<div dir="ltr"><div dir="ltr"><div>What do you more precisely mean by "The output projections do not look like the raw projections I have from the CBCT"</div><div>Are they flipped, are they all black, are they much brighter or darker, or do they not align?<br><br></div><div>If alignment: Consider if you need to sort the projections by gantry angle before visual comparison, the Xim reader just reads sequentially by the given regex, so a ProBeam CB (with two imagers) may interleave projections from different angles. This is unlikely to be a problem for a gantry with only one imager.</div><div><br></div><div>If flipped or all black: Your transformation matrix looks correct to me, so I think the problem may be elsewhere.</div><div dir="ltr"><div>It's always a mess to figure out. Be careful, that when you flip axes manually like that that you also remember to flip offsets (origin), spacing, etc. accordingly.</div><div>In particular orientation (directions), I can see it says RAI for "AnatomicalOrientation", but I think you'll need the "Orientation" tag with direction cosines if you want to specify the directions manually.</div><div><a href="https://itk.org/Wiki/ITK/MetaIO/Documentation#MetaObject_Tags">https://itk.org/Wiki/ITK/MetaIO/Documentation#MetaObject_Tags</a></div><div><br></div><div>All this being said, I would suggest to instead use ITK's readers and the built-in filters for image transformation if that's even necessary, to avoid the hell of trying to keep track of all these values manually.</div><div><br></div><div>If intensity is darker or brighter: Check if you have preprocessed the CB projections correctly for bow-tie filter and the like.</div><div><br></div><div>I hope this gives a hint to where the problem might be.</div><div><br></div><div>/Andreas<br clear="all"><div><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><p style="margin-bottom:0.0001pt"><span lang="EN-US" style="color:rgb(31,73,125)"><span lang="EN-US" style="font-size:11pt;line-height:16.8667px;font-family:Calibri,sans-serif">__________________________________</span></span></p><p style="margin-bottom:0.0001pt"><span lang="EN-US" style="color:rgb(31,73,125)"><span lang="EN-US" style="font-size:11pt;line-height:16.8667px;font-family:Calibri,sans-serif">Andreas Gravgaard Andersen</span></span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Danish Center for Particle Therapy, </span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Aarhus University Hospital<u></u><u></u></span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span lang="DA" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Palle Juul-Jensens Blvd. 99,</span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span lang="DA" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">8200, Aarhus</span></p><div><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span lang="DA" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Mail: <a href="mailto:agravgaard@protonmail.com" target="_blank">agravgaard@protonmail.com</a></span></p><p style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:"Times New Roman",serif;color:black"><span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt">Cell: </span><span style="color:rgb(31,73,125);font-family:Calibri,sans-serif;font-size:11pt"> </span><a value="+4523382411" style="font-family:Calibri,sans-serif;font-size:11pt;color:rgb(17,85,204)">+45 3165 8140</a></p></div></div></div></div></div></div></div></div></div></div><br></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 26 May 2020 at 05:08, Brani Rusanov <<a href="mailto:Brani_Rusanov@hotmail.com">Brani_Rusanov@hotmail.com</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">
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Hi all,</div>
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I am attempting to forward project a CT volume (previously registered to a CBCT volume) using the geometry of a CBCT volume to generate raw projections. I also have access to the raw CBCT projections. I have used rktprojections to stack the raw CBCT projections
and generate .mhd/raw files. </div>
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Next, I used rtkvariabprobeamgeometry on the scan.xml file that came with the raw CBCT projections to generate a RTK compatible geometry.xml file. </div>
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Next, I have stacked the registered CT dicoms into a .mhd/raw format. The trouble I'm having is creating the projections using rtkforwardprojections. Specifically, I cannot find the correct transformmatrix in the CT header to tell rtkforwardprojetions the conversion
