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<font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">Thanks Brad. Just another question: I used the </span></font><span style="font-size:11pt"><font face="Courier, Courier New">setPixelAsInt16 </font><font face="Calibri, Verdana, Helvetica, Arial">method, but it works per voxel. The issue is that I have to loop over 3 dimensions from within Matlab to call this method to construct an image object. This looping is extremely time consuming in Matlab. So a method where I can pass the entire 3D matrix would be very efficient for Matlab.<br>
<br>
Registration wrappers would be great and we all certainly look forward to having them.<br>
<br>
- Aditya<br>
<br>
<br>
<br>
On 4/19/12 9:44 AM, "Bradley Lowekamp" <<a href="blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>> wrote:<br>
<br>
</font></span><blockquote><span style="font-size:11pt"><font face="Calibri, Verdana, Helvetica, Arial">Hello,<br>
<br>
There are examples in the MICCAI 2011 tutorial presentation:<br>
<br>
<a href="http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK#SimpleITK_tutorial_at_MICCAI_2011">http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK#SimpleITK_tutorial_at_MICCAI_2011</a><br>
<br>
And there are those that are in the source code and in the Doxygen:<br>
<br>
<a href="http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK#SimpleITK_tutorial_at_MICCAI_2011">http://www.vtk.org/Wiki/ITK_Release_4/SimpleITK#SimpleITK_tutorial_at_MICCAI_2011</a><br>
<br>
Registration is still underdevelopment and it forthcoming. We have gone through a few prototypes and have settled on one but there is still a good bit of work to do.<br>
<br>
Brad<br>
<br>
<br>
On Apr 18, 2012, at 5:16 PM, <a href="aptea@mskcc.org">aptea@mskcc.org</a> wrote:<br>
<br>
</font></span><blockquote><span style="font-size:11pt"><font face="Calibri, Verdana, Helvetica, Arial">Re: [Insight-users] SimpleITK / jar wrapper? <br>
Thanks Brad. It works like a charm!!<br>
<br>
I tested it by reading in a Dicom image and calculating statistics on it. I am specifically interested in image Registration and Segmentation. Are there any examples for those?<br>
<br>
Thanks,<br>
Aditya<br>
<br>
<br>
On 4/18/12 4:29 PM, "Bradley Lowekamp" <<a href="blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a> <x-msg:<a href="//25/blowekamp@mail.nih.gov">//25/blowekamp@mail.nih.gov</a>> > wrote:<br>
<br>
</font></span><blockquote><span style="font-size:11pt"><font face="Calibri, Verdana, Helvetica, Arial">Hello,<br>
<br>
It appears that the Wrapping read me is a bit out of date. It would be good if you could add this issue to the SimpleITK issue tracker:<br>
<br>
<a href="https://itk.icts.uiowa.edu/jira/browse/SIMPLEITK">https://itk.icts.uiowa.edu/jira/browse/SIMPLEITK</a><br>
<br>
This visual guide is mostly current:<br>
<br>
<a href="http://www.vtk.org/Wiki/A_visual_guide_to_SimpleITK_in_Java">http://www.vtk.org/Wiki/A_visual_guide_to_SimpleITK_in_Java</a><br>
<br>
I believe the bit you need are:<br>
<br>
SimpleITK-build/Wrapping/simpleitk-0.5.0.jar<br>
SimpleITK-build/Wrapping/simpleitk-javadoc-0.5.0.jar<br>
SimpleITK-build/Wrapping/simpleitk-source-0.5.0.jar<br>
<br>
Then there is the needed java native shared library which currently is here:<br>
<br>
SimpleITK-build/lib/libSimpleITKJava.jnilib<br>
<br>
Which has moved since the release version from SimpleITK-build/Wrapping.<br>
<br>
<br>
<br>
On Apr 18, 2012, at 4:08 PM, <a href="aptea@mskcc.org">aptea@mskcc.org</a> <x-msg:<a href="//25/aptea@mskcc.org">//25/aptea@mskcc.org</a>> wrote:<br>
<br>
</font></span><blockquote><span style="font-size:11pt"><font face="Calibri, Verdana, Helvetica, Arial">Re: [Insight-users] SimpleITK / jar wrapper? <br>
Hello Brad,<br>
<br>
Thanks for your reply. I tried to build SimpleITK using the following procedure:<br>
</font></span><font size="1"><font face="Courier, Courier New"><span style="font-size:7pt">git clone --recursive <font color="#3866BB"><a href="http://itk.org/SimpleITK.git">http://itk.org/SimpleITK.git</a><br>
</font>mkdir SimpleITK-build<br>
cd SimpleITK-build<br>
</span></font></font><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt"><br>
Then, I used “make” to build SimpleITK. It ran until 32% completion, and gave the following message:<br>
<br>
</span></font><font size="1"><font face="Courier, Courier New"><span style="font-size:8pt">Linking CXX shared module ../lib/simpleitk.bundle<br>
ld: framework not found ruby<br>
collect2: ld returned 1 exit status<br>
make[5]: *** [lib/simpleitk.bundle] Error 1<br>
make[4]: *** [Wrapping/CMakeFiles/simpleitk.dir/all] Error 2<br>
make[3]: *** [all] Error 2<br>
