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<p style="margin-top:0;margin-bottom:0">Thanks, Sir for your quick response. I think is very helpful with the insightful and the approach you have outlined. I will look at it to see if I can use it for my purpose. Will let you and the GATE users know of the
progress. I really appreciate the help. I<br>
Best regards,</p>
<p style="margin-top:0;margin-bottom:0">Emmanuel</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Maikol Salas Ramirez <mmsalas@gmail.com><br>
<b>Sent:</b> Wednesday, 13 June 2018 12:47:57 PM<br>
<b>To:</b> Emmanuel Marfo<br>
<b>Subject:</b> Re: [Gate-users] Material image dose scoring</font>
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<div dir="ltr"><font face="arial, helvetica, sans-serif">Hi Emmanuel,</font>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">I think, it is not possible to use the material decomposed images directly in GATE without a table, one option is to create mask of each material and a second is to create mesh volumes of each material and used
them like a child volumes of the contour of the normal ct image. <br>
</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">One option to start is create fraction images:<br>
</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><span style="font-family:arial,helvetica,sans-serif">When you use material decomposed images, you have mass conservation (it depend of your spectral method, but normally is like that, you have to check it), it means Mass_Fraction(HA) + Mass(Lipid)</span><span style="font-family:arial,helvetica,sans-serif">
</span><span style="font-family:arial,helvetica,sans-serif">_Fraction</span><span style="font-family:arial,helvetica,sans-serif">
</span><span style="font-family:arial,helvetica,sans-serif">+ Mass(Water)</span><span style="font-family:arial,helvetica,sans-serif">_Fraction</span><span style="font-family:arial,helvetica,sans-serif">
</span><font face="arial, helvetica, sans-serif">= 1. </font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">The problem here is how to transform your images in fraction images, I had a previous experience but with Water/Fat images but from MRI. For my MRI experiment I calculated the fat fraction and the water fraction
(1-fat fraction).</font></div>
<div><font face="arial, helvetica, sans-serif"><br>
</font></div>
<div><font face="arial, helvetica, sans-serif">In your case you can do the same:</font></div>
<div><font face="arial, helvetica, sans-serif">1- HA_Fraction = HA_Voxel_Value / (
<span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">
HA_Voxel_Value + <span style="float:none; display:inline">Lipid_Voxel_Value + <span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">
Water_Voxel_Value).</span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline">2-
Lipid_Fraction = Lipid_Voxel_Value / (</span><span style="float:none; display:inline"><span> </span></span><span style="float:none; display:inline">HA_Voxel_Value + <span> </span><span style="float:none; display:inline">Lipid_Voxel_Value + <span> </span><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">Water_Voxel_Value).</span></span></span>
<br>
</span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline">3-
Water_Fraction = Water_Voxel_Value / (</span><span style="float:none; display:inline"><span> </span></span><span style="float:none; display:inline">HA_Voxel_Value + <span> </span><span style="float:none; display:inline">Lipid_Voxel_Value + <span> </span><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">Water_Voxel_Value).</span></span></span>
<br>
</span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><br>
</span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline">I did this calculation with
your images using ImageJ and it works pretty easy, you just need to sum all the three images and divide each one by the sum, if you chose one voxel you will see that the sum is 1. The attached image shows the three images.
<br>
</span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><br>
</span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline">The only artifact
here is i<span style="line-height:115%; font-family:Arial,sans-serif">n voxel with air or with a zero value you will have NaN value, you have to fix them (given the zero value), ImageJ has an option to do that. </span>
</span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><br>
</span></span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><font face="arial, helvetica, sans-serif">--------------</font></span></span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><font face="arial, helvetica, sans-serif">This
is what I can see, the main point is that a normal voxel in a CT images has a composition of material and what you have in each voxel is a effective atomic number and effective density, with spectral CT you separate the material and you have to take care to
use the individual images because you lost anatomical information information.</font></span></span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><font face="arial, helvetica, sans-serif"><br>
</font></span></span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><font face="arial, helvetica, sans-serif">Sorry
I think, I could not help you to much.</font></span></span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><font face="arial, helvetica, sans-serif"><br>
</font></span></span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><font face="arial, helvetica, sans-serif">Best
regards</font></span></span></span></span></font></div>
<div><font face="arial, helvetica, sans-serif"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="float:none; display:inline"><span style="background-color:rgb(255,255,255); float:none; display:inline"><span style="line-height:115%; font-family:Arial,sans-serif"><font face="arial, helvetica, sans-serif">Maikol</font><br>
</span></span></span></span></font></div>
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<div class="x_gmail_quote">2018-06-12 10:50 GMT+02:00 Emmanuel Marfo <span dir="ltr">
<<a href="mailto:emmanuel.marfo@postgrad.otago.ac.nz" target="_blank">emmanuel.marfo@postgrad.otago<wbr>.ac.nz</a>></span>:<br>
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<p style="margin-top:0px; margin-bottom:0px">Hello</p>
<p style="margin-top:0px; margin-bottom:0px">Thanks for the quick response. Please, the images are density images obtained by dividing linear attenuation(energy information) values by mass attenuation(material basis). </p>
<p style="margin-top:0px; margin-bottom:0px">Attached is a dropbox link of a folder containing the material decomposed images for your assessment. thanks</p>
