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<div>Dear Iván,</div>
<div><br>
</div>
<div>Thank you very much for breaking it down into steps. It was very helpful.</div>
<div><br>
</div>
<div>I tried my first simulation with the attenuation image as my phantom and placed a point source in the rat body. I resized the image to have very large voxels to accelerate the simulation. It seems to work.</div>
<div><br>
</div>
<div>Then I used the activity image (with the same size of the attenuation image) as the source.. again it seems to work. I have to check with smaller voxel size and higher activity for final check.</div>
<div><br>
</div>
<div>Thanks again and best regards,</div>
<div><br>
</div>
<div>Parisa<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div style="font-family:Times New Roman; color:#000000; font-size:16px">
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<div id="divRpF501014" style="direction:ltr"><font size="2" face="Tahoma" color="#000000"><b>From:</b> Gate-users [gate-users-bounces@lists.opengatecollaboration.org] on behalf of Límbano Iván López Coello [vancoello@gmail.com]<br>
<b>Sent:</b> 06 February 2019 22:20<br>
<b>To:</b> Parisa Khateri<br>
<b>Cc:</b> gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> Re: [Gate-users] implementing MOBY into GATE<br>
</font><br>
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<div></div>
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<div dir="ltr">
<div dir="ltr">
<div dir="ltr">Hello Parisa
<div><br>
</div>
<div>Sure, I will comment my experience:<span id="gmail-selectionBoundary_1549485867748_15625180610229417" class="gmail-rangySelectionBoundary" style="line-height:0"></span></div>
<div><br>
</div>
<div>After generate the MOBY/ROBY Phantom you have to go to the <span class="gmail-pwa-mark gmail-pwa-mark-done">
<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">logfile</span></span></span> (<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">it
is created</span></span></span> at the same time that the phantom) to see which attenuation values you have for each tissue an example is below (look for the Linear Attenuation Coefficients):</div>
<div>
<div><img src="cid:ii_jrtnyqxe0" alt="image.png" width="378" height="318"><br>
</div>
</div>
<div>These values will be useful later for the segmentation and to define sources and detectors, when you create a phantom with the MOBY application, it will generate 3 files, an attenuation image, an activity image and the
<span class="gmail-pwa-mark gmail-pwa-mark-done">log file</span>, I used the attenuation image for the simulations.</div>
<div>this attenuation image will be in .bin format, I changed the extension file from .bin to<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done"> .</span></span>raw</span> once
you have done this, <span class="gmail-pwa-mark gmail-pwa-mark-done"><span></span></span>create a header,
<span class="gmail-pwa-mark gmail-pwa-mark-done">an example of my header <span class="gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">is presented</span></span></span></span> below:</div>
<div><br>
</div>
<div><span id="gmail-selectionBoundary_1549486409900_7611517119097935" class="gmail-rangySelectionBoundary" style="line-height:0"></span>
<div><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">ObjectType</span></span> = Image</div>
<div><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">NDims</span></span> = 3</div>
<div><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">DimSize</span></span> = 256 256 739</div>
<div><br>
</div>
<div><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">ElementType</span></span> = MET_FLOAT</div>
<div><br>
</div>
<div><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">ElementSpacing</span></span> = 0.145 0.145 0.145</div>
<div><br>
</div>
<div><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">ElementByteOrderMSB</span></span> = False</div>
<div>Element</div>
<div><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">DataFile</span></span> = MOBY<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">.</span></span>raw</div>
</div>
<div><span id="gmail-selectionBoundary_1549486410484_22102339294734752" class="gmail-rangySelectionBoundary" style="line-height:0"></span><br>
</div>
<div><br>
</div>
<div>you can create in a <span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">txt</span></span> file, and when you complete it with the information
<span></span>you need, save it as<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done"> .</span></span><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">mhd</span></span>
extension</div>
<div><br>
</div>
<div>until now you will have:</div>
<div><br>
</div>
