<div><div><div><div style="border-color:rgb(255,255,255)" dir="auto">Hi Xinjie,</div><div style="border-color:rgb(255,255,255)" dir="auto"><br></div><div style="border-color:rgb(255,255,255)" dir="auto">Thank you for your advice for converting format.</div></div></div><div></div></div><div><div style="border-color:rgb(255,255,255)" dir="auto"><br></div><div style="border-color:rgb(255,255,255)"><span style="border-color:rgb(0,0,0);color:rgb(0,0,0)">> </span><span style="border-color:rgb(0,0,0);color:rgb(0,0,0)">does this process '</span><span style="border-color:rgb(80,0,80);color:rgb(80,0,80)">Process > Math > Add: Add the attenuation coefficient</span><span style="border-color:rgb(0,0,0);color:rgb(0,0,0)">' need any outer info or it did calculation based on the image you input? </span><br></div><div style="border-color:rgb(255,255,255)"><br></div></div><div><div><div style="border-color:rgb(255,255,255)">Attenuation coefficients were outer information. I looked it up on XCOM. <span>I am simulating a simple structure phantom like the NEMA phantom </span>and consist of two materials, water and air. Thus, it was<span> not difficult to add the values manually. </span><span>For complex phantoms, adding the attenuation coefficient may be a bit complicated.</span></div><div style="border-color:rgb(255,255,255)"><span><br></span></div><div style="border-color:rgb(255,255,255)"><span><br></span></div><div style="border-color:rgb(255,255,255)"><span><br></span></div><div style="border-color:rgb(255,255,255)"><span>Best,</span></div><div style="border-color:rgb(255,255,255)"><span>Suguru</span></div><div style="border-color:rgb(255,255,255)"><span><br></span></div><div><br></div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2020年7月16日(木) 23:51 Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>>:<br></div></div></div></div><div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)"><div dir="ltr">Hi Suguru,<div><br></div></div></blockquote></div></div></div></div><div><div><div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)"><div dir="ltr"><div>Thanks for your reply, really appreciate it! </div><div><br></div><div>From my understanding, the attenuation map/correction image helps improve the real reconstructed image quality because it is
based on the different tissues or parts of the phantom. So how does ImageJ generate the attenuation correction image by adding coefficients without any other look-up-table or atlas? I mean, <span style="border-color:rgb(0,0,0);color:rgb(0,0,0)">does this process '</span><span style="border-color:rgb(80,0,80);color:rgb(80,0,80)">Process > Math > Add: Add the attenuation coefficient</span><span style="border-color:rgb(0,0,0);color:rgb(0,0,0)">' need any outer info or it did calculation based on the image you input? </span></div><div><br></div><div>PS: For image format conversion, I recommend you use Medcon instead of AMIDE because it looks like there are some little bugs in AMIDE conversion.</div><div><br></div><div>Best,</div><div>Xinjie</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 15, 2020 at 4:33 PM Suguru Katsube <<a href="mailto:sug.katsu@gmail.com" target="_blank">sug.katsu@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)"><div dir="ltr"> Hi, Xinjie<br><br><br>1) Which kind of phantom are you using? Normal phantom or voxelized phantom?<br>I made normal phantom. <br><br>2) What tool did you use for generating the attenuation image? GATE or CASToR?<br>Attenuation image was generated outside the CASToR. I made attenuation image using ImageJ.<br>In ImageJ, <br>File > New > Image: A fresh stack image is opened.<br>Image > properties: Set the pixel size<br>Edit > Selection > Specify: Set regions<br>Process > Math > Add: Add the attenuation coefficient<br>File > save As > Raw Data<br><br>ImageJ didn't seem to support interfile format without a plugin. So I used AMIDE to convert the file format.<br>In AMIDE, <br>File > Import File(Specify) > Raw Data<br>File > Export Data Set<div><br></div><div>It may not be a very wise approach. I hope this helps you.</div><div><br></div><div>Best regards,</div><div>Suguru</div><div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2020年7月16日(木) 5:30 Suguru Katsube <<a href="mailto:sug.katsu@gmail.com" target="_blank">sug.katsu@gmail.com</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)"><div dir="ltr">Hi, Xinjie<br><br><br>1) Which kind of phantom are you using? Normal phantom or voxelized phantom?<br>I made normal phantom. <br><br>2) What tool did you use for generating the attenuation image? GATE or CASToR?<br>Attenuation image was generated outside the CASToR. I made attenuation image using ImageJ.<br>In ImageJ, <br>File > New > Image: A fresh stack image is opened.<br>Image > properties: Set the pixel size<br>Edit > Selection > Specify: Set regions<br>Process > Math > Add: Add the attenuation coefficient<br>File > save As > Raw Data<br><br>ImageJ didn't seem to support interfileformat without a plugin. So I used AMIDE to convert the file format.