<p style="margin-top:0px; margin-bottom:0px"><a href="https://www.dropbox.com/sh/zxfio5azk4q6osb/AADw0a1BMYQiPnqFjMgwdCnYa?dl=0" class="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319OWAAutoLink" id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPlnk330578" disabled="" target="_blank">https://www.dropbox.com/sh/zxf<wbr>io5azk4q6osb/AADw0a1BMYQiPnqFj<wbr>MgwdCnYa?dl=0</a></p>
<div id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPBorder_GT_15287933942890.2901239450969866" style="margin-bottom:20px; overflow:auto; width:100%; text-indent:0px">
<table id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPContainer_15287933942850.9431737051670686" cellspacing="0" style="width:90%; background-color:rgb(255,255,255); overflow:auto; padding-top:20px; padding-bottom:20px; margin-top:20px; border-top:1px dotted rgb(200,200,200); border-bottom:1px dotted rgb(200,200,200)">
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<div id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPImageContainer_15287933942860.523681359473239" style="background-color:rgb(255,255,255); height:128px; margin:auto; display:table; width:128px">
<a id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPImageAnchor_15287933942870.8818418690919838" href="https://www.dropbox.com/sh/zxfio5azk4q6osb/AADw0a1BMYQiPnqFjMgwdCnYa?dl=0" disabled="" target="_blank" style="display:table-cell; text-align:center"><img id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPThumbnailImageID_15287933942870.42754814793871154" width="128" height="128" style="display:inline-block; max-width:250px; max-height:250px; height:128px; width:128px; border-width:0px; vertical-align:bottom" src="https://cfl.dropboxstatic.com/static/images/icons128/folder_dropbox.png"></a></div>
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<td id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319TextCell_15287933942870.6173573598772124" colspan="2" style="vertical-align:top; padding:0px; display:table-cell">
<div id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPRemovePreviewContainer_15287933942870.354328013542929">
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<div id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPTitle_15287933942870.334403355865428" style="color:rgb(0,120,215); font-weight:normal; font-size:21px; font-family:wf_segoe-ui_light,"Segoe UI Light","Segoe WP Light","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; line-height:21px">
<a id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPUrlAnchor_15287933942880.11144699600538988" href="https://www.dropbox.com/sh/zxfio5azk4q6osb/AADw0a1BMYQiPnqFjMgwdCnYa?dl=0" disabled="" target="_blank" style="text-decoration:none">material
images from spectral CT</a></div>
<div id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPMetadata_15287933942880.62823753261166" style="margin:10px 0px 16px; color:rgb(102,102,102); font-weight:normal; font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; font-size:14px; line-height:14px">
<a href="http://www.dropbox.com" target="_blank">www.dropbox.com</a></div>
<div id="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPDescription_15287933942880.9817824926763286" style="display:block; color:rgb(102,102,102); font-weight:normal; font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; font-size:14px; line-height:20px; max-height:100px; overflow:hidden">
Shared with Dropbox</div>
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<p style="margin-top:0px; margin-bottom:0px">Best regards,</p>
<p style="margin-top:0px; margin-bottom:0px">Emmanuel</p>
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<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Maikol Salas Ramirez <<a href="mailto:mmsalas@gmail.com" target="_blank">mmsalas@gmail.com</a>><br>
<b>Sent:</b> Tuesday, 12 June 2018 5:45:25 PM<br>
<b>To:</b> Emmanuel Marfo<br>
<b>Cc:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecolla<wbr>boration.org</a><br>
<b>Subject:</b> Re: [Gate-users] Material image dose scoring</font>
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<div dir="auto">Hi Emmanuel,</div>
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<div dir="auto"><br>
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<div dir="auto">When you said <span style="font-family:Calibri,Helvetica,sans-serif; word-spacing:1px; background-color:rgb(255,255,255)">material decomposed image, are you talking about Rho/Z image (effective density and atomic number - image)?</span></div>
<div dir="auto">What info do you have in your image?</div>
<div dir="auto"><br>
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<div dir="auto"><font face="Calibri, Helvetica, sans-serif"><span style="word-spacing:1px; background-color:rgb(255,255,255)">Best regards</span></font></div>
<div dir="auto"><font face="Calibri, Helvetica, sans-serif"><span style="word-spacing:1px; background-color:rgb(255,255,255)">Maikol</span></font></div>
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<div class="x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319x_gmail_quote">
<div>El El mar, 12 jun 2018 a las 0:34, Emmanuel Marfo <<a href="mailto:emmanuel.marfo@postgrad.otago.ac.nz" target="_blank">emmanuel.marfo@postgrad.otago<wbr>.ac.nz</a>> escribió:<br>
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<p style="margin-top:0px; margin-bottom:0px">Hello Gate Users,</p>
<p style="margin-top:0px; margin-bottom:0px">Please, I need help on this or if anyone has the knowledge of how it can be done I would be grateful.<span style="font-size:12pt"> I am using a</span> spectral<span style="font-size:12pt"> CT system to obtained material
decomposed image based on mass attenuation and energy information. I want </span>
to<span style="font-size:12pt"> do dose deposition on the material </span>decomposed<span style="font-size:12pt"> images without the use of
</span>Schneider<span style="font-size:12pt"> material converter employed in GATE. My problem is I want to know if GATE architecture supports it and second I can not import the material decomposed image into GATE because is always requesting for a conversion
text file. Can I bypass it? Can someone help me, please? Thanks</span></p>
<p style="margin-top:0px; margin-bottom:0px"><span style="font-size:12pt"><br>
</span></p>
<p style="margin-top:0px; margin-bottom:0px">Best regards,</p>
<p style="margin-top:0px; margin-bottom:0px">Emmanuel Marfo</p>
<p style="margin-top:0px; margin-bottom:0px">Student</p>
<p style="margin-top:0px; margin-bottom:0px">University of Otago</p>
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