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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Yes, you can load raw files into 3D Slicer. You just have to create a small text file that specifies how your raw file should be interpreted (pixel type, image
size, spacing). For example, if you have a raw file ‘myimage.raw’ create a text file called ‘myimage.nhdr’ in the same directory with the following content:<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:"Courier New";color:#1F497D">NRRD0004<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">type:
<b>short</b><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">dimension: 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">space: left-posterior-superior<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">sizes:
<b>256 256 130</b><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">space directions:
<b>(1.0,0,0) (0,1.0,0) (0,0,1.0)<o:p></o:p></b></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">kinds: domain domain domain<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">endian: little<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">encoding: raw<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">space origin: (0.0,0.0,0.0)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D">data file: myimage.raw<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">Probably you only need to change
<i>type</i> (probably uchar, short, or double – see all options here: <a href="http://teem.sourceforge.net/nrrd/format.html#basic">
http://teem.sourceforge.net/nrrd/format.html#basic</a>), <i>sizes</i> (image size in pixels), and
<i>space directions</i> (change 1.0 values to image spacing values).<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 create your images in Matlab then you can use nrrdwrite.m to write your matrix into a raw file along with a .nhdr text header file (<a href="https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/">https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/</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">You can load the image by drag-and-dropping the .nrrd file into 3DSlicer application window.<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"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Community [mailto:community-bounces@itk.org]
<b>On Behalf Of </b>Ivan Hidrovo<br>
<b>Sent:</b> Monday, June 12, 2017 1:05 PM<br>
<b>To:</b> community@itk.org<br>
<b>Subject:</b> Re: [ITK] Question about applying registration transformation to another data set<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello community, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Can you kindly tell me <br>
1) if you can input a threshold to an image on ITK when implementing an algorithm?
<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">For example when running registration I wish to use only voxel values within a lower and higher threshold<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">2) Also,do you know if you can use raw files in Slicer3D? we had difficulty putting raw data into slicer and hence switched to ITK<o:p></o:p></p>
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<p class="MsoNormal">Thank you,<o:p></o:p></p>
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<p class="MsoNormal">Ivan <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, Jun 9, 2017 at 12:08 PM, Ivan Hidrovo <<a href="mailto:ivan.hidrovo@gmail.com" target="_blank">ivan.hidrovo@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hello all,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">We are registering 2 data sets A and B using ImageRegistration8.cxx. We get an output dataset C registered to A and also some matrix numbers which we believe to be the rigid registration parameters.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"> We need to apply the same registration transformation to another data set (of a different modality) -- is there a way to use this code or another code to apply a given transformation to an image.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Or do we need to make small changes to the code to do this.<o:p></o:p></p>
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<p class="MsoNormal">thanks,<o:p></o:p></p>
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<p class="MsoNormal">Ivan<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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