<html>

<head>

<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">

<style type="text/css" style="display:none;"> P {margin-top:0;margin-bottom:0;} </style>

</head>

<body dir="ltr">

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

Hi everyone,</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

<br>

</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

I was not able to reproduce the incorrect behavior in later tests with the same macros and voxelized source, so interfile also seems to work just fine in 9.2. I did update ROOT to a newer version before the new tests, but I doubt it should have any effect in

 this case. I guess there might be a certain combination that causes issues, but at the moment I have no idea what might have been the cause.</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

<br>

</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

In a nutshell, using interfile is completely viable too.</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

<br>

</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

As a sidenote, I don't think the size of the CT/phantom voxels/matrix should have any effect on the source position, but it can cause wrong attenuation if the anatomic locations are in different locations.<br>

</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

<br>

</div>

<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">

Regards,

<div>Ville-Veikko Wettenhovi<br>

</div>

</div>

<div id="appendonsend"></div>

<hr style="display:inline-block;width:98%" tabindex="-1">

<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Julia Franziska Brosch-Lenz <jbrosch@bccrc.ca><br>

<b>Sent:</b> Friday, July 15, 2022 21:37<br>

<b>To:</b> 'BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)' <mark.baker23@nhs.net>; Ville-Veikko Wettenhovi <ville-veikko.wettenhovi@uef.fi>; gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>

<b>Subject:</b> RE: Voxelised Source Placement Confusion</font>

<div> </div>

</div>

<style>

<!--

@font-face

        {font-family:"Cambria Math"}

@font-face

        {font-family:Calibri}

@font-face

        {font-family:"Segoe UI"}

p.x_MsoNormal, li.x_MsoNormal, div.x_MsoNormal

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Times New Roman",serif}

a:link, span.x_MsoHyperlink

        {color:#0563C1;

        text-decoration:underline}

a:visited, span.x_MsoHyperlinkFollowed

        {color:#954F72;

        text-decoration:underline}

p

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Times New Roman",serif}

p.x_msonormal0, li.x_msonormal0, div.x_msonormal0

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Times New Roman",serif}

p.x_xxmsonormal, li.x_xxmsonormal, div.x_xxmsonormal

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Times New Roman",serif}

p.x_xxmsonormal0, li.x_xxmsonormal0, div.x_xxmsonormal0

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Times New Roman",serif}

p.x_xxxmsonormal, li.x_xxxmsonormal, div.x_xxxmsonormal

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Times New Roman",serif}

p.x_xxxmsonormal0, li.x_xxxmsonormal0, div.x_xxxmsonormal0

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Times New Roman",serif}

p.x_xxxxmsonormal, li.x_xxxxmsonormal, div.x_xxxxmsonormal

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:11.0pt;

        font-family:"Calibri",sans-serif}

p.x_xxxxmsochpdefault, li.x_xxxxmsochpdefault, div.x_xxxxmsochpdefault

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:12.0pt;

        font-family:"Calibri",sans-serif}

p.x_xxxmsochpdefault, li.x_xxxmsochpdefault, div.x_xxxmsochpdefault

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:10.0pt;

        font-family:"Times New Roman",serif}

p.x_xxmsochpdefault, li.x_xxmsochpdefault, div.x_xxmsochpdefault

        {margin:0cm;

        margin-bottom:.0001pt;

        font-size:10.0pt;

        font-family:"Times New Roman",serif}

span.x_xxmsohyperlink

        {color:#0563C1;

        text-decoration:underline}

span.x_xxmsohyperlinkfollowed

        {color:#954F72;

        text-decoration:underline}

span.x_xxxmsohyperlink

        {color:#0563C1;

        text-decoration:underline}

span.x_xxxmsohyperlinkfollowed

        {color:#954F72;

        text-decoration:underline}

span.x_xxxxmsohyperlink

        {color:#0563C1;

        text-decoration:underline}

span.x_xxxxmsohyperlinkfollowed

        {color:#954F72;

        text-decoration:underline}

span.x_xxxxemailstyle17

        {font-family:"Calibri",sans-serif;

