<div dir="ltr"><span style="font-size:12.8px">Thank you for your reply!</span><br style="font-size:12.8px"><span style="font-size:12.8px">I have some binary data which I load in Matlab and I reshape them to obtain my 3D image. I perform 2D semi-automatic segmentation (based on active contours and b-splines) where I obtain both the curve as a set of points as well as binary images which I then multiple with my original image. I then use isosurfaces to get the 3D model. </span><br style="font-size:12.8px"><div style="font-size:12.8px">What I want is to avoid performing the semi-automatic segmentation on each slice so I thought of creating a binary 3D model with missing slices and then do the interpolation. I will study now the "grow from seeds effect" and working with scripts on Slicer since I haven't done this before.. </div><div style="font-size:12.8px"><br></div><div style="font-size:12.8px">Best,</div><div style="font-size:12.8px">Thanos</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 21, 2017 at 3:27 PM, Andras Lasso <span dir="ltr"><<a href="mailto:lasso@queensu.ca" target="_blank">lasso@queensu.ca</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">





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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">It should be easy to write an executable like that. It can be either a standalone executable, or – if you want to use other effects or you don’t want to set up
 a build environment on multiple platforms and create distribution mechanism (software download page and/or app store) – then you can do it using 3D Slicer and a small Python script. See for example how to apply a Segment Editor effect in a script here: <a href="https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#How_to_run_segment_editor_effects_from_a_script" target="_blank">https://www.slicer.org/wiki/<wbr>Documentation/Nightly/<wbr>ScriptRepository#How_to_run_<wbr>segment_editor_effects_from_a_<wbr>script</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">How the rest of your pipeline is implemented (image loading, visualization, contouring, etc)?<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Andras<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></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"> thanos thanos [mailto:<a href="mailto:thanosxania@gmail.com" target="_blank">thanosxania@gmail.com</a>]
<br>
<b>Sent:</b> Thursday, September 21, 2017 8:22 AM<br>
<b>To:</b> Andras Lasso <<a href="mailto:lasso@queensu.ca" target="_blank">lasso@queensu.ca</a>><br>
<b>Cc:</b> <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a></span></p><div><div class="h5"><br>
<b>Subject:</b> Re: [ITK] [ITK-users] New Submission: ND morphological contour interpolation<u></u><u></u></div></div><p></p><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Hello Andras,<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Thank you very much for your answer. I already tried Slicer and the Segment Editor and it works fine. I was wondering if I can make an executable that I could use for my data (for example an .nrrd segmented volume with some slices missing). <u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Best regards,<u></u><u></u></p>
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<p class="MsoNormal">Thanos<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">On Wed, Sep 20, 2017 at 6:25 PM, Andras Lasso <<a href="mailto:lasso@queensu.ca" target="_blank">lasso@queensu.ca</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">If you want to see what the morphological contour interpolation filter can do, then download nightly version of 3D Slicer (<a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.slicer.org&data=02%7C01%7Classo%40queensu.ca%7Ca08e625765f04a0fac1408d500eb5119%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636415933050412732&sdata=ADd9uXu9%2FX%2BkJr5FW1P1vKgLtvzgpx8b8tQtel%2FWgE4%3D&reserved=0" target="_blank">www.slicer.org</a>)
 and try "Fill between slices" effect. Some information about the tool is available at 
<a href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fslicer.readthedocs.io%2Fen%2Flatest%2Fuser_guide%2Fmodule_segmenteditor.html&data=02%7C01%7Classo%40queensu.ca%7Ca08e625765f04a0fac1408d500eb5119%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636415933050412732&sdata=Dz2kfKpmJrib0je7bRayRVmqmCTLvmAbnQUL6eu92sU%3D&reserved=0" target="_blank">
http://slicer.readthedocs.io/<wbr>en/latest/user_guide/module_<wbr>segmenteditor.html</a>, but if you are stuck at any point then you can ask help at
<a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdiscourse.slicer.org&data=02%7C01%7Classo%40queensu.ca%7Ca08e625765f04a0fac1408d500eb5119%7Cd61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636415933050412732&sdata=SWrqY0hKYfYPc7UhOP%2FuAjl2WZDM%2F2pgEusdpmNG1Pk%3D&reserved=0" target="_blank">
https://discourse.slicer.org</a> - all questions are answered, typically within a few hours.<br>
<br>
Andras<br>
<br>
-----Original Message-----<br>
From: Community [mailto:<a href="mailto:community-bounces@itk.org" target="_blank">community-bounces@itk.<wbr>org</a>] On Behalf Of thanos<br>
Sent: Wednesday, September 20, 2017 10:21 AM<br>
To: <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a><br>
Subject: Re: [ITK] [ITK-users] New Submission: ND morphological contour interpolation<br>
<br>
Hello,<br>
<br>
Is there maybe an example for the morphological contour interpolation?<br>
I am working on Matlab for the segmentation of some 3D data and since I am currently segmenting semi-automatically slice by slice, it would be great if I could use this class..<br>
I also have a quite silly question.. I am aware about the "test" folder and data but I don't really understand what is used for... I had a look on the Software Guide on the chapter "How to create a module" but I still don't get it..<br>
<br>
Thank you very much.<br>
<br>
Best regards,<br>
Thanos<br>
<br>
<br>
<br>
--<br>
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