div><br></div></blockquote></div><br><br clear="all"><br>-- <br><div><div dir="ltr"><div><span style="font-family:'Times New Roman';font-size:medium"><table style="width:638px" border="0" cellpadding="0"><tbody><tr style="height:37.5pt"><td style="width:228px;height:37.5pt;padding-top:0.75pt;padding-right:0.75pt;padding-bottom:0.75pt;padding-left:0.75pt" align="left" valign="top"><b><span style="font-family:Arial,Helvetica;font-size:8pt">LEMAÎTRE Guillaume</span><span style="font-size:8pt;font-family:Helvetica"><br></span><font size="1"><span style="font-family:Arial">PhD Candiate<br>MSc Erasmus Mundus ViBOT (Vision-roBOTic)<br></span></font><span style="font-size:7.5pt;font-family:Arial" lang="EN-GB"><font color="#000000">MSc Business Innovation and Technology Management<br></font></span></b><span style="font-size:7.5pt;font-family:Arial" lang="EN-GB"><b><br></b><font color="#0DB02B"><a href="mailto:g.lemaitre58@gmail.com" target="_blank">g.lemaitre58@gmail.com</a><br><br></font></span><p></p></td><td style="width:400px;height:37.5pt;padding-top:0.75pt;padding-right:0.75pt;padding-bottom:0.75pt;padding-left:0.75pt" align="left" valign="top"><span style="font-size:8pt"><b><span style="font-family:Arial,Helvetica"><font color="#000000">ViCOROB - Computer Vision and Robotic Team</font></span></b></span><span style="font-size:7.5pt;font-family:Arial"><font color="#000000"><br>Universitat de Girona, Campus Montilivi, Edifici P-IV 17071 Girona<br>Tel. <a href="tel:%2B34%20972%2041%2098%2012" value="+34972419812" target="_blank">+34 972 41 98 12</a> - Fax. <a href="tel:%2B34%20972%2041%2082%2059" value="+34972418259" target="_blank">+34 972 41 82 59</a> </font></span><br><span lang="EN-GB"><a href="http://vicorob.udg.es/" style="font-family:Arial;font-size:7.5pt" target="_blank">http://vicorob.udg.es/</a><br><font color="#000000"><b><font face="Arial, Helvetica"><span style="font-size:11px">LE2I - Le Creusot</span></font><br></b><font face="Arial" size="1">IUT Le Creusot, Laboratoire LE2I, 12 rue de la Fonderie, 71200 Le Creusot<br>Tel. <a href="tel:%2B33%203%2085%2073%2010%2090" value="+33385731090" target="_blank">+33 3 85 73 10 90</a></font></font><span style="font-family:Arial;font-size:x-small"> - Fax. <a href="tel:%2B33%203%2085%2073%2010%2097" value="+33385731097" target="_blank">+33 3 85 73 10 97</a></span><span style="font-family:Arial;font-size:x-small"> </span><span style="font-family:Arial;font-size:x-small"><br></span><span style="font-family:Arial;font-size:7.5pt" lang="EN-GB"><a href="http://le2i.cnrs.fr" target="_blank">http://le2i.cnrs.fr</a></span></span></td></tr></tbody></table></span></div><div style="text-align:left"><img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103962984/config/le2i.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103388011/config/vico.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103887254/config/ub.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340103809482/config/udg.png">  <img src="https://sites.google.com/site/glemaitre58/_/rsrc/1340104225210/config/vibot.png"></div><a href="https://sites.google.com/site/glemaitre58/" target="_blank">https://sites.google.com/site/glemaitre58/</a><br>Vice - Chairman of A.S.C. Fours UFOLEP<br>Chairman of A.S.C. Fours FFC<br>Webmaster of <a href="http://ascfours.free.fr" target="_blank">http://ascfours.free.fr</a></div></div>
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