<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Dan,<br>
See the website, download page, for instructions how to access the svn repository.
<br>
Cheers,<br>
Stefan<br>
<br>
<div class="moz-cite-prefix">On 08/04/2013 16:33, Dan Xu wrote:<br>
</div>
<blockquote cite="mid:CAM+PfKGzTTgPjJPmgrfniyzM37eBjPsPkrq1yFVijby-0p6WcQ@mail.gmail.com" type="cite">
<div>Hi Chris,</div>
<div>Thank you for your detailed reply. Could you let me know how to get your files? I assume that you have modified the original Elastix. Sorry I'm not familar with "trunkpublic".</div>
<div> </div>
<div>Thanks,</div>
<div>Dan<br>
<br>
</div>
<div class="gmail_quote">On Mon, Apr 8, 2013 at 3:05 AM, Chris Bouwman <span dir="ltr">
<<a moz-do-not-send="true" href="mailto:Chris.Bouwman@pie.nl" target="_blank">Chris.Bouwman@pie.nl</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px
          0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div vlink="blue" link="blue" lang="NL">
<div>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt">Hello Stefan, Dan,</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Here a small guideline to generate and use elastix dll:</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><u><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">generate project using CMAKE</span></font></u></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">To Generate the dll, get the latest files from the trunkpublic.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Generate the project using CMake (remove checkmark from setting ELASTIX BUILD EXECUTABLE).</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">The following types are used on the interface:</span></font></p>
<p class="MsoNormal"><u><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">images:</span></font></u><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">itk::image<TPixel,VImageDimension></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Note that these image must be passed to the dll as a itk::DataObject::Pointer, this can be reached by calling GetPointer() on the itk::image.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">note that the pixel type of mask images must be unsigned char!</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">The result image pixeltype must be the type as specified in the registration parameters (parameter "ResultImagePixelType"). Note that
 for now elastix can only handle short and unsigned short pixel types.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><u><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">registration parameters:</span></font></u></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Are passed to the dll as a ParameterMapType being a std::map<> containing a string holding the Parametername and a vector<std::string>
 containing one or more parameter values.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><u><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">todo</span></font></u></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">For now the dll can only generate a result image. I also added functionality that enables the user to get the applied transformation.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Furthermore I adapted the code to generate a transformix dll.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">However, I have not committed these changes to the trunckpublic so far.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Dan, I do not know what Blitz++ is, so I don't now if that works.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Regards,</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB">Chris Bouwman.</span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial"><span style="FONT-FAMILY:Arial;COLOR:navy;FONT-SIZE:10pt" lang="EN-GB"> </span></font></p>
<div>
<div style="TEXT-ALIGN:center" class="MsoNormal" align="center"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt" lang="EN-US">
<hr align="center" size="2" width="100%">
</span></font></div>
<p class="MsoNormal"><b><font face="Tahoma"><span style="FONT-FAMILY:Tahoma;FONT-SIZE:10pt;FONT-WEIGHT:bold" lang="EN-US">From:</span></font></b><font face="Tahoma"><span style="FONT-FAMILY:Tahoma;FONT-SIZE:10pt" lang="EN-US"> Dan Xu [mailto:<a moz-do-not-send="true" href="mailto:danxu2008@gmail.com" target="_blank">danxu2008@gmail.com</a>]
<br>
<b><span style="FONT-WEIGHT:bold">Sent:</span></b> donderdag 4 april 2013 22:03<br>
<b><span style="FONT-WEIGHT:bold">To:</span></b> S. Klein<br>
<b><span style="FONT-WEIGHT:bold">Cc:</span></b> Elastix; Chris Bouwman<br>
<b><span style="FONT-WEIGHT:bold">Subject:</span></b> Re: question on Elastix</span></font><span lang="EN-US"></span></p>
</div>
<div>
<div class="h5">
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">Hi Stefan</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">Thank you very much for the information.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">Chris,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">Could you shed some light on how to call/modify Elastix functions so that it accepts 3D image data (e.g., multidimensional array in Blitz++) in memory as input?</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">Thank you,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">Dan</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt"><br>
<br>
 </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">On Thu, Apr 4, 2013 at 9:45 AM, S. Klein <<a moz-do-not-send="true" href="mailto:s.klein@erasmusmc.nl" target="_blank">s.klein@erasmusmc.nl</a>> wrote:</span></font></p>
<div bgcolor="#FFFFFF" text="#000000">
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt">Hi Dan,
<br>
Thanks for your interest in elastix. I forward your mail to the mailing list. You can subscribe to this via the website.
<br>
Chris Bouwman (cc, but I think he's on the list as well) has developed a library interface for elastix. It's still work in progress, but you could already give it a try.<br>
Chris, could you give a few hints on how to start?<br>
Cheers,<br>
Stefan </span></font></p>
<div>
<div>
<p style="MARGIN-BOTTOM:12pt" class="MsoNormal"><font face="Times New
                              Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
<div>
<p class="MsoNormal"><font face="Times New
                                Roman" size="3"><span style="FONT-SIZE:12pt">On 03/04/2013 20:31, Dan Xu wrote:</span></font></p>
</div>
<blockquote style="MARGIN-TOP:5pt;MARGIN-BOTTOM:5pt" type="cite">
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt">Dear Stefan,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt">I'm trying to use your wonderfully put-together Elastix for some image volume registration. The command line based registration works
 fine. What I'd really like to do is to call your functions from my main c++ code (where tons of other functionalities, including image reconstruction, exist).
</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt">Could you give me some suggestions on how I should call/modify your functions so that it accepts 3D image data in memory as input, instead
 of from files? I'd also like to supply the parameters through input arguments, rather than from a file if possible.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt">The 3D image data format I use is the multidimensional array format in Blitz.</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt">Thanks a lot,</span></font></p>
</div>
<div>
<p class="MsoNormal"><font face="Times New
                                  Roman" size="3"><span style="FONT-SIZE:12pt">Dan</span></font></p>
</div>
</blockquote>
<p class="MsoNormal"><font face="Times New
                              Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
</div>
<pre cols="72"><font color="#888888" face="Courier New"><span style="COLOR:#888888;FONT-SIZE:10pt">-- </span></font></pre>
<pre><font color="#888888" face="Courier New"><span style="COLOR:#888888;FONT-SIZE:10pt">Stefan Klein</span></font></pre>
<pre><font color="#888888" face="Courier New"><span style="COLOR:#888888;FONT-SIZE:10pt"><a moz-do-not-send="true" href="tel:%2B31%2010%207043049" target="_blank" value="+31107043049">+31 10 7043049</a></span></font></pre>
<pre><font color="#888888" face="Courier New"><span style="COLOR:#888888;FONT-SIZE:10pt"><a moz-do-not-send="true" href="http://www.bigr.nl/people/StefanKlein" target="_blank">http://www.bigr.nl/people/StefanKlein</a></span></font></pre>
</div>
</div>
<p class="MsoNormal"><font face="Times New Roman" size="3"><span style="FONT-SIZE:12pt"> </span></font></p>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</blockquote>
<br>
<pre class="moz-signature" cols="72">-- 
Stefan Klein
+31 10 7043049
<a class="moz-txt-link-freetext" href="http://www.bigr.nl/people/StefanKlein">http://www.bigr.nl/people/StefanKlein</a></pre>
</body>
</html>