<div dir="ltr"><div dir="ltr"><div>Hi,</div><div>1/ This implementation is known to have some issues and I think it should be revisited. I have opened an issue to track this</div><div><a href="https://github.com/SimonRit/RTK/issues/454">https://github.com/SimonRit/RTK/issues/454</a></div><div>If I remember correctly, someone identified at some point a problem with the patient mask, which was selecting air instead. In any case, the SPR might have no influence because one hits the <a href="http://www.openrtk.org/Doxygen/classrtk_1_1BoellaardScatterCorrectionImageFilter.html#ae8752f068ecb8b3208b360c1375ae0a6">non negativity constraints</a>. If you're willing to contribute, the <a href="https://github.com/SimonRit/RTK/blob/master/include/rtkBoellaardScatterCorrectionImageFilter.hxx#L64-L107">code</a> is fairly simple so feel free to investigate.</div><div>2/ I think that the problem is that FDK expect a full scan and you have a short scan. So the projections next to the gap get a huge weight. You need to apply Parker weighting similarly to rtkfdk, see <a href="https://github.com/SimonRit/RTK/blob/master/applications/rtkfdk/rtkfdk.cxx#L102-L117">here</a>.</div><div>From what I see in the code, the volume is not centered on the isocenter. I would also correct it with<br></div><div><font size="2"><span style="font-size:10pt"><pre style="background-color:rgb(43,43,43);color:rgb(169,183,198);font-family:"JetBrains Mono",monospace;font-size:9.8pt"><pre style="background-color:rgb(43,43,43);color:rgb(169,183,198);font-family:"JetBrains Mono",monospace;font-size:9.8pt">originVol = [-(sizeOutputVol[<span style="color:rgb(104,151,187)">0</span>] / <span style="color:rgb(104,151,187)">2 </span>- <span style="color:rgb(104,151,187)">0.5</span>) * spacingVol[<span style="color:rgb(104,151,187)">0</span>]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">-(sizeoutputVol[1] / 2 - 0.5) * spacingVol[1]</span><span style="color:rgb(204,120,50)">, </span>-(sizeOutputVol[<span style="color:rgb(104,151,187)">2</span>] / <span style="color:rgb(104,151,187)">2 -</span> <span style="color:rgb(104,151,187)">0.5</span>) * spacingVol[<span style="color:rgb(104,151,187)">2</span>]]<br></pre></pre></span></font></div></div><div>I hope it helps. Good luck with all this!</div><div>Simon<br></div><div><div class="gmail_quote"><div dir="ltr" class="gmail_attr"><br></div><div dir="ltr" class="gmail_attr">On Fri, Nov 5, 2021 at 4:07 PM Maspero, M. (Matteo) <<a href="mailto:M.Maspero@umcutrecht.nl">M.Maspero@umcutrecht.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div id="gmail-m_7158141332472973541divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<p>Dear rtk-users,</p>
<p><br>
</p>
<p>First of all a huge thanks to the developers of RTK, what a very powerful tool. Here I am am with a couple of points:</p>
<p><br>
</p>
<p>1) Boellaard scatter: after having performed multiple rtkfkd recons with different "spr" settings (from the complied C++ version), I could not find any differences between the reconstructed images. It seems like the scatter-to-primary ratio does not impact
the recon. Is this to be expected/does anyone experience the same?</p>
<p><br>
</p>
<p>2) F<span style="font-size:12pt">inally I had some time to dig in the python wrapped side of RTK and run some very basic recons on Elekta raw (XVI release > 5) data - based on the FirstRecon example - for benchmarking purposes. However, I do not get to the
desired result. I am pretty sure that is something quite superficial on my side, but any help is very welcome.</span></p>
<p><span style="font-size:12pt">So the reconstruction starts from the following projections:</span></p>
<p><span style="font-size:12pt"><img size="54921" id="gmail-m_7158141332472973541img413685" style="max-width: 99.9%;" src="cid:17d08ff76b07d6722a1"><br>
I get with the compiled version of C++</span></p>
<p><span style="font-size:12pt"><img size="86799" id="gmail-m_7158141332472973541img339014" style="max-width: 99.9%;" src="cid:17d08ff76b2be0c196f2"><br>
while when trying my own recon, I get</span></p>