<div>MOBY<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">.</span></span>raw (attenuation image)</div>
<div>MOBY<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">.</span></span><span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">mhd</span></span>
<span class="gmail-pwa-mark gmail-pwa-mark-done"><span class="gmail-pwa-mark gmail-pwa-mark-done">( </span></span>Meta Image Header)</div>
<div>Attenuation Linear coefficients for the ROI <span class="gmail-pwa-mark gmail-pwa-mark-done">
<span class="gmail-pwa-mark gmail-pwa-mark-done">that </span></span>you want to simulate.</div>
<div><br>
</div>
<div>for GATE you can create a macro to confirm if the phantom was imported correctly then use that macro to import disabling the visualization because consumes a lot of computing resources please see my example below:</div>
<div>
<div><br>
</div>
<div><br>
</div>
<div>#=====================================================</div>
<div># GEOMETRY&VISUALIZATION</div>
<div>#=====================================================</div>
<div><br>
</div>
<div><br>
</div>
<div>/gate/geometry/<span class="gmail-pwa-mark gmail-pwa-mark-done">setMaterialDatabase</span><span class="gmail-pwa-mark gmail-pwa-mark-done"> .</span>./data/<span class="gmail-pwa-mark gmail-pwa-mark-done">GateMaterials</span>.db</div>
<div><br>
</div>
<div><br>
</div>
<div>#World</div>
<div>/vis/open OGLI</div>
<div>/<span class="gmail-pwa-mark gmail-pwa-mark-done">vis</span>/scene/create</div>
<div>/<span class="gmail-pwa-mark gmail-pwa-mark-done">vis</span>/scene/add/volume</div>
<div><br>
</div>
<div>/<span class="gmail-pwa-mark gmail-pwa-mark-done">vis</span>/scene/add/axes 0 0 0 500 mm</div>
<div><br>
</div>
<div>/vis/<span class="gmail-pwa-mark gmail-pwa-mark-done">sceneHandler</span>/attach</div>
<div><br>
</div>
<div>/gate/world/geometry/<span class="gmail-pwa-mark gmail-pwa-mark-done">setXLength</span> 50 cm</div>
<div><br>
</div>
<div>/gate/world/geometry/<span class="gmail-pwa-mark gmail-pwa-mark-done">setYLength</span> 50 cm</div>
<div><br>
</div>
<div>/gate/world/geometry/<span class="gmail-pwa-mark gmail-pwa-mark-done">setZLength</span> 50 cm</div>
<div><br>
</div>
<div>/gate/world/<span class="gmail-pwa-mark gmail-pwa-mark-done">setMaterial</span> Air</div>
<div><br>
</div>
<div>/gate/world/<span class="gmail-pwa-mark gmail-pwa-mark-done">vis</span>/<span class="gmail-pwa-mark gmail-pwa-mark-done">setVisible</span> 1</div>
<div><br>
</div>
<div>/gate/world/<span class="gmail-pwa-mark gmail-pwa-mark-done">vis</span>/<span class="gmail-pwa-mark gmail-pwa-mark-done">forceWireframe</span></div>
<div><br>
</div>
<div># Voxel phantom</div>
<div><br>
</div>
<div>/gate/world/daughters/name mouse</div>
<div>/gate/world/daughters/insert <span class="gmail-pwa-mark gmail-pwa-mark-done">ImageRegularParametrisedVolume</span></div>
<div><br>
</div>
<div>/gate/mouse/geometry/<span class="gmail-pwa-mark gmail-pwa-mark-done">setRangeToMaterialFile</span>
<span class="gmail-pwa-mark gmail-pwa-mark-done"> .</span>./data/<b><span class="gmail-pwa-mark gmail-pwa-mark-done">Range_MOBY</span>.txt</b></div>
<div><br>
</div>
<div>/gate/mouse/geometry/<span class="gmail-pwa-mark gmail-pwa-mark-done">setImage</span>
<span class="gmail-pwa-mark gmail-pwa-mark-done"> .</span>./data/MOBY<span class="gmail-pwa-mark gmail-pwa-mark-done">.</span><span class="gmail-pwa-mark gmail-pwa-mark-done">mhd</span></div>
<div><br>
</div>
<div>/gate/mouse/<span class="gmail-pwa-mark gmail-pwa-mark-done">setSkipEqualMaterials</span> 0</div>
<div><br>
</div>
<div><br>
</div>
<div>/gate/mouse/<span class="gmail-pwa-mark gmail-pwa-mark-done">vis</span>/<span class="gmail-pwa-mark gmail-pwa-mark-done">forceWireframe</span></div>
<div><br>
</div>
<div><br>
</div>
</div>
<div>the file<b> <span class="gmail-pwa-mark gmail-pwa-mark-done">Range_MOBY</span></b> was created using the Linear attenuation coefficients as shown below:</div>
<div><br>
</div>
<div>
<div>19 #number of the structures(tissues)</div>
<div><br>
</div>
<div>0 57.5345 Air ( every tissue is defined in a range of linear attenuation values that you found in the logfile of MOBY)</div>
<div><br>
</div>
<div>16.6851 16.6853 Lung</div>
<div><br>
</div>
<div>33.3449 33.3451 Adipose</div>
<div><br>
</div>
<div>55.1011 55.1013 Pancreas</div>
<div><br>
</div>
<div>55.7452 55.7454 Brain</div>
<div><br>
</div>
<div>56.5967 56.5969 Intestine</div>
<div><br>
</div>
<div>56.6229 56.6231 Muscle</div>
<div><br>
</div>
<div>56.7398 56.7400 Heart</div>
<div><br>
</div>
<div>56.9961 56.9963 Kidney</div>
<div><br>
</div>
<div>57.2666 57.2668 Liver</div>
<div><br>
</div>
<div>58.2013 58.2015 Spleen</div>
<div><br>
</div>
<div>58.4943 58.4945 Blood</div>
<div><br>
</div>
<div>59.1105<span style="white-space:pre"> </span>59.1107 Body</div>
<div><br>
