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Hi Andreas,</div>
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Your input is invaluable, thanks for your suggestions! You are correct, I am attempting to apply the a priori scatter correction. Is the normalisation procedure you mentioned regarding the calibration-chamber similar to what has been mentioned on page 63-64
of this thesis (<a href="https://pdfs.semanticscholar.org/d90c/d77b61d10d2c24df0686bc0be1f38424d67d.pdf" id="LPlnk674520">https://pdfs.semanticscholar.org/d90c/d77b61d10d2c24df0686bc0be1f38424d67d.pdf</a>), specifically Norm Chamber (NC) values located in
raw projection header?<br>
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I will admit, I am a complete novice when it comes to C coding and using RTK. For correctly normalising the Varian projections do you recommend installing your "cbctrecon" package? If so, which function performs the Varian normalisation? Or can the normalisation
be done by scaling the projection pixel values manually? My plan is to manually scale the CB projections and perform a reconstruction until the HU looks right. A more robust method is preferable, however. </div>
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Your advice is greatly appreciated,</div>
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Brani</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Andreas Andersen <andreasga22@gmail.com><br>
<b>Sent:</b> Tuesday, 26 May 2020 7:15 PM<br>
<b>To:</b> Brani Rusanov <brani_rusanov@hotmail.com><br>
<b>Cc:</b> rtk-users@public.kitware.com <rtk-users@public.kitware.com><br>
<b>Subject:</b> Re: [Rtk-users] Unable to Forward Project CT Volume With Correct Orientation</font>
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<div dir="ltr">I'm happy to hear it worked!
<div><br>
I don't know the complete Varian pipeline for correction, there should in addition to subtracting the bow-tie be something like a calibration-chamber-based correction, but I have not figured out how to do this (let me know if you do)
<div>RTK does not have filters to take care of this (yet). It would be possible to do, but you'd have to know which image in the calibration folder is the correct one. (There may be several and I think they are named by the local Varian engineers - not standardised)</div>
<div>I do a simple subtraction in my own OpenCL implementation, but looping through projections, extracting 2D from 3D, and using the ITK subtraction image filter would probably be simpler.</div>
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<div>(<i>If I should find documentation from Varian describing this process with some standard, I'll write it into the reader for Xim images. However, I'm afraid their own solution might specific to each gantry or engineering team</i>)</div>
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<div>It could sound like you want to do the "a priori scatter correction", I've implemented this for Varian based projections (hnd and xim), see:
<a href="https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgitlab.com%2Fagravgaard%2Fcbctrecon&data=02%7C01%7C%7C63220d57e95844eb634508d8016629c0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637260885580829813&sdata=Hiyv%2BwFoqjeHcqAH3jIG%2B5aiyqKnurLJ0qQ6ax4N3ug%3D&reserved=0" originalsrc="http://gitlab.com/agravgaard/cbctrecon" shash="Yv4+mp7e7Ji8AEif19n2j6FBtHjqE/gWn42ffuq2Wgsouw/Wg/gYSEFgar2rALFmVzo+zC+z7mxvL9F37b2lCrFvuu81IlBwY0TrkF2hDRyvwTq9gmPxR2Lu/Xt2Olu0u/CXKQUJ0vuyOXhKosK9LEFiLHcsRO3Ne5bMolMAPsE=">
gitlab.com/agravgaard/cbctrecon</a> (The Develop branch should be preferred at the moment)</div>
<div>The correction factor from the original Elekta implementation doesn't work without a normalisation as mentioned above, so I'm doing some tricks to ensure correctness of projection intensity for the subtraction, but I hope to implement a solution/normalisation
based on numbers from the machine instead.</div>
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<div>/Andreas<br clear="all">
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<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>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Danish Center for Particle Therapy, </span></p>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Aarhus University Hospital<u></u><u></u></span></p>
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<span lang="DA" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Palle Juul-Jensens Blvd. 99,</span></p>
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<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>
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<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>
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<div dir="ltr" class="x_gmail_attr">On Tue, 26 May 2020 at 12:37, Brani Rusanov <<a href="mailto:brani_rusanov@hotmail.com">brani_rusanov@hotmail.com</a>> wrote:<br>
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Hi Andreas,</div>
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You are correct, I had failed to flip the y and z coordinates of the offset parameter in the header. I had thought that the transformmatrix would take care of this. Now the simulated projection looks as desired. Thank you!</div>
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You mentioned the possibility of applying pre-processing on the CB projections for a bow-tie filter. Do you know what kind of pre-processing is available within RTK for bow-tie filters? I ask because I plan on subtracting the measured CBCT projections from
the simulated CT-registered projections. However, the measured CBCT projections have the characteristic attenuation pattern on the left and right side of the image corresponding to a bow-tie filter. Can RTK remove these two regions of greater attenuation? </div>
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Also, would you happen to know if rtkprojections, when converting the raw projection float values to attenuation, is compatible with Varian raw projection data? I ask this because the studies I have read that perform this procedure use Elekta projection data.