<br>In AMIDE, <br>File > Import File(Specify) > Raw Data<br>File > Export Data Set<div><br></div><div>It may not be a very wise approach. I hope this helps you.</div><div><br></div><div>I hope we can continue to share information with each other as we are all interested in the same field.<br></div><div><br></div><div>Best regards, </div><div>Suguru<br><div><br></div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2020年7月15日(水) 23:43 Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)"><div dir="ltr">Hi Suguru,<div><br></div><div>I am also curious about how to generate the attenuation correction image and have a few questions, could you share some experience about that?</div><div><br></div><div>1) Which kind of phantom are you using? Normal phantom or voxelized phantom?</div><div>2) What tool did you use for generating the attenuation image? GATE or CASToR?</div><div><br></div><div>Any reply will be highly appreciated! Thank you!</div><div><br></div><div>Best,</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Jul 15, 2020 at 6:29 AM Suguru Katsube <<a href="mailto:sug.katsu@gmail.com" target="_blank">sug.katsu@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)"><div dir="ltr">Dear Thibaut Merlin,<div><br></div><div>Thank you for your quick response. <br></div><div>Successfully, I made the attenuation image. Then, I made **.cdh and **.cdf with attenuaton correrction using castor-GATERootToCastor (This is list-mode format for reconstructing with scatter and random correction). <br></div><div><br></div><div>When I run castor-recon, the message below was displayed.</div><div><br></div><div><b>***** oSensitivityGenerator::InitializeAttenuationFiles() -> Attenuation correction is included in the data file while it is not in the sensitivity computation !<br>***** oSensitivityGenerator::Initialize() -> A problem occurred while initializing the attenuation files !<br>***** castor-recon() -> A problem occurred while initializing the sensitivity generator !<br></b></div><div><br></div><div>I know that the attenuation image MUST be providen to the castor-recon exe as well, in order to perform sensitivity image computation for PET list-mode. How should I provide attenuation image to reconstruct the data?<br></div><div><br></div><div>Thank you in advance.</div><div>Best regards,</div><div><br></div><div>Suguru</div><div><br></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">2020年6月30日(火) 0:00 tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">Thibaut.Merlin@univ-brest.fr</a>>:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)">
<div>
<p>Hi Suguru,</p>
<p>Attenuation image must be in interfile format, and must be in
cm-1. The dimensions/voxel sizes will be interpolated to the
reconstruction image dimensions, so you don't need to provide an
image with the exact same dimensions than for the reconstruction.
Additionally, you should make sure that the reconstruction image
dimensions are large enough to include all attenuated materials of
the attenuation image, otherwise the attenuation correction will
be incorrect. </p>
<p>Regarding the image itself, you should generate it from the
geometry of the phantom you use in the GATE simulation, or derive
it directly from the phantom image if you used a voxelized
phantom.</p>
<p>Hope this helps,</p>
<p>Thibaut<br>
</p>
<p><br>
</p>
<div>On 29/06/2020 09:57, Suguru Katsube
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi all,
<div><br>
</div>
<div>I am trying to reconstruct a GATE root file (PET).<br>
I want to apply attenuation correction and reconstruct it. The
manual states I need an attenuation image, how do I create it
? The phantom was designed on a GATE and no CT images were
acquired. There are many unclear points such as image format,
number of pixels, number of slices, alignment, etc. Can I
create the attenuation image using a root file or mac file?</div>
<div><br>
Any advice is appreciated.<br clear="all">
<div><br>
</div>
<div>Best regards, </div>
<div><br>
</div>
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<pre cols="72" style="font-family:monospace">--
Thibaut MERLIN -- PhD
Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
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Tel: 06.75.12.24.90</pre>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><b><font style="color:rgb(0,0,0)">....................................................