</div>
<div>59.1771 59.1773 Lymph</div>
<div><br>
</div>
<div>60.3382 60.3384 Cartilage</div>
<div><br>
</div>
<div>65.4576 65.4578 SpineBone</div>
<div><br>
</div>
<div>71.8001 71.8003 Skull</div>
<div><br>
</div>
<div>82.1753 82.1755 RibBone</div>
</div>
<div><span id="selectionBoundary_1549487199034_14036015846009842" class="rangySelectionBoundary" style="line-height:0"></span><span id="selectionBoundary_1549487199230_2920590683593014" class="rangySelectionBoundary" style="line-height:0"></span><span id="selectionBoundary_1549487199724_8892523791751288" class="rangySelectionBoundary" style="line-height:0"></span><br>
</div>
<div><br>
</div>
<div>doing these steps you will <span></span>import and see your phantom in the GATE enviroment like this:</div>
<div>
<div><img src="cid:ii_jrtovp081" alt="image.png" width="319" height="181"><br>
</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Then for the simulation you have to define positioning, source, detectors, etc.</div>
<div><br>
</div>
<div>let me know if you need more information.</div>
<div><br>
</div>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">El mié., 6 feb. 2019 a las 12:06, Parisa Khateri (<<a href="mailto:parisa.khateri@cern.ch" rel="noopener noreferrer" target="_blank">parisa.khateri@cern.ch</a>>) escribió:<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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<div style="direction:ltr; font-family:Tahoma; color:rgb(0,0,0); font-size:10pt">
<div>Hi Iván,</div>
<div><br>
</div>
<div>I was wondering if you could solve this issue. If so, I would really appreciate if you could share your experience with me. I am totally new to Gate voxelized simulation and need some help to import MOBY/ROBY outputs into gate and run a voxelized simulation.</div>
<div><br>
</div>
<div>Thank you in advance and kind regards,</div>
<div><br>
</div>
<div>Parisa</div>
<div><br>
</div>
<div style="font-family:"Times New Roman"; color:rgb(0,0,0); font-size:16px">
<hr>
<div id="gmail-m_6136591214261167327divRpF653153" style="direction:ltr"><font size="2" face="Tahoma" color="#000000"><b>From:</b> Gate-users [<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" rel="noopener noreferrer" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>]
on behalf of Límbano Iván López Coello [<a href="mailto:vancoello@gmail.com" rel="noopener noreferrer" target="_blank">vancoello@gmail.com</a>]<br>
<b>Sent:</b> 24 October 2017 04:24<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" rel="noopener noreferrer" target="_blank">
gate-users@lists.opengatecollaboration.org</a><br>
<b>Subject:</b> [Gate-users] implementing MOBY into GATE<br>
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<div>Hello all</div>
<div> My name is Iván, I am quite new in this area my final proyect consist in a few experiments using different sizes of MOBY and 67Ga, but I am stuck in how import succesfully the MOBY into GATE<br>
</div>
<div><br>
</div>
<div>I have a few questions I hope you can help me:</div>
<div><br>
</div>
<div><br>
</div>
1.- I have checked the forums for this question, but it is still not clear for me, I have created a phantom with the MOBY software, it gave me two files:<br>
<br>
</div>
Act.bin and Atn.bin, I see that I need to convert them to a 16 bit inter file, but I am using ImageJ to perform the conversion, my steps were:<br>
<br>
</div>
Import the file then edit>options>conversions: uncheck scale when converting then I changed the image type to 16 bit and finally save it as a RAW.<br>
<br>
</div>
I would like to know if that is ok or Do I need to use another software?<br>
<br>
</div>
<br>
</div>
2.- I have checked that after the conversion to 16 bit I need to convert again to a i33 with a header h33 with a xmedcon software, I am using Ubuntu 16.04 and I am getting issues during installations of this xmedcon about JAVA JDK 8, so I am not able to perform
this conversion yet , I was checking that there is a windows version that I will try to install but in the mean time I would like to know if there is another way to perform the conversion and get my images with a header?<br>
<br>
<br>
</div>
3.- I was trying to do the example that is in GATE webpage that is named pre-clinical dosimetry that has a voxelized mouse phantom, I ran it and looks that it worked but when I enabled the visual mac I can not see the phantom, for now I just want to see a voxelized
phantom by just running the visual mac.. I checked the data folder and I see that the header is in a .iff file and the images are in a .img file. How can I run just the visual mac and see the mouse phantom?<br>
<br>
<br>
</div>
Thank you<br>
</div>
Best Regards from México<br>
</div>
Iván<br>
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