        color:windowtext}

span.x_xxxemailstyle24

        {font-family:"Calibri",sans-serif;

        color:#1F497D}

span.x_xxemailstyle30

        {font-family:"Calibri",sans-serif;

        color:#1F497D}

span.x_xxemailstyle31

        {font-family:"Calibri",sans-serif;

        color:#1F497D}

span.x_EmailStyle37

        {font-family:"Calibri",sans-serif;

        color:#1F497D}

span.x_EmailStyle38

        {font-family:"Calibri",sans-serif;

        color:#1F497D}

span.x_EmailStyle39

        {font-family:"Calibri",sans-serif;

        color:windowtext}

.x_MsoChpDefault

        {font-size:10.0pt}

@page WordSection1

        {margin:72.0pt 72.0pt 72.0pt 72.0pt}

div.x_WordSection1

        {}

-->

</style>

<div lang="EN-CA" link="#0563C1" vlink="#954F72">

<div class="x_WordSection1">

<p class="x_MsoNormal"><span lang="DE" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Hi Mark, hi Ville-Veikko,</span></p>

<p class="x_MsoNormal"><span lang="DE" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">I can confirm that there is

<u>no issue</u> with the voxelized source shift in Gate version 9.2 when you use mhd files.

</span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">I highly recommend to convert your files to mhd format that should ease it for you. Plus I noticed your PET and CT are not having the same voxel and matrix

 size. This is an issue too, they not only have to be registered, but also resampled to the same voxel and matrix size. Then you need to shift the source image (=PET in your case) by half of it’s size.

</span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">I attach the example that I gave you in my answer to your previous email back in April again:</span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span style="color:#1F497D">Here an example from one of my simulations: my source image matrix is 256x256x1000. My voxel size is 0.145x0.145x0.145 mm^3. That makes a total image size of 37.12 37.12 145 mm^3. That means the command line

 for my source is:</span></p>

<p class="x_MsoNormal"><span style="color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span style="color:#1F497D"># Source has always to be shifted to -1/2 of its total length in x,y,z</span></p>

<p class="x_MsoNormal"><span style="color:#1F497D">/gate/source/YOURSOURCE/setPosition -18.56 -18.56 -72.5 mm</span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Please try 1) resample your CT to PET size and then 2) convert PET and resampled CT to mhd format, and 3) apply the shift as explained above. You should not

 encounter any issue anymore.</span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Best,</span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Julia</span></p>

<p class="x_MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<div>

<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">

<p class="x_MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Gate-users <gate-users-bounces@lists.opengatecollaboration.org>

<b>On Behalf Of </b>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)<br>

<b>Sent:</b> July 15, 2022 8:45 AM<br>

<b>To:</b> Ville-Veikko Wettenhovi <ville-veikko.wettenhovi@uef.fi>; gate-users@lists.opengatecollaboration.org<br>

<b>Subject:</b> Re: [Gate-users] Voxelised Source Placement Confusion</span></p>

</div>

</div>

<p class="x_MsoNormal"> </p>

<table class="x_MsoNormalTable" border="0" cellspacing="3" cellpadding="0">

<tbody>

<tr>

<td style="border:solid black 1.0pt; background:lightyellow; padding:0cm 7.5pt 0cm 7.5pt">

<p><span style="color:black">This email came from an </span><b><span style="color:red">EXTERNAL SENDER.</span>

</b><span style="color:black">If you think this message is suspicious, please do not open any attached files or links, and forward it as an attachment to

</span><span style="color:blue"><a href="mailto:spammail@bccrc.ca">spammail@bccrc.ca</a>

</span></p>

</td>

</tr>

</tbody>

</table>

<p class="x_MsoNormal"><span lang="EN-GB"> </span></p>

<div>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Hi Ville-Veikko</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Apologies for the delay in replying. Between leave and short-staffing in my department, I’ve not been able to get back to my project for a while.