The output attenuation values for my measured projection data in air region is about ~2 mm-1 after conversion with rtkprojections. Whereas, I previously converted the HU of the registered CT volume to attenuation using the formula: mu = (HU + 1024)/2^16 which
shows air to be ~0.019mm-1 once forward projected.</div>
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Thank you kindly for your advice,</div>
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Brani</div>
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<div id="x_gmail-m_7439177778697677005divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Andreas Andersen <<a href="mailto:andreasga22@gmail.com" target="_blank">andreasga22@gmail.com</a>><br>
<b>Sent:</b> Tuesday, 26 May 2020 4:51 PM<br>
<b>To:</b> Brani Rusanov <<a href="mailto:Brani_Rusanov@hotmail.com" target="_blank">Brani_Rusanov@hotmail.com</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a> <<a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a>><br>
<b>Subject:</b> Re: [Rtk-users] Unable to Forward Project CT Volume With Correct Orientation</font>
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<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>
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<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>
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<div>If flipped or all black: Your transformation matrix looks correct to me, so I think the problem may be elsewhere.</div>
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<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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fitk.org%2FWiki%2FITK%2FMetaIO%2FDocumentation%23MetaObject_Tags&data=02%7C01%7C%7C63220d57e95844eb634508d8016629c0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637260885580839808&sdata=v2SPprbq57AoHf3VyamdMKStgCNsVK0HozMmmJbI3dM%3D&reserved=0" originalsrc="https://itk.org/Wiki/ITK/MetaIO/Documentation#MetaObject_Tags" shash="gWbyKywawBejy2Wr/CoMvDF9ILnjdjMXaLYW0g0fIfO2jEBpociHWLHKgYTOdzJSUDHR7TqmcT+EfuLWVaj0nw8FSyrGA9UNd/PQ9tqS624GDAWrc/spOQ6G78qtIPZQHbIIPZhYzBKYTR04NzoKkPGaBfqbxIq9kE63edCJXW0=" target="_blank">https://itk.org/Wiki/ITK/MetaIO/Documentation#MetaObject_Tags</a></div>
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<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>
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<div>If intensity is darker or brighter: Check if you have preprocessed the CB projections correctly for bow-tie filter and the like.</div>
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<div>I hope this gives a hint to where the problem might be.</div>
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<div>/Andreas<br clear="all">
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<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>
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<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>
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<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>
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<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
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<div dir="ltr">On Tue, 26 May 2020 at 05:08, Brani Rusanov <<a href="mailto:Brani_Rusanov@hotmail.com" target="_blank">Brani_Rusanov@hotmail.com</a>> wrote:<br>
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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://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.semanticscholar.org%2Fpaper%2Fnuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray%2F1ec27be3617dfc4e03bba86dcd92db8f3323de21%2Ffigure%2F3&data=02%7C01%7C%7C63220d57e95844eb634508d8016629c0%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637260885580849808&sdata=%2BcHqKs1UZFalgC6Aug0OUp8qmGor5gm2ubuS5FmwoJg%3D&reserved=0" originalsrc="https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3" shash="T9akAcCP1GG25LwvRT5QrUcpLJEX01lbqA0Asl13MtNJRQMrlartizgBUx1YR1wczM7LCU7NXDBqAOzguiin9Ri2DY4ndhKv6cWfXUsnJVPHqOi4d23jTB+qDUp26p3BoDiX/tutRcuVcNb+HKkaa5Z3hNY6ti7V8Uyu6LRFHtA=" rel="noopener noreferrer" target="_blank" style="margin:0px">https://www.semanticscholar.org/paper/nuclear-science-and-technology-Radiation-Quantities-Brink-McNitt-Gray/1ec27be3617dfc4e03bba86dcd92db8f3323de21/figure/3</a>
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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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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>
<br>
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>
<div style="margin:0px; font-size:12pt; font-family:Calibri,Helvetica,sans-serif; background-color:rgb(255,255,255)">
<span style="margin:0px"><br>
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<span style="margin:0px">Thank you kindly for your response,</span></div>
<div style="margin:0px; font-size:12pt; font-family:Calibri,Helvetica,sans-serif; background-color:rgb(255,255,255)">
<span style="margin:0px">Brani</span></div>
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