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<p class="MsoNormal">Please post 3D Slicer specific question to the Slicer forum:<o:p></o:p></p>
<p class="MsoNormal"><a href="https://discourse.slicer.org">https://discourse.slicer.org</a><o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Andras<o:p></o:p></p>
<p class="MsoNormal"><a name="_MailEndCompose"><o:p> </o:p></a></p>
<span style="mso-bookmark:_MailEndCompose"></span>
<p class="MsoNormal"><b>From:</b> Community [mailto:community-bounces@itk.org] <b>
On Behalf Of </b>Ivan Hidrovo<br>
<b>Sent:</b> Monday, June 12, 2017 5:45 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></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hello community,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">I know that this is not an itk related question, but does anybody know how to input my own created 0-1 bit mask for general registration (BRAINS) in 3D slicer?
<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 Mon, Jun 12, 2017 at 2:31 PM, Andras Lasso <<a href="mailto:lasso@queensu.ca" target="_blank">lasso@queensu.ca</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">You must follow my example exactly. Lines are not allowed to be removed or reordered.<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">Andras<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>From:
</b><a href="mailto:ivan.hidrovo@gmail.com" target="_blank">Ivan Hidrovo</a><br>
<b>Sent: </b>Monday, June 12, 2017 3:28 PM<br>
<b>To: </b><a href="mailto:lasso@queensu.ca" target="_blank">Andras Lasso</a><o:p></o:p></p>
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<p class="MsoNormal"><br>
<b>Subject: </b>Re: [ITK] Question about applying registration transformation to another data set<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Dear Andras,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">We tried this :<br>
<br>
type: int<br>
dimension: 3<br>
sizes: 91 106 115<br>
endian: little<br>
encoding: raw<br>
data file: m1d0_ROIRegboxS.raw<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">It loaded nothing (at least not visible in the windows open)<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">but when we tried a mhd format it appears to show it:<br>
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<b>ObjectType = Image<br>
NDims = 3<br>
DimSize = 91 106 115<br>
ElementType = MET_INT<br>
ElementDataFile = m1d0_ROIRegboxS.raw</b><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">What are we doing wrong in the nrrd format.<o:p></o:p></p>
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<p class="MsoNormal">Can we go ahead with mhd ?<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 Mon, Jun 12, 2017 at 12:29 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">Dear Andras,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Thank you. <o:p></o:p></p>
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<p class="MsoNormal"><span class="m4012298218212017936hoenzb"><span style="color:#888888">-Ivan
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Jun 12, 2017 at 12:19 PM, Andras Lasso <<a href="mailto:lasso@queensu.ca" target="_blank">lasso@queensu.ca</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="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:</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">NRRD0004</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">type:
<b>short</b></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">dimension: 3</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">space: left-posterior-superior</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">sizes:
<b>256 256 130</b></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">space directions:
<b>(1.0,0,0) (0,1.0,0) (0,0,1.0)</b></span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">kinds: domain domain domain</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">endian: little</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">encoding: raw</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">space origin: (0.0,0.0,0.0)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Courier New";color:#1F497D">data file: myimage.raw</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Probably you only need to change
<i>type</i> (probably uchar, short, or double – see all options here: <a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fteem.sourceforge.net%2Fnrrd%2Fformat.html%23basic&data=02%7C01%7Classo%40queensu.ca%7Cf9bded9ae6454207bc0008d4b1c928e2%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636328924909734583&sdata=2WkBPYI0I%2FtaXtqiMxzdBPPtB8W7FoDXM%2B6JfMXBU3w%3D&reserved=0" target="_blank">
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).</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="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://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsubversion.assembla.com%2Fsvn%2Fslicerrt%2Ftrunk%2FMatlabBridge%2Fsrc%2FMatlabCommander%2Fcommandserver%2F&data=02%7C01%7Classo%40queensu.ca%7Cf9bded9ae6454207bc0008d4b1c928e2%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636328924909734583&sdata=WWT2Wu4ATC51JBOE7TFoFSx7O9u5USw0qVAYZ6YC1H0%3D&reserved=0" target="_blank">https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/</a>).</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">You can load the image by drag-and-dropping the .nrrd file into 3DSlicer application window.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Andras</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>From:</b> Community [mailto:<a href="mailto:community-bounces@itk.org" target="_blank">community-bounces@itk.org</a>]
<b>On Behalf Of </b>Ivan Hidrovo<br>
<b>Sent:</b> Monday, June 12, 2017 1:05 PM<br>
<b>To:</b> <a href="mailto:community@itk.org" target="_blank">community@itk.org</a><br>
<b>Subject:</b> Re: [ITK] Question about applying registration transformation to another data set<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello community,
<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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="mso-margin-top-alt:auto;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="mso-margin-top-alt:auto;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" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank you,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Ivan
<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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="mso-margin-top-alt:auto;margin-bottom:12.0pt">Hello all,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;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="mso-margin-top-alt:auto;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="mso-margin-top-alt:auto;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" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Ivan<o:p></o:p></p>
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