 I think I’m using version 9.0 but I would have to check.</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">I have a plan to try both approaches (interfile and rolling back to 8.2) and I’ll report back with my own findings. Probably won’t be until the

 end of next week unfortunately though.</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<div>

<p class="x_MsoNormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Mark Baker</span></b></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Principal Clinical Scientist</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Imaging Physics (Ionising)</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span></p>

<p class="x_MsoNormal"><i><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">(he, him)</span></i></p>

<p class="x_MsoNormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871"> </span></b></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCW Tel:  0151 556 5030

</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCL Tel: 0151 318 8438</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Email:

</span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">

</span></p>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7C3c8b9c8490ec4c9053c408da66911aa4%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637935070801985131%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nK63QmzrM74hJBaNsVaaUiOpgiBgyD4X%2B8NSHZoGACk%3D&reserved=0" originalsrc="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" shash="GIQHIUA8sLPs2W3Tf/3a+YlIs0PA8W6BQ2t2OODjA9gldwdtxUhEscR1/M+LLfQeLyCADlXMvviYTpj72FLUHALaJ0bYdpVNFlnFvRGjy75YmuYjQiUIJ53jeUcgVTElpqMiW3sXjQkV5eZMyKOmqMpyafTM+dwUIWnOktVyoLE="><span style="color:#4472C4">Microsoft

 Teams (click here)</span></a></span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"></span></p>

</div>

<p class="x_MsoNormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span></p>

<div>

<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">

<p class="x_MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>

<br>

<b>Sent:</b> 12 July 2022 16:32<br>

<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>>;

<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>

<b>Subject:</b> Re: Voxelised Source Placement Confusion</span></p>

</div>

</div>

<p class="x_MsoNormal"><span lang="EN-GB"> </span></p>

<table class="x_MsoNormalTable" border="0" cellspacing="0" cellpadding="0" align="left" width="100%" style="width:100.0%; margin-left:.45pt; margin-right:.45pt">

<tbody>

<tr style="height:10.5pt">

<td style="background:#910A19; padding:5.25pt 1.5pt 5.25pt 1.5pt; height:10.5pt">

<p class="x_MsoNormal" style=""> </p>

</td>

<td width="100%" style="width:100.0%; background:#FDF2F4; padding:0cm 3.75pt 0cm 6.25pt; height:10.5pt">

<p class="x_MsoNormal" style=""><span style="font-size:9.0pt; font-family:"Segoe UI",sans-serif; color:#212121">This message originated from outside of NHSmail. Please do not click links or open attachments unless you recognise the sender and know the content

 is safe. </span></p>

</td>

</tr>

</tbody>

</table>

<div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Hi Mark,</span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Have you had any progress? What GATE version are you using by the way? I did some tests myself, and it seems that voxelized sources are

 either broken in GATE v9.2 or then the documentation is outdated. The shift that worked previously (at least in 8.2), now shifts the source in completely different location. In fact, using the original rule, the source seems to be shifted completely out of

 the scanner FOV in the current version.</span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Has the voxelized source example been tested/validated for the current version?</span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Regards,

</span></p>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Ville-Veikko Wettenhovi</span></p>

</div>

</div>

<div class="x_MsoNormal" align="center" style="text-align:center"><span lang="EN-GB">

<hr size="2" width="98%" align="center">

</span></div>

<div id="x_divRplyFwdMsg">

<p class="x_MsoNormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black">From:</span></b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black"> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>><br>

<b>Sent:</b> Wednesday, June 29, 2022 10:59<br>

<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>>;

<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>

<b>Subject:</b> Re: Voxelised Source Placement Confusion</span><span lang="EN-GB">

</span></p>

<div>

<p class="x_MsoNormal"><span lang="EN-GB"> </span></p>

</div>

</div>

<div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Hi Mark,</span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Sorry for the late response. I've not used DICOM images myself with GATE ever so I really can't comment them. One possibility is if you

 convert the DICOM images into interfile or MetaImage files and then try again. Those have always worked fine in my case.</span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span></p>

</div>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Regards,

</span></p>

<div>

<p class="x_MsoNormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Ville-Veikko Wettenhovi</span></p>

</div>

</div>

<div class="x_MsoNormal" align="center" style="text-align:center"><span lang="EN-GB">

