<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Title" content="">
<meta name="Keywords" content="">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Arial;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.msoIns
{mso-style-type:export-only;
mso-style-name:"";
text-decoration:underline;
color:teal;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body bgcolor="white" lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal">Hello Sara,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">As you correctly identified, the problem is with the version of SimpleITK. The addition of the meta-data dictionaries to the series reader was done after the release of version 1.0.0.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">As an immediate solution, you will need to build SimpleITK yourself. For Anaconda we have a build recipe on github:
<a href="https://github.com/SimpleITK/SimpleITKCondaRecipe#process">https://github.com/SimpleITK/SimpleITKCondaRecipe#process</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Please follow the detailed instructions there (read all of the instructions before you start the build as you will need to change the version of SimpleITK you are building, currently set to 1.0.0 and you need master).<o:p></o:p></p>
<p class="MsoNormal"><o:p></o:p></p>
<p class="MsoNormal"> regards<o:p></o:p></p>
<p class="MsoNormal"> Ziv<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Sara Gh <sg.ele.eng@gmail.com><br>
<b>Date: </b>Friday, June 23, 2017 at 11:47 AM<br>
<b>To: </b>"Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]" <zivrafael.yaniv@nih.gov><br>
<b>Cc: </b>"community@itk.org" <community@itk.org><br>
<b>Subject: </b>Re: [ITK] Problem with Writing Dicom Series<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Dear Ziv,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Thank you for your reply.</span>
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">I tried the sample code; however, I am getting below error:</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">'ImageSeriesReader' object has no attribute 'MetaDataDictionaryArrayUpdateOn'. Do you know how I should fix that? I have installed SimpleITK using python binary package for the Anaconda and currently,
its version is simpleitk 1.0.0-py27_0.</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><br>
<br>
</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Sincerely,</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Sara</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Wed, Jun 21, 2017 at 10:41 AM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <<a href="mailto:zivrafael.yaniv@nih.gov" target="_blank">zivrafael.yaniv@nih.gov</a>> wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello Sara,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Please take a look at this example on readthedocs (part of the Examples found in the SimpleITK source):<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="http://simpleitk.readthedocs.io/en/latest/Examples/DicomSeriesReadModifyWrite/Documentation.html" target="_blank">http://simpleitk.readthedocs.io/en/latest/Examples/DicomSeriesReadModifyWrite/Documentation.html</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Writing a valid DICOM series which contains all of the tag information you need may be tricky, depending on the information you need to encode in the meta-data dictionary (private
tags etc.).<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">As a side note, the problem you have with the series writer is that it is writing each of the images into its own series.
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> hope this helps<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Ziv<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Sara Gh <<a href="mailto:sg.ele.eng@gmail.com" target="_blank">sg.ele.eng@gmail.com</a>><br>
<b>Date: </b>Wednesday, June 21, 2017 at 10:19 AM<br>
<b>To: </b>"<a href="mailto:community@itk.org" target="_blank">community@itk.org</a>" <<a href="mailto:community@itk.org" target="_blank">community@itk.org</a>><br>
<b>Subject: </b>[ITK] Problem with Writing Dicom Series</span><o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello,
<o:p></o:p></p>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I have a question regarding writing Dicom series using SimpleITK in Python. I read a 3D scan, resampled it, and stored it as a Dicom series. However, when I try to read the stored
data, I am unable to load the whole 3D images and it only displays one of the slices. It seems that the header is corrupted. I would be thankful if someone could help me to fix this issue. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Here is my write method:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">def WriteDicomSeries(imagein,outDir):<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> writer = sitk.ImageSeriesWriter()<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> filenames = [ outDir+'MR_{0:04}.dcm'.format(i) for i in range(imagein.GetSize()[2])] <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> writer.SetFileNames(filenames)<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> writer.Execute(imagein)<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Sara<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</div>
</div>
</body>
</html>