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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">Hi Atik,</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">Sorry for the delay!<br>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">I didn't look into this couple of years ago! But here is a working example for the mouse atlas voxelized phantom.</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">1- Back then GATE didn't read DICOM files so I had to use Interfile format (see attached *.h33 and *.i33).</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">2- Since using the whole mouse phantom is computationally intensive (even with a cluster computing), I kept the chest and truncated the rest of the mouse body.</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">Here are responses to your questions:</span></p>
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<strong style="background: transparent; margin-top:0pt; margin-bottom:0pt"><span style="background: transparent; margin-top:0pt; margin-bottom:0pt">How to define this file in GATEfor the given atlas data?</span></strong></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">I've attached a file 'Voxel_mouse.mac' where you can see how I have defined the atlas data in GATE.</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> </span><strong style="background: transparent; margin-top:0pt; margin-bottom:0pt"><span style="background: transparent; margin-top:0pt; margin-bottom:0pt">All the elements are also defined
in text files. </span></strong></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">If you're not using a whole-body mouse as a voxelized phantom, you don't have to define all organ labels in the text file, you can specify just the ones that exist in the region you're
studying (like brain structures for example).</span></p>
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<strong style="background: transparent; margin-top:0pt; margin-bottom:0pt"><span style="background: transparent; margin-top:0pt; margin-bottom:0pt">My problem is, that I do not know the interval defined in the attenuation range file.</span></strong></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">In the case of the atlas, you just add the tissue composition of each organ in the GATE material database, and then you specify these materials in the attenuation range file. I have attached
an attenuation range file, for the same attached voxelized mouse phantom, take a look on it. </span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">in the attached attenuation range file, you will find these names: SoftTissue, Heart, Water, Pancreas and here is how I have defined the Heart into the GATE material database: </span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt">Heart: d=1.05 g/cm3 ; n=11</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Hydrogen ; f=0.104</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Carbon ; f=0.139</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Nitrogen ; f=0.029</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Oxygen ; f=0.718</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Sodium ; f=0.001</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Phosphor ; f=0.002</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Sulfur ; f=0.002</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Chlorine ; f=0.002</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Potassium ; f=0.003</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Calcium ; f=0.0</span></p>
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<span style="background: transparent; margin-top:0pt; margin-bottom:0pt"> +el: name=Scandium ; f=0.0</span></p>
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I hope it helps,<br>
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Mahdjoub<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>De :</b> Atiq Ur Rahman <atiqchep@gmail.com><br>
<b>Envoyé :</b> samedi 22 février 2020 10:46<br>
<b>À :</b> Mahdjoub Hamdi <mahdjoub.hamdi@hotmail.fr><br>
<b>Objet :</b> Re: [Gate-users] How to access Dicom Images of small Animals (RAT, Cat, Frog)</font>
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<div dir="ltr">Dear Mahdjoub Hamdi,
<div>In the Atlas data file, we have three the files. In usual .dcm phantoms we use to provide an attenuation_range.txt file which is shown below. How to define this file in the gate for the given atlas data? All the elements are also defined in a text files.
My problem is , that I do not know the interval define in the attenuation range file. </div>
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<div><img alt="image.png" width="459" height="164" data-outlook-trace="F:1|T:1" src="cid:4c45f4de-95aa-4a5e-8753-bec00fe32728"><br>
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<div>old and New and code....</div>
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<div><img alt="image.png" width="472" height="247" data-outlook-trace="F:1|T:1" src="cid:29bcdee7-74db-4367-ad9e-eec644a8d567"><br>
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<div>Attenuation range file..</div>
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<div><img alt="image.png" width="421" height="127" data-outlook-trace="F:1|T:1" src="cid:acc5369c-f1f4-407f-b450-118e09d775d9"><br>
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<div>How I can writ new Material conversion file. The given atlas data file, materials are described but the interval or ranges are not known.</div>
<div>Regards</div>
<div>Atiq</div>
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<div dir="ltr" class="x_gmail_attr">On Sat, Feb 22, 2020 at 12:04 AM Mahdjoub Hamdi <<a href="mailto:mahdjoub.hamdi@hotmail.fr">mahdjoub.hamdi@hotmail.fr</a>> wrote:<br>
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Hi Atik,</div>
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Take a look here: <a href="https://neuroimage.usc.edu/neuro/Digimouse" id="x_gmail-m_-403349848869549423LPNoLP926777" target="_blank">
https://neuroimage.usc.edu/neuro/Digimouse</a>.</div>
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This is the Digimouse project, where you can find coregistered PET/CT and cryosection mouse image plus the Atlas.</div>
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You don't have to use them as Dicom format, you can use them as an interfile format where the binary file is short integer.<br>
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I used to work with these images for small animal radiation therapy, let me know if you face any issues.</div>
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Thanks,</div>
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Mahdjoub<br>
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<div id="x_gmail-m_-403349848869549423divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>De :</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>>
de la part de Atiq Ur Rahman <<a href="mailto:atiqchep@gmail.com" target="_blank">atiqchep@gmail.com</a>><br>
<b>Envoyé :</b> vendredi 21 février 2020 06:26<br>
<b>À :</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Objet :</b> [Gate-users] How to access Dicom Images of small Animals (RAT, Cat, Frog)</font>
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<div dir="ltr">Dear Users,
<div>I have simulated a PET with small geometric efficiency. I want to try some animal CT dicom Images as Phantom. Can you please point me some free online repository, database or someone share if he have for study and research purposes. I have surfed but
somehow not able to find any free resource.</div>
<div>Regards</div>
<div>Atiq</div>
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