<hr size="2" width="98%" align="center">

</span></div>

<div id="x_x_divRplyFwdMsg">

<p class="x_MsoNormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black">From:</span></b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black"> BAKER, Mark (THE CLATTERBRIDGE CANCER

 CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>><br>

<b>Sent:</b> Thursday, June 23, 2022 14:55<br>

<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>>; Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>;

<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>

<b>Subject:</b> RE: Voxelised Source Placement Confusion</span><span lang="EN-GB">

</span></p>

<div>

<p class="x_MsoNormal"><span lang="EN-GB"> </span></p>

</div>

</div>

<div>

<div>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Hi Ville-Veikko (and everyone else)</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Apologies for the delay in getting this data back, I’ve not had much project time recently. I’ve attached a single slice from each of the PET

 and CT data, and as far as I can tell, the data looks correct.</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<div>

<p class="x_xxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Mark Baker</span></b><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Principal Clinical Scientist</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Imaging Physics (Ionising)</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><i><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">(he, him)</span></i><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871"> </span></b><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCW Tel:  0151 556 5030

</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCL Tel: 0151 318 8438</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Email:

</span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">

</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7C3c8b9c8490ec4c9053c408da66911aa4%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637935070801985131%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nK63QmzrM74hJBaNsVaaUiOpgiBgyD4X%2B8NSHZoGACk%3D&reserved=0" originalsrc="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" shash="GIQHIUA8sLPs2W3Tf/3a+YlIs0PA8W6BQ2t2OODjA9gldwdtxUhEscR1/M+LLfQeLyCADlXMvviYTpj72FLUHALaJ0bYdpVNFlnFvRGjy75YmuYjQiUIJ53jeUcgVTElpqMiW3sXjQkV5eZMyKOmqMpyafTM+dwUIWnOktVyoLE="><span style="color:#4472C4">Microsoft

 Teams (click here)</span></a></span><span lang="EN-GB"></span></p>

</div>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<div>

<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">

<p class="x_xxmsonormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org">gate-users-bounces@lists.opengatecollaboration.org</a>>

<b>On Behalf Of </b>BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST)<br>

<b>Sent:</b> 17 June 2022 09:27<br>

<b>To:</b> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>;

<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>

<b>Subject:</b> Re: [Gate-users] Voxelised Source Placement Confusion</span><span lang="EN-GB"></span></p>

</div>

</div>

<p class="x_xxmsonormal"><span lang="EN-GB"> </span></p>

<table class="x_MsoNormalTable" border="0" cellspacing="0" cellpadding="0" align="left" width="100%" style="width:100.0%; margin-left:.45pt; margin-right:.45pt">

<tbody>

<tr style="height:10.5pt">

<td style="background:#910A19; padding:5.25pt 1.5pt 5.25pt 1.5pt; height:10.5pt">

<p class="x_xxmsonormal" style=""> </p>

</td>

<td width="100%" style="width:100.0%; background:#FDF2F4; padding:0cm 3.75pt 0cm 6.25pt; height:10.5pt">

<p class="x_xxmsonormal" style=""><span style="font-size:9.0pt; font-family:"Segoe UI",sans-serif; color:#212121">This message originated from outside of NHSmail. Please do not click links or open attachments unless you recognise the sender and know the content

 is safe. </span></p>

</td>

</tr>

</tbody>

</table>

<div>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">I think so. I got the information direct from the header files, with both imageJ and Weasis. I’m away from my data at the moment, but when

 I am back I’ll attach a sample slice with the header attached, in case I’m being a complete numpty.</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<div>

<p class="x_xxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Mark Baker</span></b><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Principal Clinical Scientist (Interim)</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Imaging Physics (Ionising)</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><i><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">(he, him)</span></i><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871"> </span></b><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCW Tel:  0151 556 5030

</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCL Tel: 0151 318 8438</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Email:

