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<p style="margin-top:0;margin-bottom:0">Dear Maikol/GATE-Users,</p>
<p style="margin-top:0;margin-bottom:0">Please, I followed your prescribed method and worked successfully. However, the importation of the behaviour of the mouse mesh volume(bones) in the mother volume is unexpected. I expected the size of the mouse mesh volume
to be smaller and located inside the mother volume. Attached is the picture of how the entire geometry looks like. Please, can anyone help me rectify this problem? Thanks for your help so far.</p>
<p style="margin-top:0;margin-bottom:0">Best regards,</p>
<p style="margin-top:0;margin-bottom:0">Emmanuel</p>
</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Emmanuel Marfo<br>
<b>Sent:</b> Monday, 18 June 2018 9:05:05 PM<br>
<b>To:</b> Maikol Salas Ramirez<br>
<b>Subject:</b> Re: [Gate-users] Material image dose scoring</font>
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<p style="margin-top:0; margin-bottom:0">Thanks very much for your response. I will work on it and let you know the outcome.</p>
<p style="margin-top:0; margin-bottom:0">best regards,</p>
<p style="margin-top:0; margin-bottom:0">Emmanuel</p>
</div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Maikol Salas Ramirez <mmsalas@gmail.com><br>
<b>Sent:</b> Monday, 18 June 2018 8:58:51 PM<br>
<b>To:</b> Emmanuel Marfo<br>
<b>Subject:</b> Re: [Gate-users] Material image dose scoring</font>
<div> </div>
</div>
<meta content="text/html; charset=utf-8">
<div>
<div dir="ltr">Hi,
<div><br>
</div>
<div>I just realize that just with the first step you will have the water+bone+fat mask because all the voxel most have to be 1 and air will be zero or NaN (1 after fix).</div>
<div><br>
</div>
<div>Now, with your question, the idea is to do not leave gaps. You start in step 1 with a full mask, then step by step you remove bone and fat, water can be considered a common material. </div>
<div>If you just get the water material you will have to apply a threshold value for water and you could have gaps between volume.</div>
<div><br>
</div>
<div>In step 3, you will have to select a threshold value for bone, with this value you will decide what is bone and what is not bone in the bone image, you will lost some info but it is the only way if you want to segment the would body. </div>
<div><br>
</div>
<div><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">In step 4, again </span><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">you will have to select a threshold value
for fat, with the same implication.</span><br>
</div>
<div><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><br>
</span></div>
<div><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">In step 5, the rest in the mask of step 2 will be water.</span></div>
<div><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><br>
</span></div>
<div><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">You also can try to start with water instead of bone, but I found that bone is better for the high contrast and fat second, because fat has a more specific localization
in the body.</span></div>
<div><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline"><br>
</span></div>
<div>Best regards<br>
</div>
<div><span style="font-size:small; background-color:rgb(255,255,255); float:none; display:inline">Maikol</span></div>
<div><br>
</div>
<div> </div>
</div>
<div class="x_x_gmail_extra"><br>
<div class="x_x_gmail_quote">2018-06-18 10:35 GMT+02:00 Emmanuel Marfo <span dir="ltr">
<<a href="mailto:emmanuel.marfo@postgrad.otago.ac.nz" target="_blank">emmanuel.marfo@postgrad.otago.ac.nz</a>></span>:<br>
<blockquote class="x_x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div id="x_x_m_-5505382561369211157divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0; margin-bottom:0">Thanks for the reply. This process below is for me to make sure I understood the method clearly and ask a question another question. Perhaps I will also be able to know the answer through some measurements </p>
<p style="margin-top:0; margin-bottom:0">First step</p>
<p style="margin-top:0; margin-bottom:0"></p>
<ol style="margin-bottom:0px; margin-top:0px">
<li><span style="font-size:12pt"></span>Obtain mass density probabilities for the materials concerned (such as bone, fat and water). The summation of their probabilities should be 1. Fix all NaN.</li></ol>
Second step
<p></p>
<p style="margin-top:0; margin-bottom:0">2. Create a mask from the summed materials (wate+fat+bone)</p>
<p style="margin-top:0; margin-bottom:0">3. Create a mask and a mesh volume from the bone. Subtract the bone mask from <span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">(water+fat+bone)
mask leaving (water+fat )mask</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">4 <span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">Create
a mask and a </span>mesh<span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"> volume from the fat. Subtract the fat mask from </span><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">(water+fat)
mask leaving pure water mask</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">5.
Create a mesh volume of water from a water mask.</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">6.