<p><span style="font-size:12pt"><img size="63784" id="gmail-m_7158141332472973541img319115" style="max-width: 99.9%;" src="cid:17d08ff76b2bd8523f33"><br>
<br>
</span></p>
<p></p>
<p><span style="font-size:12pt">To me, it seems that the geometry/axis orientation is somewhat incorrect. Trying to facilitate coming up with some suggestions, I put at the end of the mail an excerpt of the code, maybe you spot the issue right away. If you
may appreciate a dataset to reproduce the problem, just let me know. Again, any suggestion is welcome, especially if a quick look from someone else may speed up things on this side.</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Thank you very much in advance.</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Best Regards and have a great weekend,</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Matteo</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<div id="gmail-m_7158141332472973541Signature">
<div id="gmail-m_7158141332472973541divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols">
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
<div style="font-family:Tahoma;font-size:13px">
<div><font size="2"><span style="font-size:10pt">
<div> Matteo Maspero</div>
<div>| Clinical scientist/Postdoc<br>
| Radiotherapy, Imaging and Cancer</div>
<div><span style="font-size:10pt">| Computational Imaging Group <a href="http://www.compimag.org" id="gmail-m_7158141332472973541LPNoLP" target="_blank">www.compimag.org</a></span></div>
<div>| Center for Image Sciences<br>
| University Medical Center Utrecht</div>
<div><span style="font-family:Tahoma;font-size:13.3333px">| Free on Wednesdays</span><br>
| Room Q.02.2.315<br>
| P.O. 85500<br>
| Heidelberglaan 100, 3508 GA Utrecht, Netherlands<br>
| E: <a href="mailto:m.maspero@umcutrecht.nl" target="_blank">m.maspero@umcutrecht.nl</a><br>
| Tel +31-8875 67492 / <span style="font-family:Tahoma;font-size:13.3333px">+31-614956534</span><br>
| Fax +31-8875 55850<br>
</div>
<div><br>
</div>
<div>--------------------- code excerpt ----</div>
<div>
<pre style="background-color:rgb(43,43,43);color:rgb(169,183,198);font-family:"JetBrains Mono",monospace;font-size:9.8pt"><span style="color:rgb(204,120,50)"></span><pre style="background-color:rgb(43,43,43);color:rgb(169,183,198);font-family:"JetBrains Mono",monospace;font-size:9.8pt"><span style="color:rgb(204,120,50)">import </span>sys<br><span style="color:rgb(204,120,50)">import </span>os<br><span style="color:rgb(204,120,50)">import </span>matplotlib.pyplot <span style="color:rgb(204,120,50)">as </span>plt<br><span style="color:rgb(204,120,50)">import </span>glob<br><span style="color:rgb(204,120,50)">import </span>itk<br><span style="color:rgb(204,120,50)">from </span>itk <span style="color:rgb(204,120,50)">import </span>RTK <span style="color:rgb(204,120,50)">as </span>rtk <br><span style="color:rgb(128,128,128)"># image definition<br></span>CPUImageType = rtk.Image[itk.F<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span>]<br><br><span style="color:rgb(128,128,128)"># TMP, pt_dir are the folders with the data <br></span><span style="color:rgb(128,128,128)"># Flags<br></span>Flag_saveProj = <span style="color:rgb(106,135,89)">"on"<br></span><span style="color:rgb(106,135,89)"><br></span><span style="color:rgb(128,128,128)"># geometry -> read xml<br></span>geometryReader = rtk.ThreeDCircularProjectionGeometryXMLFileReader.New()<br>geometryReader.SetFilename(TMP + <span style="color:rgb(106,135,89)">"elektaGeometry"</span>)<br>geometryReader.GenerateOutputInformation()<br>geometry = geometryReader.GetGeometry()<br><br><span style="color:rgb(128,128,128)"># List of filenames<br></span>fileNames = <span style="color:rgb(136,136,198)">list</span>()<br><span style="color:rgb(128,128,128)"># Get list of all files in a given directory sorted by name<br></span>fileNames = <span style="color:rgb(136,136,198)">sorted</span>( <span style="color:rgb(136,136,198)">filter</span>( os.path.isfile<span style="color:rgb(204,120,50)">,<br></span><span style="color:rgb(204,120,50)"> </span>glob.glob(pt_dir + <span style="color:rgb(106,135,89)">'*his'</span>)))<br><br>projReader = rtk.ProjectionsReader[CPUImageType].New()<br>projReader.SetFileNames(fileNames)<br>projections = projReader.GetOutput()<br><span style="color:rgb(128,128,128)"># plot the projections<br></span>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">1</span>); plt.imshow(projections[<span style="color:rgb(104,151,187)">55</span><span style="color:rgb(204,120,50)">, </span>:<span style="color:rgb(204,120,50)">, </span>:]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'Proj X'</span>)<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">2</span>); plt.imshow(projections[:<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">55</span><span style="color:rgb(204,120,50)">, </span>:]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'Proj Y'</span>)<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span>); plt.imshow(projections[:<span style="color:rgb(204,120,50)">, </span>:<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">50</span>]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'Proj Z'</span>)<br>plt.show()<br><br><span style="color:rgb(128,128,128)"># Writer<br></span><span style="color:rgb(204,120,50)">if </span>Flag_saveProj == <span style="color:rgb(106,135,89)">"on"</span>:<br> <span style="color:rgb(136,136,198)">print</span>(<span style="color:rgb(106,135,89)">'Writing projections image...'</span>)<br> itk.imwrite(projections<span style="color:rgb(204,120,50)">, </span>TMP + <span style="color:rgb(106,135,89)">'projections.mha'</span>)<br> itk.imwrite(projections<span style="color:rgb(204,120,50)">, </span>TMP + <span style="color:rgb(106,135,89)">'projections.gipl'</span>)<br><br><span style="color:rgb(128,128,128)"># Reconstruction parameter<br></span>spacingVol = [<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">1</span>] <span style="color:rgb(128,128,128)"># resolution of the recon<br></span>sizeOutputVol = [<span style="color:rgb(104,151,187)">256</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">256</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">256</span>] <span style="color:rgb(128,128,128)"># FOV = S -> [270, 270, 264]<br></span>originVol = [-(sizeOutputVol[<span style="color:rgb(104,151,187)">0</span>] / <span style="color:rgb(104,151,187)">2 </span>+ <span style="color:rgb(104,151,187)">0.5</span>) * spacingVol[<span style="color:rgb(104,151,187)">0</span>]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">0.</span><span style="color:rgb(204,120,50)">, </span>-(sizeOutputVol[<span style="color:rgb(104,151,187)">2</span>] / <span style="color:rgb(104,151,187)">2 </span>+ <span style="color:rgb(104,151,187)">0.5</span>) * spacingVol[<span style="color:rgb(104,151,187)">2</span>]]<br><br><span style="color:rgb(128,128,128)"># Create (an empty) reconstructed image<br></span>constantImageSource = rtk.ConstantImageSource[CPUImageType].New()<br>constantImageSource.SetOrigin(originVol)<br>constantImageSource.SetSpacing(spacingVol)<br>constantImageSource.SetSize(sizeOutputVol)<br>constantImageSource.SetConstant(<span style="color:rgb(104,151,187)">0.</span>)<br>source = constantImageSource.GetOutput()<br><br><span style="color:rgb(128,128,128)"># FDK reconstruction<br></span><span style="color:rgb(136,136,198)">print</span>(<span style="color:rgb(106,135,89)">'Reconstructing...'</span>)<br>FDKCPUType = rtk.FDKConeBeamReconstructionFilter[CPUImageType]<br>feldkamp = FDKCPUType.New()<br>feldkamp.SetInput(<span style="color:rgb(104,151,187)">0</span><span style="color:rgb(204,120,50)">, </span>source)<br>feldkamp.SetInput(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span>projections)<br>feldkamp.SetGeometry(geometry)<br>feldkamp.GetRampFilter().SetTruncationCorrection(<span style="color:rgb(104,151,187)">0.0</span>)<br>feldkamp.GetRampFilter().SetHannCutFrequency(<span style="color:rgb(104,151,187)">0.0</span>)<br>imageFDK = feldkamp.GetOutput()<br><br><span style="color:rgb(128,128,128)"># plot the reconstructed image<br></span>im = imageFDK<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">1</span>); plt.imshow(im[<span style="color:rgb(104,151,187)">55</span><span style="color:rgb(204,120,50)">, </span>:<span