[Gate-users] Weird Blips in F18 data

Thu Dec 9 16:49:16 CET 2021

Hi

I’ve “solved” the issue by using QGSP_BERT instead of QGSP_BERT_EMV as the physics list. However, I still get the incredibly high energy Edep Spectrum at 0.5MeV (12GeV high in this case). Now I need to read up on the various physics lists, I think, and try and see if I am using the right on (particularly as _EMV is considerably faster).

This leads to a more general question for the mailbase. Obviously, how many primaries you want depends a lot on the purpose of the simulation and the errors you are happy with, but I have no feel for what is a good number (without going into my error analysis yet). What is a typical number of primaries that you might use for a certain task?

Thank you

[cid:image003.png at 01D7ED14.502D8BD0]

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: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net>
Sent: 09 December 2021 09:18
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net>; David Sarrut <david.sarrut at creatis.insa-lyon.fr>
Cc: gate-users at lists.opengatecollaboration.org
Subject: RE: [Gate-users] Weird Blips in F18 data

Hi David

I’m still seeing the same effect even with a single core. I’ve attached the output files for a 150000 event I ran, plus my initial mac files (for the single core). Obviously, the actual data is too big to send via email, but I can provide a link to the original CT/PET data and also the output MHA files if needed.

[cid:image004.png at 01D7ED11.08043780]

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: 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)
Sent: 08 December 2021 15:37
To: David Sarrut <david.sarrut at creatis.insa-lyon.fr<mailto:david.sarrut at creatis.insa-lyon.fr>>
Cc: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Weird Blips in F18 data

Hi David

Sorry for the delay in responding. I’m away from my machine at the moment, but I will try a single core tomorrow. However, the images showed these effects on the root files of the individual cores (i.e. before they were merged) and I think this would be the same as running a single core (to my limited knowledge). I will do one to confirm however.

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: David Sarrut <david.sarrut at creatis.insa-lyon.fr<mailto:david.sarrut at creatis.insa-lyon.fr>>
Sent: 07 December 2021 07:15
To: BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>>
Cc: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Weird Blips in F18 data

Hello Mark,

can you try with a single core (no merging), even with a "low" statistics, to see if it also occurs ?

thanks
David

On Thu, Dec 2, 2021 at 4:52 PM BAKER, Mark (THE CLATTERBRIDGE CANCER CENTRE NHS FOUNDATION TRUST) <mark.baker23 at nhs.net<mailto:mark.baker23 at nhs.net>> wrote:
Hi everyone

I’m running a relatively simple simulation of a NEMA IQ phantom, looking at the dose deposited within it by F18. My sim has a CT scan loaded as the geometry (with HU determined from the StoichHU example) and the F18 scan as the source. Physics are loaded as GQSP_BERT_EMV.  The macro is split into 4 to run on 4 separate cores, then merged together afterwards using hadd for the root files. My source definition is Fluor18 with e+ particle, 6585s setforcedhalflife and true for setforcedunstableflag (unfortunately my code is on a different machine to my emails so I can’t cope and paste directly).

I’m getting some interesting results in my tracklength and edepspectrum root files (see attached). The tracklength seems to get a little bit of a blip at pretty much 1mm, which I’m finding hard to explain. Additionally, on the Edep there appears to be an event (or possibly several) which deposits 20GeV from an energy of around 0.5MeV. The reason that I think it might be several events is that the same point is visible on the individual root files as well as the merged file. My actual edep and dose images look pretty good.

These examples are from merged root files from 4x25000 events so probably not amazing statistically but are quick enough for me to run and trouble shoot. I’ve ran slightly more events and still see the same effects, but I will run a longer simulation (4x200M or something) overnight to see if I get the same effects (and rule out a statistics related issue).

Does anyone have any clues or suggests are to where to look to troubleshoot this?

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)

Honorary Lecturer, Dept. of Physics
University of Liverpool

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