[Gate-users] TPSPencilBeam source description

Thu Sep 19 21:29:11 CEST 2019

Hallo Jakob!

I should check in more details but it seems to me that your plan name is an empty string. I am not fully sure this can be parsed by the code as well as the clitkDicomRTPlan2Gate...

Can you check this first maybe ? I hope it will already help you...

Best
Alessio

> On 19.09.2019, at 17:07, jbaran <jbaran at ifj.edu.pl> wrote:
>
> Dear Gate Community,
>
> I would like to continue the thread and ask one more question regarding the TPS plan based simulations. I used clitkDicomRTPlan2Gate program to convert TPS plan to Gate format and get the 'Segmentation fault (core dumped)' but the file has been produced. When I tried to run the simulation I get an error as follows:
>
> [Beam-0] source description file specifies energy spread in MeV
> [Beam-0] (This overrides whatever you configured for the 'setSigmaEnergyInMeVFlag' in the configuration of TPSPencilBeam.)
> [Beam-0] [TPSPencilBeam] Source description file successfully loaded.
> GateSourceTPSPencilBeam.cc (l.238): Something went wrong while parsing plan description file "plan_description.txt":
> wrong number of values (1) on line 25 of plan_description.txt, expected 3 value(s) of type d
>
> I checked the plan description file (plan_description.txt) and it looks as follows (a few first lines):
>
> #TREATMENT-PLAN-DESCRIPTION
> #PlanName
>
> #NumberOfFractions
> 37
> ##FractionID
> 1
> ##NumberOfFields
> 10
> ###FieldsID
> 1
> ###FieldsID
> 2
> ###FieldsID
> 3
> ###FieldsID
> 4
> ###FieldsID
> 5
> ###FieldsID
> 6
> ###FieldsID
> 7
> ###FieldsID
> 8                   <----------- line no. 25
> ###FieldsID
> 9
> ###FieldsID
> 10
> #TotalMetersetWeightOfAllFields
> 483
>
> I am wondering if anyone of you have similar problem and might have an idea how to solve that. I use GATE 8.2.
>
> All the best,
> Jakub
>
>> On 2019-08-21 15:06, David Boersma wrote:
>> Hi Jakub,
>> Yes, sorry, this is a relatively new (~1 year old) addition to the
>> "source properties" in GateSourceTPSPencilBeam.
>> We ("GateRTion" crowd) are even thinking about changing it yet again.
>> 😊
>> If the treatment plans that you work with are specifying the spot
>> weights in "number of ions" (option "setSpotIntensityAsNbIons" true),
>> then in principle you do not need to worry about this, the monitor
>> calibration will be ignored (add a dummy polynomial, maybe you can
>> even omit it).
>> If it does use MU as a spot weight unit, then during commsissioning of
>> your TPS you or your medical physicist colleagues probably had to
>> provide tables/curves of N/MU as function of beam energy. A polynomial
>> fit to those data would be good first try for a good N/MU calibration
>> in the source properties file. Maybe another possibility: fit them
>> together with the energy polynomials, if you happen to have a set of
>> IDD curves with absolute calibration.
>> In older versions of Gate (8.0 and older) the N/MU calibration was
>> hardcoded in GateSourceTPSPencilBeam. I made a polynomial fit to that
>> calibration function and inserted it in the source properties file of
>> the "dosimetry/dosimetry/protontherapy" example:
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGateContrib%2Fblob%2Fmaster%2Fdosimetry%2Fdosimetry%2Fprotontherapy%2Fdata%2FSource-Properties.txt&data=02%7C01%7Calessio.elia%40medaustron.at%7C5dd37b44a36b4611511008d73d131ace%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637045024575026484&sdata=EuZslewecVtw6PmINMpO2Lbq7cYnqGo2cI%2Fv1Lq4b6c%3D&reserved=0
>> A few years ago, when I was working in Uppsala, I compared this
>> function with the measured calibration curve of the Skandion clinic.
>> Amazingly, they were completely compatible within the accuracy of the
>> measurement. If the treatment machines for which you are going to
>> perform simulations are similar to those at Skandion, then I bet that
>> you can be optimistic about the similarity of your curve with that
>> "standard calibration curve". 😊
>> About the planned change to this functionality: right now, only the
>> shape of the N/MU curve matters, not the overall normalization factor.
>> The spot weights (be it in N or in MU) are effectively renormalized to
>> the number of requested primaries: if you request 10 times more
>> primaries, then the DoseActor will record a 10 times higher dose. In
>> order to compare with TPS dose, you need to rescale the distributions
>> with NTPS/NMC. It has been suggested that the dose actor should apply
>> this rescaling factor directly (this is technically not so hard, using
>> the particle weight). This probably wouldn't affect the source
>> properties file, but it would put stronger requirements on the quality
>> of the fit that you provide (not only the shape, but the normalization
>> will matter too). For the implementation, we need to take care that
>> this will work correctly with variable number of primaries (for the
>> SaveData functionality of the dose actor, e.g. with "everyNseconds",
>> or in combination with the "stop on script" actor).
>> HTH,
>> David
>> -------------------------
>> VON: Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
>> im Auftrag von jbaran <jbaran at ifj.edu.pl>
>> GESENDET: Mittwoch, 21. August 2019 13:18:44
>> AN: Gate Users
>> BETREFF: [Gate-users] TPSPencilBeam source description
>> Dear Gate Community,
>> According to the TPSPencilBeam source description
>> (https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwiki.opengatecollaboration.org%2Findex.php%2FUsers_Guide%3ASource%23TPS_Pencil_Beam_source&data=02%7C01%7Calessio.elia%40medaustron.at%7C5dd37b44a36b4611511008d73d131ace%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637045024575026484&sdata=x%2FKPEyltVYTwevt86ORM%2BNneQ9%2FL8SRrwwa1kTmIpU4%3D&reserved=0)
>> I have to provide 9 polynomials. I dealt with all of them. However I
>> have a problem to describe the beam monitor calibration in number of
>> particles per monitor unit (N/MU). Unfortunately, there is no
>> description of that in that example:
>> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGateContrib%2Fblob%2Fmaster%2Fdosimetry%2FRadiotherapy%2Fexample5%2Fdata%2FSource-Properties.txt&data=02%7C01%7Calessio.elia%40medaustron.at%7C5dd37b44a36b4611511008d73d131ace%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637045024575026484&sdata=Uhtw2bHssh0rNvmvgfrWPRzDLaC6Kwme11l%2BRV1G4Ew%3D&reserved=0
>> .
>> Is anyone have similar problem and could provide the proper way of
>> doing
>> that.
>> All the best,
>> Jakub
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