</span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">

</span><span lang="EN-GB"></span></p>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7C3c8b9c8490ec4c9053c408da66911aa4%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637935070801985131%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nK63QmzrM74hJBaNsVaaUiOpgiBgyD4X%2B8NSHZoGACk%3D&reserved=0" originalsrc="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" shash="GIQHIUA8sLPs2W3Tf/3a+YlIs0PA8W6BQ2t2OODjA9gldwdtxUhEscR1/M+LLfQeLyCADlXMvviYTpj72FLUHALaJ0bYdpVNFlnFvRGjy75YmuYjQiUIJ53jeUcgVTElpqMiW3sXjQkV5eZMyKOmqMpyafTM+dwUIWnOktVyoLE="><span style="color:#4472C4">Microsoft

 Teams (click here)</span></a></span><span lang="EN-GB"></span></p>

</div>

<p class="x_xxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<div>

<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">

<p class="x_xxmsonormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>

<br>

<b>Sent:</b> 16 June 2022 15:23<br>

<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>>;

<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>

<b>Subject:</b> Re: Voxelised Source Placement Confusion</span><span lang="EN-GB"></span></p>

</div>

</div>

<p class="x_xxmsonormal"><span lang="EN-GB"> </span></p>

<table class="x_MsoNormalTable" border="0" cellspacing="0" cellpadding="0" align="left" width="100%" style="width:100.0%; margin-left:.45pt; margin-right:.45pt">

<tbody>

<tr style="height:10.5pt">

<td style="background:#910A19; padding:5.25pt 1.5pt 5.25pt 1.5pt; height:10.5pt">

<p class="x_xxmsonormal" style=""> </p>

</td>

<td width="100%" style="width:100.0%; background:#FDF2F4; padding:0cm 3.75pt 0cm 6.25pt; height:10.5pt">

<p class="x_xxmsonormal" style=""><span style="font-size:9.0pt; font-family:"Segoe UI",sans-serif; color:#212121">This message originated from outside of NHSmail. Please do not click links or open attachments unless you recognise the sender and know the content

 is safe. </span></p>

</td>

</tr>

</tbody>

</table>

<div>

<div>

<p class="x_xxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Hi Mark,</span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">The macros seem fine. Are you sure the relevant dimensions and the size of voxels are present and correct in the PET data header file?</span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Regards,

</span><span lang="EN-GB"></span></p>

<div>

<p class="x_xxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Ville-Veikko Wettenhovi</span><span lang="EN-GB"></span></p>

</div>

</div>

<div class="x_MsoNormal" align="center" style="text-align:center"><span lang="EN-GB">

<hr size="2" width="98%" align="center">

</span></div>

<div id="x_x_x_divRplyFwdMsg">

<p class="x_xxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black">From:</span></b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black"> BAKER, Mark (THE CLATTERBRIDGE

 CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>><br>

<b>Sent:</b> Thursday, June 16, 2022 17:08<br>

<b>To:</b> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>;

<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>

<b>Subject:</b> RE: Voxelised Source Placement Confusion</span><span lang="EN-GB">

</span></p>

<div>

<p class="x_xxmsonormal"><span lang="EN-GB"> </span></p>

</div>

</div>

<div>

<div>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Hi Ville-Veikko</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you for your reply. The relevants macs are attached to this email. I have 8 mains in total (one for each core) which are identical apart

 from the first one has visualisation. The current offset was just something I was trying but I can’t seem to get any of the numbers to truly work.</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D">Thank you</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<div>

<p class="x_xxxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Mark Baker</span></b><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Principal Clinical Scientist</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Imaging Physics (Ionising)</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><i><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">(he, him)</span></i><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871"> </span></b><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCW Tel:  0151 556 5030

</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">CCCL Tel: 0151 318 8438</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">Email:

</span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#006871">

</span><span lang="EN-GB"></span></p>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#4472C4"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7C3c8b9c8490ec4c9053c408da66911aa4%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637935070801985131%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=nK63QmzrM74hJBaNsVaaUiOpgiBgyD4X%2B8NSHZoGACk%3D&reserved=0" originalsrc="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" shash="GIQHIUA8sLPs2W3Tf/3a+YlIs0PA8W6BQ2t2OODjA9gldwdtxUhEscR1/M+LLfQeLyCADlXMvviYTpj72FLUHALaJ0bYdpVNFlnFvRGjy75YmuYjQiUIJ53jeUcgVTElpqMiW3sXjQkV5eZMyKOmqMpyafTM+dwUIWnOktVyoLE="><span style="color:#4472C4">Microsoft