make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2<br>
make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2<br>
make: *** [all] Error 2<br>
</span></font></font><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt"><br>
It did create simpleitk-0.4.0.jar file under SimpleITK-build/Wrapper directory. Then, I tried to use this .jar file within Matlab. For this, I added the file to classpath, but I am not able to load the classes within this file as described in the examples. For example, </span></font><font size="1"><font face="Courier, Courier New"><span style="font-size:9pt">org.itk.simple.ImageFileReader </span></font></font><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">could not be accessed and so on. The documentation under <a href="http://www.itk.org/SimpleITKDoxygen/html/Wrapping.html">http://www.itk.org/SimpleITKDoxygen/html/Wrapping.html</a> mentions that I should get </span></font><font size="1"><font face="Courier, Courier New"><span style="font-size:9pt">org.itk.simple.jar </span></font></font><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">file that contains the required classes. But I did not get this file when I built SimpleITK. So I am confused about where to find the java classes that wrap ITK functions.<br>
<br>
Thanks,<br>
Aditya<br>
<br>
<br>
<br>
On 4/18/12 3:49 PM, "Bradley Lowekamp" <<a href="blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a> <x-msg:<a href="//25/blowekamp@mail.nih.gov">//25/blowekamp@mail.nih.gov</a>> <x-msg:<a href="//497/blowekamp@mail.nih.gov">//497/blowekamp@mail.nih.gov</a> <x-msg:<a href="//497/blowekamp@mail.nih.gov">//497/blowekamp@mail.nih.gov</a>> > > wrote:<br>
<br>
</span></font><blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">Hello,<br>
<br>
The SimpleITK Getting Started wiki page a a section for Binaries:<br>
<br>
<a href="http://www.itk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Binaries">http://www.itk.org/Wiki/ITK_Release_4/SimpleITK/GettingStarted#Binaries</a><br>
<br>
Which points to SourceForge for the Java Binaries:<br>
<br>
<a href="http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/Java/">http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/Java/</a><br>
<br>
<br>
Where there is a download for Java for MacOSX 10.6:<br>
<br>
</span><font size="2"><span style="font-size:10pt">SimpleITK-0.4.0-Java-maxosx-10.6-intel.zip <<a href="http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/Java/SimpleITK-0.4.0-Java-maxosx-10.6-intel.zip/download">http://sourceforge.net/projects/simpleitk/files/SimpleITK/0.4.0/Java/SimpleITK-0.4.0-Java-maxosx-10.6-intel.zip/download</a>> <br>
</span></font><span style="font-size:11pt"><br>
This would likely also work for macOSX 10.7 as well.<br>
<br>
I also would like to know what was the issue when you tried to compile SimpleITK on OSX.<br>
<br>
Thanks,<br>
Brad<br>
<br>
<br>
<br>
On Apr 18, 2012, at 3:32 PM, <a href="aptea@mskcc.org">aptea@mskcc.org</a> <x-msg:<a href="//25/aptea@mskcc.org">//25/aptea@mskcc.org</a>> <x-msg:<a href="//497/aptea@mskcc.org">//497/aptea@mskcc.org</a> <x-msg:<a href="//497/aptea@mskcc.org">//497/aptea@mskcc.org</a>> > wrote:<br>
<br>
</span></font><blockquote><font face="Calibri, Verdana, Helvetica, Arial"><span style="font-size:11pt">SimpleITK / jar wrapper? <br>
Are SimpleITK Wrapper .jar files available for download?<br>
I failed to build SimpleITK for Mac OS X, so was wondering if I could use the binaries directly?<br>
Many thanks!<br>
<br>
<br>
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</span></font><font size="4"><span style="font-size:14pt">Bradley Lowekamp </span></font><font size="1"><span style="font-size:9pt"> <br>
<br>
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</span></font><font size="4"><span style="font-size:14pt"><a href="blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a> <x-msg:<a href="//25/blowekamp@mail.nih.gov">//25/blowekamp@mail.nih.gov</a>> <x-msg:<a href="//497/blowekamp@mail.nih.gov">//497/blowekamp@mail.nih.gov</a> <x-msg:<a href="//497/blowekamp@mail.nih.gov">//497/blowekamp@mail.nih.gov</a>> > <br>
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<br>
</span></font><font size="4"><span style="font-size:14pt">Medical Science and Computing for<br>
</span></font><font size="1"><span style="font-size:9pt"><br>
</span></font><font size="4"><span style="font-size:14pt">Office of High Performance Computing and Communications<br>
</span></font><font size="1"><span style="font-size:9pt"><br>
</span></font><font size="4"><span style="font-size:14pt">National Library of Medicine <br>
</span></font><font size="1"><span style="font-size:9pt"><br>
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