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Hi,
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<div>When you generated your voxelized phantom files, you also generated a log file (*_log). If you look at that file, you will find a list of materials under "Linear Attenuation Coefficients (1/pixel)". These are the pixel values that represent each material.
For example, if a pixel has value 0.0467, you look at that list and figure out what material it is (in my case, this corresponds to water).</div>
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<div>Now, remember that the XCAT produces 32-bit real images. Gate, however, needs 16-bit unsigned integer images. So, you need to convert your phantom to 16-bit unsigned integer using the method of your choice (Matlab, ImageJ, etc.). You also need to figure
out what conversion is used to go from 32-bit real to 16-bit unsigned integer. I usually used a simple linear scale. Now, you need to convert your list of materials with pixel values in 32-bit real to 16-bit unsigned int. For example, if the rib bone is the
highest value in your image (e.g. 0.0686 in 32-bit), it would become 65535 in 16-bit unsigned (using a linear scale).</div>
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<div>Once you have your phantom in 16-bit unsigned int format, you need your range translator as described in the Gate User's Guide. The first two columns (the range) will be the 16-bit pixel values that you converted from your log file. In this case, there
is no range, so you can write down the same number for both columns or you can give it a small range if there is no overlap over different materials. Then you write the name of the materials to which this corresponds (use the name that is found in the Gate
materials database). Then you can add the visiblity options.</div>
<div><br>
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<div>I hope this helps!</div>
<div><br>
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<div>Cheers,<br>
<div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Marc</div>
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<div><br>
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<div>__________________________</div>
<div><br>
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<div>Marc Chamberland, MSc</div>
PhD candidate<br>
Department of Physics<br>
Carleton University<br>
Ottawa (ON)</div>
</span></div>
<br>
<div>
<div>On May 19, 2014, at 16:17, Wei Deng <<a href="mailto:wdeng@oakland.edu">wdeng@oakland.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">Thank you very much. So my question is how to form the attenuation map in Gate using XCAT-phantom attenuation data. For example, The attenuation data 'heart_atten.bin' was generated with the program XCAT, with the attenuation coefficient 0.009789/voxel
or 0.1000/cm, how could I read the attenuation data for simulation in Gate?<br>
<br>
thank you so much.<br>
Best regards,<br>
<br>
Wei<br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Mon, May 19, 2014 at 11:48 PM, Marc Chamberland <span dir="ltr">
<<a href="mailto:MarcChamberland@cmail.carleton.ca" target="_blank">MarcChamberland@cmail.carleton.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Wei,
<div><br>
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<div>The attenuation range does not give the actual attenuation coefficients. Read the user's guide: <a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Voxelized_Source_and_Phantom#Conversion_into_material_definitions" target="_blank">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Voxelized_Source_and_Phantom#Conversion_into_material_definitions</a></div>
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<div>The first two numbers on a line represent the range of voxel values for which the voxel will be assigned the material on the line (so Gate knows the attenuation coefficients by knowing what material the voxel is). The last four numbers on the line are
simply the visualization parameters, i.e. what color this specific material will be on the screen and how transparent it will be. It has nothing to do with the attenuation coefficients.</div>
<div><br>
</div>
<div>I hope this helps.</div>
<div><br>
</div>
<div>Cheers,<br>
<div><span style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; border-spacing: 0px;">
<div style="word-wrap:break-word">
<div>Marc</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>__________________________</div>
<div><br>
</div>
<div>Marc Chamberland, MSc</div>
PhD candidate<br>
Department of Physics<br>
Carleton University<br>
Ottawa (ON)</div>
</span></div>
<br>
<div>
<div>
<div class="h5">
<div>On May 19, 2014, at 9:30, Wei Deng <<a href="mailto:wdeng@oakland.edu" target="_blank">wdeng@oakland.edu</a>> wrote:</div>
<br>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">Hello, gaters. There is a question when I am studying the voxelized phantom. It read 'AttenuationRange.dat' to form the attenuation map in VoxelizedPhantom.mac in the examplePET. However the last column of 'AttenuationRange.dat' is not discripted
as 'attenuation coefficient' but 'Tansparency'. Who can tell me the relationship between 'attenuation coefficient' and 'Tansparency'? Should I replace the 'Tansparency' with my 'attenuation coefficient' when forming the attenuation map?
<br>
My phantom was created by XCAT. Is there any documentation (or are there examples) for integrating XCAT-phantom<br>
attenuation data into a gate simulation?<br>
<br>
thank you so much for your attention.<br>
Best regards,<br>
<br>
Wei<br>
</div>
</div>
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