[Gate-users] TPSPencilBeam source description

Fri Sep 20 08:48:41 CEST 2019

Hello Alessio,

you are right. I change that and the number of fractions to 1 and the 
error is not longer valid.
However there is another problem with the clitkDicomRTPlan2Gate program. 
It seems the conversion is not proper at some point. Like I wrote at the 
beginning the program gives me an Segmentation fault and in fact the 
resulted plan file compatible with GATE doesn't contain all energy 
layers (a few last ControlPointIndices are missing).
Is anyone from of you have similar problem and know the solution or 
should I dig in the VV software source code?

All the best,
Jakub

On 2019-09-19 21:29, Elia Alessio wrote:
> 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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