from DICOM to IEC geometry. The output projections do not look like the raw projections I have from the CBCT. This may be a stupid question, but I cannot figure it out. From my own estimation, the transformation should be 1 0 0 0 0 -1 0 1 0 based on this diagram
(<a href="https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3" rel="noopener noreferrer" style="margin:0px" target="_blank">https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3</a>
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<div style="margin:0px 12px 0px 0px;height:104.547px;overflow:hidden"><a href="https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3" style="margin:0px" target="_blank"><img alt="" height="104" width="240" style="margin: 0px; display: block;" src="https://ai2-s2-public.s3.amazonaws.com/figures/2017-08-08/1ec27be3617dfc4e03bba86dcd92db8f3323de21/14-Figure1.4-1.png"></a></div>
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<div style="margin:0px 8px 12px 0px;font-weight:300;font-size:21px;font-family:wf_segoe-ui_light,"Segoe UI Light","Segoe WP Light","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif">
<a href="https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3" style="margin:0px" target="_blank">Figure 1.4 from nuclear science
and technology Radiation Quantities and Units , Dose to the Patients , and Image Quality in Computed Tomography ( CT ) ( RAD UNITS ) Author : | Semantic Scholar</a></div>
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Figure 1.4 (left) The IEC patient coordinate system (the patient is lying in supine position); (right) transformation of coordinates between the IEC and DICOM coordinate systems [IEC, 2000] (cited in ICRU Report 71, 2004, page 35) - "nuclear science and technology
Radiation Quantities and Units , Dose to the Patients , and Image Quality in Computed Tomography ( CT ) ( RAD UNITS ) Author :"</div>
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<a href="http://www.semanticscholar.org" target="_blank">www.semanticscholar.org</a></div>
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My questions are: Is this the correct transformmatrix to apply?<br>
Do I need to also change the offset values in order to get the correct projections? <br>
Could this have something to do with the fact that I am using variant data?<br>
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The .mhd for the registered CT is:<br>
<span style="margin:0px">ObjectType = Image<br>
</span>
<div style="margin:0px">NDims = 3<br>
</div>
<div style="margin:0px">BinaryData = True<br>
</div>
<div style="margin:0px">BinaryDataByteOrderMSB = False<br>
</div>
<div style="margin:0px">CompressedData = False<br>
</div>
<div style="margin:0px">TransformMatrix = 1 0 0 0 0 -1 0 1 0<br>
</div>
<div style="margin:0px">Offset = -131.03451538085938 -131.03451538085938 -91.809638977050781 <br>
</div>
<div style="margin:0px">CenterOfRotation = 0 0 0<br>
</div>
<div style="margin:0px">AnatomicalOrientation = RAI<br>
</div>
<div style="margin:0px">ElementSpacing = 0.51285523409720002 0.51285523409720002 1.9958648681640625<br>
</div>
<div style="margin:0px">DimSize = 512 512 93<br>
</div>
<div style="margin:0px">ElementType = MET_DOUBLE<br>
</div>
<span style="margin:0px">ElementDataFile = CIRS_6A.raw<br>
</span><br>
Similarly, the .mhd for the raw CBCT projections is:<br>
<span style="margin:0px">ObjectType = Image<br>
</span>
<div style="margin:0px">NDims = 3<br>
</div>
<div style="margin:0px">BinaryData = True<br>
</div>
<div style="margin:0px">BinaryDataByteOrderMSB = False<br>
</div>
<div style="margin:0px">CompressedData = False<br>
</div>
<div style="margin:0px">TransformMatrix = 1 0 0 0 1 0 0 0 1<br>
</div>
<div style="margin:0px">Offset = -198.46200000000002 -148.798 0<br>
</div>
<div style="margin:0px">CenterOfRotation = 0 0 0<br>
</div>
<div style="margin:0px">AnatomicalOrientation = RAI<br>
</div>
<div style="margin:0px">ElementSpacing = 0.38800000000000001 0.38800000000000001 1<br>
</div>
<div style="margin:0px">DimSize = 1024 768 501<br>
</div>
<div style="margin:0px">ElementType = MET_FLOAT<br>
</div>
<span style="margin:0px">ElementDataFile = CIRS_6A_SCGH_P.raw</span><br>
</div>
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<span style="margin:0px">Thank you kindly for your response,</span></div>
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<span style="margin:0px">Brani</span></div>
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