Now, we have three masks and three meshes of water, bone and fat materials. The water mesh volume serves as the mother volume while the bone and fat mesh serves as the daughter volumes.</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><br>
</span></span></p>
<p style="margin-top:0; margin-bottom:0"><span style="font-family:Calibri,Helvetica,sans-serif,EmojiFont,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px"><span style="color:rgb(0,111,201)">The
question with the pure water mask, why do we have to add water</span><span style="color:rgb(0,111,201)">,fat</span><span style="color:rgb(0,111,201)"> and bone mask, </span><span style="color:rgb(0,111,201)">and then</span><span style="color:rgb(0,111,201)">
subtracting fat and bone mask to get pure water mask? Can`t we just get the water mask and mesh volume from the water mass fraction
</span><span style="color:rgb(0,111,201)">image.</span></span></p>
</div>
<hr style="display:inline-block; width:98%">
<div id="x_x_m_-5505382561369211157divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><span class=""><b>From:</b> Maikol Salas Ramirez <<a href="mailto:mmsalas@gmail.com" target="_blank">mmsalas@gmail.com</a>><br>
</span><b>Sent:</b> Monday, 18 June 2018 7:58:44 PM
<div>
<div class="x_x_h5"><br>
<b>To:</b> Emmanuel Marfo<br>
<b>Subject:</b> Re: [Gate-users] Material image dose scoring</div>
</div>
</font>
<div> </div>
</div>
<div>
<div class="x_x_h5">
<div>
<div dir="ltr">Hi Emmanuel,
<div><br>
</div>
<div>Yes, you are right. </div>
<div>There is a possibility to have some voxels with pure bone, therefore it is better to include bone in the principal mask to have a complete volume. </div>
<div>Sorry, I did not see that.</div>
<div><br>
</div>
<div><br>
</div>
<div>Best regards.</div>
<div>Maikol</div>
</div>
<div class="x_x_m_-5505382561369211157x_gmail_extra"><br>
<div class="x_x_m_-5505382561369211157x_gmail_quote">2018-06-18 9:36 GMT+02:00 Emmanuel Marfo
<span dir="ltr"><<a href="mailto:emmanuel.marfo@postgrad.otago.ac.nz" target="_blank">emmanuel.marfo@postgrad.<wbr>otago.ac.nz</a>></span>:<br>
<blockquote class="x_x_m_-5505382561369211157x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div id="x_x_m_-5505382561369211157x_m_-2290038695161413218divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0; margin-bottom:0">Hello Maikol,</p>
<p style="margin-top:0; margin-bottom:0">Please, I have a question about subtracting bone and fat mask from water + fat maks to get pure water mask. Why are we not summing water, fat and bone mask and then subtract bone and fat mask from them but instead water
+ fat mask only? </p>
<p style="margin-top:0; margin-bottom:0">Best regards,</p>
<p style="margin-top:0; margin-bottom:0">Emmanuel</p>
</div>
<hr style="display:inline-block; width:98%">
<div id="x_x_m_-5505382561369211157x_m_-2290038695161413218divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><span><b>From:</b> Maikol Salas Ramirez <<a href="mailto:mmsalas@gmail.com" target="_blank">mmsalas@gmail.com</a>><br>
</span><span><b>Sent:</b> Friday, 15 June 2018 12:03:46 AM<br>
</span>
<div>
<div class="x_x_m_-5505382561369211157x_h5"><b>To:</b> Emmanuel Marfo<br>
<b>Subject:</b> Re: [Gate-users] Material image dose scoring</div>
</div>
</font>
<div> </div>
</div>
<div>
<div class="x_x_m_-5505382561369211157x_h5">
<div>
<div dir="ltr">Hi Emmanuel,
<div><br>
</div>
<div>I am not an expect, but I will recommend some possible steps:</div>
<div><br>
</div>
<div>1- You sum the fat and water images and than transform the image in a mask, I mean all the voxel with a value higher than zero, yo set them to 1.</div>
<div><br>
</div>
<div>2- Segment the bone image, for example you can use a threshold, which all the voxels with a value higher than
<b>0.1 (this value you have to decided)</b> in the bone image will assigned a value of 1, then you will have a bone mask, then you subtract it from the first mask (step 1). At same time you use the bone mask to create a mesh volume, you can do this procedure
in 3DSlicer or in ImageJ (using 3d viewer). </div>
<div> </div>
<div>3- in this point you have a three masks (<b>water + fat</b>, <b>bone</b>, <b>
water + fat - bone</b> ) and one mesh volume (bone) </div>
<div><br>
</div>
<div>4- You take the fat image, and you make a mask of this image (again you have to chose a threshold value). Also you can make a mesh volume of this mask.</div>
<div><br>
</div>
<div>5- Now you substract from the <b style="font-size:small; background-color:rgb(255,255,255)">
water + fat - bone </b><span style="font-size:small; background-color:rgb(255,255,255)">mask the fat image, then you will have a mask of pure water. Then you can create a new mesh for water.</span></div>
<div><span style="font-size:small; background-color:rgb(255,255,255)"><br>
</span></div>
<div>You can do all of this steps with ImageJ, and it is very important that each time that you create a new mask, you have to apply some filter to smooth the mask and avoid holes (please see the effect over the image of the imageJ funtion in Process->Binary
and Process->filter), also go through all the images to check the mask. Only after this fine tune you have to do mask subtractions.</div>
<div><br>
</div>
<div>At end you will have three mesh files and thre masks. The water-mesh in the mother volume and the fat an bone are child volumes.</div>
<div><br>
</div>
<div>Let me now if it works. I hope, It will help you.</div>
