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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If you need access to Matlab, ITK (SimpleITK), VTK, numpy, etc. in the same environment then you may consider using 3D Slicer with the MatlabBridge extension.
All the functions are available from the Python console and also from a graphical user interface.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">To access Matlab functions you only need to write a small XML file that describes the input and output data types. All the inputs and outputs (images, point
sets, transformations, scalar&vector values, etc.) are then automatically transferred to/from Matlab, so you don’t have to worry about writing and reading files. Graphical user interface is generated automatically for your Matlab function, too, so you can
define all the inputs on the Slicer GUI, run your Matlab function with a single click, and see the results immediately.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">More info:<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Demo video:
<a href="http://screencast.com/t/TgAVE6Wa8mf">http://screencast.com/t/TgAVE6Wa8mf</a><o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">3D Slicer:
<a href="http://ww.slicer.org">http://ww.slicer.org</a><o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:Symbol;color:#1F497D"><span style="mso-list:Ignore">·<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MatlabBridge:
<a href="https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Extensions/MatlabBridge">
https://www.slicer.org/slicerWiki/index.php/Documentation/4.3/Extensions/MatlabBridge</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Andras<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">________________________________</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Andras Lasso, PhD</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Senior Medical Image Computing & Applications Engineer<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Associate Director<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Laboratory for Percutanous Surgery<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">School of Computing<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Queen’s University</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Kingston, ON, CANADA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Arial","sans-serif";color:#595959">Web:
<a href="http://perk.cs.queensu.ca/">http://perk.cs.queensu.ca</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> community-bounces@itk.org [mailto:community-bounces@itk.org]
<b>On Behalf Of </b>Samuel Pichardo<br>
<b>Sent:</b> Thursday, December 12, 2013 10:33 AM<br>
<b>To:</b> zhq; ITK</span><span style="font-size:10.0pt;font-family:"PMingLiU","serif";color:windowtext">论坛</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"><br>
<b>Subject:</b> Re: [ITK Community] [Insight-users] I hope ITK read data from matlab , what should I do ?<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You could use Python to make the link between Matlab file and VTK<br>
<br>
read the file with numpy with <br>
<a href="http://docs.scipy.org/doc/scipy/reference/tutorial/io.html">http://docs.scipy.org/doc/scipy/reference/tutorial/io.html</a><br>
<br>
<br>
and save in VTK through the VTK wrapper<br>
<br>
<a href="https://code.google.com/p/devide/wiki/NumPyToVTK">https://code.google.com/p/devide/wiki/NumPyToVTK</a><br>
<br>
be sure of saving the Matlab file with -V6 option<br>
<br>
On 13-12-12 08:12 AM, zhq wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif"">Dear all :
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> I run matlab code , and get a data which is save as mat format file . Then , I wish segment the data with ITK . How can I read the data with ITK .<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> Can I save the data as vtk format file and then to read it with ITK ?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> The follow is what I has done :<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> ( In matlab :)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> save('MRI.vtk','MRAImgs') % the MRAImgs is the mat format data , I want to save the data as vtk format<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> ( In ITK :)<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> typedef itk::ImageFileReader<InternalImageType> ReaderType ; <o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> ReaderType::Pointer reader = ReaderType::New();<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> reader->SetFileName("G:\\Graduation Design\\ITK code\\MRI.vtk");<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> try<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> {<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> reader->Update();<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> }<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> catch( itk::ExceptionObject & excep )<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> <span class="apple-tab-span">
</span> {<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> std::cerr << "Exception caught !" << std::endl;<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> std::cerr << excep << std::endl;<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> system("pause");<o:p></o:p></span></p>
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<p class="MsoNormal"><span class="apple-tab-span"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""></span></span><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> }<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> But a error appears:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> <img border="0" width="655" height="250" id="_x0000_i1025" src="cid:image001.png@01CEF72D.36726A20"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> What should I do ?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""> Thanks in advance !<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif"">zhq<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
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<o:p></o:p></p>
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