 Teams (click here)</span></a></span><span lang="EN-GB"></span></p>

</div>

<p class="x_xxxmsonormal"><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:#1F497D"> </span><span lang="EN-GB"></span></p>

<div>

<div style="border:none; border-top:solid #E1E1E1 1.0pt; padding:3.0pt 0cm 0cm 0cm">

<p class="x_xxxmsonormal"><b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt; font-family:"Calibri",sans-serif"> Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi">ville-veikko.wettenhovi@uef.fi</a>>

<br>

<b>Sent:</b> 16 June 2022 14:46<br>

<b>To:</b> BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>>;

<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a><br>

<b>Subject:</b> Re: Voxelised Source Placement Confusion</span><span lang="EN-GB"></span></p>

</div>

</div>

<p class="x_xxxmsonormal"><span lang="EN-GB"> </span></p>

<table class="x_MsoNormalTable" border="0" cellspacing="0" cellpadding="0" align="left" width="100%" style="width:100.0%; margin-left:.45pt; margin-right:.45pt">

<tbody>

<tr style="height:10.5pt">

<td style="background:#910A19; padding:5.25pt 1.5pt 5.25pt 1.5pt; height:10.5pt">

<p class="x_xxxmsonormal" style=""> </p>

</td>

<td width="100%" style="width:100.0%; background:#FDF2F4; padding:0cm 3.75pt 0cm 6.25pt; height:10.5pt">

<p class="x_xxxmsonormal" style=""><span style="font-size:9.0pt; font-family:"Segoe UI",sans-serif; color:#212121">This message originated from outside of NHSmail. Please do not click links or open attachments unless you recognise the sender and know the content

 is safe. </span></p>

</td>

</tr>

</tbody>

</table>

<div>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Hi Mark,</span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Moving the voxelized source by half of each dimension should indeed work and has worked in the cases where I've used voxelized source.

 Could you share the part of the macro where you define and move the voxelized source?

</span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Another way to determine the positioning could be to form the "ground truth" image of the trues, i.e. an image where the coincidences

 are accumulated based on their source locations. Then compare that image to the attenuation image from the attenuation map actor (both with the same dimensions).</span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span><span lang="EN-GB"></span></p>

</div>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Regards,

</span><span lang="EN-GB"></span></p>

<div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black">Ville-Veikko Wettenhovi</span><span lang="EN-GB"></span></p>

</div>

<p class="x_xxxmsonormal" style="background:white"><span lang="EN-GB" style="font-family:"Calibri",sans-serif; color:black"> </span><span lang="EN-GB"></span></p>

</div>

<div class="x_MsoNormal" align="center" style="text-align:center"><span lang="EN-GB">

<hr size="2" width="98%" align="center">

</span></div>

<div id="x_x_x_x_divRplyFwdMsg">

<p class="x_xxxmsonormal"><b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black">From:</span></b><span lang="EN-GB" style="font-size:11.0pt; font-family:"Calibri",sans-serif; color:black"> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org">gate-users-bounces@lists.opengatecollaboration.org</a>>

 on behalf of BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <<a href="mailto:mark.baker23@nhs.net">mark.baker23@nhs.net</a>><br>

<b>Sent:</b> Thursday, June 16, 2022 16:27<br>

<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>><br>

<b>Subject:</b> [Gate-users] Voxelised Source Placement Confusion</span><span lang="EN-GB">

</span></p>

<div>

<p class="x_xxxmsonormal"><span lang="EN-GB"> </span></p>

</div>

</div>

<div>

<div>

<p class="x_xxxxmsonormal"><span lang="EN-GB">Hi all</span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB">I raised this query a while (or one similar) but unfortunately, I’ve not managed to get back around to my project for a while. In short, I can’t get good alignment between my CT and PET images. My understanding

 is that the voxelised PET source image should be offset by half of its size to account for it being placed in the corner of the world instead of the centre where the CT image is place. My world is 1 1 2 m and my CT data is 780 780 693 mm (512x512x213 matrix).