<div><br>
</div>
<div>Best regards</div>
<div>Maikol.</div>
<div><br>
</div>
</div>
<div class="x_x_m_-5505382561369211157x_m_-2290038695161413218x_gmail_extra"><br>
<div class="x_x_m_-5505382561369211157x_m_-2290038695161413218x_gmail_quote">2018-06-14 11:48 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>
<blockquote class="x_x_m_-5505382561369211157x_m_-2290038695161413218x_gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556divtagdefaultwrapper" dir="ltr" style="font-size:12pt; color:#000000; font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0; margin-bottom:0"><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px">Dear Sir,</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px">Please, I followed your procedure and was able to convert my images to mass density fraction for lipid, water and HA. I was also
able to correct the NaN too. </span></p>
<p style="margin-top:0; margin-bottom:0"><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px">Now I am wondering what the next step will be. Please, can I adopt your method for the MRI image(lipid/water) and see if it can
work for me. The procedure you talk about by creating a mask of each material or creating mesh volumes for each material is not quite clear to me. Can you help me with that? I have attached an interface of a plugin in ImageJ called morphological segmentation sho<wbr>wing
one of my images. I was hoping this could help me create the mask of each material. I am not sure if is the right method. I am not an expert in Imaging. I seek your guidance.</span></p>
<span>
<p style="margin-top:0; margin-bottom:0"><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px"><br>
</span></p>
<p style="margin-top:0; margin-bottom:0"><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px">>>I
</span>think,<span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px"> it is not possible to use the material decomposed images directly in GATE without a table, </span></p>
<p style="margin-top:0; margin-bottom:0"></p>
</span>
<ol style="margin-bottom:0px; margin-top:0px">
<li><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px"></span><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px">one option is to create
</span>a mask<span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px"> of each material and </span></li><li><span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px">A second is to create mesh volumes of each material and used them
</span>like a child volume<span style="color:rgb(33,33,33); font-family:arial,helvetica,sans-serif; font-size:15px"> of the contour of the normal ct image. </span><br>
</li></ol>
<font color="#212121" face="arial, helvetica, sans-serif"><span style="font-size:15px">thanks.</span></font>
<p></p>
<p style="margin-top:0; margin-bottom:0"><font color="#212121" face="arial, helvetica, sans-serif"><span style="font-size:15px">Best regards,</span></font></p>
<p style="margin-top:0; margin-bottom:0"><font color="#212121" face="arial, helvetica, sans-serif"><span style="font-size:15px">Emmanuel</span></font></p>
</div>
<hr style="display:inline-block; width:98%">
<div id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><span><b>From:</b> Maikol Salas Ramirez <<a href="mailto:mmsalas@gmail.com" target="_blank">mmsalas@gmail.com</a>><br>
</span><span><b>Sent:</b> Wednesday, 13 June 2018 12:47:57 PM<br>
<b>To:</b> Emmanuel Marfo<br>
</span>
<div>
<div class="x_x_m_-5505382561369211157x_m_-2290038695161413218x_h5"><b>Subject:</b> Re: [Gate-users] Material image dose scoring</div>
</div>
</font>
<div> </div>
</div>
<div>
<div class="x_x_m_-5505382561369211157x_m_-2290038695161413218x_h5">
<div>
<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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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_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319OWAAutoLink" id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPBorder_GT_15287933942890.2901239450969866" style="margin-bottom:20px; overflow:auto; width:100%; text-indent:0px">
<table id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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)">
<tbody>
<tr valign="top" style="border-spacing:0px">
<td id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319ImageCell_15287933942860.8895514416448271" colspan="1" style="width:250px; display:table-cell; padding-right:20px">
<div id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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>
</td>
<td id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319TextCell_15287933942870.6173573598772124" colspan="2" style="vertical-align:top; padding:0px; display:table-cell">
<div id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_m_-5586688518932082515m_-6360087027904357026gmail-m_-447624977491746132m_8061131706454315319LPRemovePreviewContainer_15287933942870.354328013542929">
</div>
<div id="x_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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_x_m_-5505382561369211157x_m_-2290038695161413218x_m_-231410338185362556x_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">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>
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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>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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