[Gate-users] Voxelised Source Placement Confusion

Fri Jun 17 10:26:34 CEST 2022

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.

Thank you

Mark Baker
Principal Clinical Scientist (Interim)
Imaging Physics (Ionising)
The Clatterbridge Cancer Centre NHS Foundation Trust
(he, him)

CCCW Tel:  0151 556 5030
CCCL Tel: 0151 318 8438
Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>
Microsoft Teams (click here)<https://teams.microsoft.com/l/chat/0/0?users=mark.baker23@nhs.net>

From: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi>
Sent: 16 June 2022 15:23
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net>; gate-users at lists.opengatecollaboration.org
Subject: Re: Voxelised Source Placement Confusion

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.
Hi Mark,

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?

Regards,
Ville-Veikko Wettenhovi
________________________________
From: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>
Sent: Thursday, June 16, 2022 17:08
To: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: RE: Voxelised Source Placement Confusion

Hi Ville-Veikko

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.

Thank you

Mark Baker

Principal Clinical Scientist

Imaging Physics (Ionising)

The Clatterbridge Cancer Centre NHS Foundation Trust

(he, him)

CCCW Tel:  0151 556 5030

CCCL Tel: 0151 318 8438

Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>

Microsoft Teams (click here)<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%7C5d632f926c7d4864dd6b08da4fa1bd80%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637909853344842248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Gipcg9n7psVEv5jWmFbdMVRGgMlzkvLES%2B4wWulf2mk%3D&reserved=0>

From: Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto:ville-veikko.wettenhovi at uef.fi>>
Sent: 16 June 2022 14:46
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: Voxelised Source Placement Confusion

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.

Hi Mark,

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?

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).

Regards,

Ville-Veikko Wettenhovi

________________________________

From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> on behalf of BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>
Sent: Thursday, June 16, 2022 16:27
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>
Subject: [Gate-users] Voxelised Source Placement Confusion

Hi all

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).

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.

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.

Thank you in advance!

Mark Baker

Principal Clinical Scientist

Imaging Physics (Ionising)

The Clatterbridge Cancer Centre NHS Foundation Trust

(he, him)

CCCW Tel:  0151 556 5030

CCCL Tel: 0151 318 8438

Email: mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>

Microsoft Teams (click here)<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%7C5d632f926c7d4864dd6b08da4fa1bd80%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637909853344842248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Gipcg9n7psVEv5jWmFbdMVRGgMlzkvLES%2B4wWulf2mk%3D&reserved=0>

Honorary Lecturer, Dept. of Physics

University of Liverpool

[CCC email footer April 2021]

************************************************************************************** ******************************

This message may contain confidential information. If you are not the intended recipient please:
i) inform the sender that you have received the message in error before deleting it; and
ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful).
Thank you for your co-operation.

NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.

For more information and to find out how you can switch visit Joining NHSmail - NHSmail Support<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsupport.nhs.net%2Farticle-categories%2Fjoining-nhsmail%2F&data=05%7C01%7C%7C5d632f926c7d4864dd6b08da4fa1bd80%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637909853344842248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gyMBRpnBLeE8jNh4ZMD1hfbwccJErznyVvBUbhvZoz8%3D&reserved=0>

************************************************************************************** ******************************

This message may contain confidential information. If you are not the intended recipient please:
i) inform the sender that you have received the message in error before deleting it; and
ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful).
Thank you for your co-operation.

NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.

For more information and to find out how you can switch visit Joining NHSmail - NHSmail Support<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsupport.nhs.net%2Farticle-categories%2Fjoining-nhsmail%2F&data=05%7C01%7C%7C5d632f926c7d4864dd6b08da4fa1bd80%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637909853344842248%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=gyMBRpnBLeE8jNh4ZMD1hfbwccJErznyVvBUbhvZoz8%3D&reserved=0>

************************************************************************************** ******************************

This message may contain confidential information. If you are not the intended recipient please:
i) inform the sender that you have received the message in error before deleting it; and
ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful).
Thank you for your co-operation.

NHSmail is the secure email, collaboration and directory service available for all NHS staff in England. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services.

For more information and to find out how you can switch visit Joining NHSmail - NHSmail Support<https://support.nhs.net/article-categories/joining-nhsmail/>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220617/21096f60/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 13489 bytes
Desc: image001.jpg
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220617/21096f60/attachment-0001.jpg>