style="color:rgb(204,120,50)">, </span>:]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'X'</span>)<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">2</span>); plt.imshow(im[:<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">55</span><span style="color:rgb(204,120,50)">, </span>:]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'Y'</span>)<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span>); plt.imshow(im[:<span style="color:rgb(204,120,50)">, </span>:<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">50</span>]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'Z'</span>); plt.show()</pre><pre style="background-color:rgb(43,43,43);color:rgb(169,183,198);font-family:"JetBrains Mono",monospace;font-size:9.8pt"><br><span style="color:rgb(128,128,128)"># Reconstruction parameter<br></span>spacingVol = [<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">1</span>] <span style="color:rgb(128,128,128)"># resolution of the recon<br></span>sizeOutputVol = [<span style="color:rgb(104,151,187)">256</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">256</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">256</span>] <span style="color:rgb(128,128,128)"># FOV = S -> [270, 270, 264]<br></span>originVol = [-(sizeOutputVol[<span style="color:rgb(104,151,187)">0</span>] / <span style="color:rgb(104,151,187)">2 </span>+ <span style="color:rgb(104,151,187)">0.5</span>) * spacingVol[<span style="color:rgb(104,151,187)">0</span>]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">0.</span><span style="color:rgb(204,120,50)">, </span>-(sizeOutputVol[<span style="color:rgb(104,151,187)">2</span>] / <span style="color:rgb(104,151,187)">2 </span>+ <span style="color:rgb(104,151,187)">0.5</span>) * spacingVol[<span style="color:rgb(104,151,187)">2</span>]]<br><br><span style="color:rgb(128,128,128)"># Create (an empty) reconstructed image<br></span>constantImageSource = rtk.ConstantImageSource[CPUImageType].New()<br>constantImageSource.SetOrigin(originVol)<br>constantImageSource.SetSpacing(spacingVol)<br>constantImageSource.SetSize(sizeOutputVol)<br>constantImageSource.SetConstant(<span style="color:rgb(104,151,187)">0.</span>)<br>source = constantImageSource.GetOutput()<br><br><span style="color:rgb(128,128,128)"># FDK reconstruction<br></span><span style="color:rgb(136,136,198)">print</span>(<span style="color:rgb(106,135,89)">'Reconstructing...'</span>)<br>FDKCPUType = rtk.FDKConeBeamReconstructionFilter[CPUImageType]<br>feldkamp = FDKCPUType.New()<br>feldkamp.SetInput(<span style="color:rgb(104,151,187)">0</span><span style="color:rgb(204,120,50)">, </span>source)<br>feldkamp.SetInput(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span>projections)<br>feldkamp.SetGeometry(geometry)<br>feldkamp.GetRampFilter().SetTruncationCorrection(<span style="color:rgb(104,151,187)">0.0</span>)<br>feldkamp.GetRampFilter().SetHannCutFrequency(<span style="color:rgb(104,151,187)">0.0</span>)<br>imageFDK = feldkamp.GetOutput()<br><br># plot the reconstructed image<br>im = imageFDK<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">1</span>); plt.imshow(im[<span style="color:rgb(104,151,187)">55</span><span style="color:rgb(204,120,50)">, </span>:<span style="color:rgb(204,120,50)">, </span>:]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'X'</span>)<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">2</span>); plt.imshow(im[:<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">55</span><span style="color:rgb(204,120,50)">, </span>:]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'Y'</span>)<br>plt.subplot(<span style="color:rgb(104,151,187)">1</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span><span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">3</span>); plt.imshow(im[:<span style="color:rgb(204,120,50)">, </span>:<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(104,151,187)">50</span>]<span style="color:rgb(204,120,50)">, </span><span style="color:rgb(170,73,38)">cmap</span>=<span style="color:rgb(106,135,89)">'gray'</span>); plt.title(<span style="color:rgb(106,135,89)">'Z'</span>); plt.show()</pre></pre>
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