</font></b><br></div><div><b><span style="font-family:"arial black",sans-serif;font-size:x-small;color:rgb(153,0,0)">Xinjie Cao</span></b><br></div><div><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)">M.E. / Ph.D. student</font></b></div><div><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)">Research Project Assistant</font></b></div><div><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)">Department of Electrical and Computer Engineering & Radiology </font></b></div><div><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)">Novel Medical Imaging Technologies Lab</font></b></div><div><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)">Health Science Center Level 8</font></b></div><div><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)">Stony Brook, NY 11794-8460 </font></b></div><div><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)">Tel: +1 (631)202-9445</font></b></div><div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)"><br></font></b></div><div><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)"><b style="font-family:"arial black",sans-serif">email: </b><a href="mailto:xinjie.cao@stonybrook.edu" style="font-family:"arial black",sans-serif" target="_blank"><b style="font-family:"arial black",sans-serif">xinjie.cao@stonybroo</b>k.edu</a></font></div><div><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)"><br></font></div><div><font size="1" face="arial black, sans-serif" style="font-family:"arial black",sans-serif;color:rgb(0,0,0)"> </font><img src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ" width="200" height="28"> <img src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" width="200" height="33"></div><div><div><b><font style="color:rgb(0,0,0)">....................................................</font></b></div><div>It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)">○●----------------------------------------------------------●○</font></div><div><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"> 勝部 俊（Suguru Katsube）</font></div><div><p style="margin:0px;line-height:normal"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"><font style="font-family:arial,sans-serif;color:rgb(0,0,0)"> 九州大学大学院</font><span style="font-family:arial,sans-serif;color:rgb(0,0,0)">医学系学府保健学専攻</span></font></p><p style="margin:0px;line-height:normal"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"> 医用量子線科学分野 修士課程2年</font></p><p style="margin:0px;line-height:normal;min-height:14px"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"> Medical Quantum Radiation Science Course<span style="line-height:normal;font-family:arial,sans-serif">,</span></font></p><p style="margin:0px;line-height:normal"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"> Department of Health Sciences<span style="line-height:normal;font-family:arial,sans-serif">,</span></font></p><p style="margin:0px;line-height:normal"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"> Graduate School of Medical Sciences<span style="line-height:normal;font-family:arial,sans-serif">,</span> </font></p><p style="margin:0px;line-height:normal"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"> Kyushu University<span style="line-height:normal;font-family:arial,sans-serif">,</span> Fukuoka<span style="line-height:normal;font-family:arial,sans-serif">,</span> Japan</font></p><p style="margin:0px;line-height:normal"><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)"><font style="font-family:arial,sans-serif;color:rgb(0,0,0)"> E-mail: </font><a href="mailto:E-mail%3Aymmk88kmmy@gmail.com" style="font-family:arial,sans-serif;color:rgb(17,85,204)" target="_blank">sug.katsu@gmail.com</a></font></p></div><div><font face="arial, sans-serif" style="font-family:arial,sans-serif;color:rgb(0,0,0)">○●----------------------------------------------------------●○</font></div></div></div></div></div></div></div></div></div>
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</div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><font face="arial, sans-serif">○●----------------------------------------------------------●○</font></div><div><font face="arial, sans-serif"> 勝部 俊（Suguru Katsube）</font></div><div><p style="margin:0px;line-height:normal"><font face="arial, sans-serif"><font color="#000000"> 九州大学大学院</font><span style="color:rgb(0,0,0)">医学系学府保健学専攻</span></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, sans-serif"> 医用量子線科学分野 修士課程2年</font></p><p style="margin:0px;line-height:normal;min-height:14px"><font color="#000000" face="arial, sans-serif"><br></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, sans-serif"> Medical Quantum Radiation Science Course<span style="line-height:normal">,</span></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, sans-serif"> Department of Health Sciences<span style="line-height:normal">,</span></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, sans-serif"> Graduate School of Medical Sciences<span style="line-height:normal">,</span> </font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, sans-serif"> Kyushu University<span style="line-height:normal">,</span> Fukuoka<span style="line-height:normal">,</span> Japan</font></p><p style="margin:0px;line-height:normal"><font face="arial, sans-serif"><font color="#000000"> E-mail: </font><a href="mailto:E-mail%3Aymmk88kmmy@gmail.com" style="color:rgb(17,85,204)" target="_blank">sug.katsu@gmail.com</a></font></p></div><div><font face="arial, sans-serif">○●----------------------------------------------------------●○</font></div></div></div></div></div></div></div></div></div>