 My PET data is 814.568 814.568 639 mm (200x200x213 matrix).</span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB">I think I was a bit confused at first, and was moving the PET source by half of its own size but then I re-read the ReadTheDocs and I think it is suggesting that I actually need to move the PET image by half of

 the world size (setPosition -500 -500 -1000 mm) but this results in a large offset. I’ve tried various combinations of half the size of the world, half the size of the PET data etc. and I think I’m just going around in circles now. Logically, I feel like the

 solution is that I move half of the world size at first to move the corner of the PET data into the centre of the world, then back by half of the PET image to put the centre of the PET in the centre of the world, but it is still offset. Any suggestions, as

 I’m tearing my hair out a little now.</span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB">Additionally, in order to test where the positioning is correct, I’m relying on the generation of secondary electrons within the water phantom in my image and looking at the NbofHits file produced. This works fine

 when the difference is obvious between the two, but I wonder if there is a better way to see the isocentre in order to 100% confirm it is correct? The reason I use secondary electrons is that positrons and gammas flood the image making it impossible to see

 the underlying CT data, plus I expect the secondary electrons to largely be created in the water and not air.</span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB">Thank you in advance!</span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><b><span lang="EN-GB" style="color:#006871">Mark Baker</span></b><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#006871">Principal Clinical Scientist</span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#006871">Imaging Physics (Ionising)</span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#006871">The Clatterbridge Cancer Centre NHS Foundation Trust</span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><i><span lang="EN-GB" style="color:#006871">(he, him)</span></i><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><b><span lang="EN-GB" style="color:#006871"> </span></b><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#006871">CCCW Tel:  0151 556 5030

</span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#006871">CCCL Tel: 0151 318 8438</span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#006871">Email: </span>

<span lang="EN-GB" style="color:#4472C4"><a href="mailto:mark.baker23@nhs.net"><span style="color:#4472C4">mark.baker23@nhs.net</span></a></span><span lang="EN-GB" style="color:#006871">

</span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#4472C4"><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fteams.microsoft.com%2Fl%2Fchat%2F0%2F0%3Fusers%3Dmark.baker23%40nhs.net&data=05%7C01%7C%7C3c8b9c8490ec4c9053c408da66911aa4%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637935070802141353%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UkmV%2B4%2FhEF5RJVprLCwhMGSSrr1%2FxS6Yu6Sn9pNBkXc%3D&reserved=0" originalsrc="https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net" shash="L8e2VIyleTfQX8MaRnV4knKOu/JegMMy5B5g1l6v49caYvPUf9qos7ia3PfeTeYylMeTbvhlIbS+JpMuozjD5J8RZezqCpdlQPaWkg8YfmTBtnIobM5mfccp8nHuaVLt9fjQ6BEOVZu2Lmw9O039WhVyC0ClEMmebSXFNEhhDS4="><span style="color:#4472C4">Microsoft

 Teams (click here)</span></a></span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><i><span lang="EN-GB" style="color:#006871">Honorary Lecturer, Dept. of Physics</span></i><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><i><span lang="EN-GB" style="color:#006871">University of Liverpool</span></i><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB" style="color:#006871"> </span><span lang="EN-GB"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"><img border="0" width="624" height="163" id="x_x_x_x_x_Picture_x0020_3" alt="CCC email footer April 2021" style="width:6.5in; height:1.7013in" data-outlook-trace="F:1|T:1" src="cid:image001.jpg@01D8983F.4A1FF6C0"></span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

<p class="x_xxxxmsonormal"><span lang="EN-GB"> </span></p>

</div>

<p class="x_xxxmsonormal" style="margin-bottom:12.0pt"><span lang="EN-GB"><br>

</span><span lang="EN-GB" style="font-size:10.0pt; font-family:"Courier New"; color:black"><br>

************************************************************************************** ******************************<br>

<br>

This message may contain confidential information. If you are not the intended recipient please:<br>

i) inform the sender that you have received the message in error before deleting it; and

<br>