dose optimization

[NatukiAdachi]

I would like to ask about dose Optimization. If the data we want to use includes RT-Dose, is it possible to only perform optimizations based on that dose?

[remocristoforetti]

Hi Natuki,
could you please specify better your request?

[NatukiAdachi]

Thank you for your reply. I would like to optimize the BED based on the overall dose that was pre-planned, like in this paper. “Voxel based BED and EQD2 Evaluation of the Radiotherapy Treatment Plan” However, even if I store the CT, RT-Struct and RT-Dose of the DICOM data I have now, a new plan will be created. I am writing code based on matRad.m. I am still new to MATRAB itself. I am still new to MATRAB itself and ignorant, so any advice would be appreciated. 2024年7月8日(月) 20:27 remocristoforetti ***@***.***>:

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Hi Natuki, could you please specify better your request? — Reply to this email directly, view it on GitHub <#741 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJIIKGQKBVOGO6QY4QVVQVLZLJZS7AVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TSOBWGQYDG> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[wahln]

Regarding BED optimization, this is now on the dev branch: https://github.com/e0404/matRad/tree/dev

I don't understand the problem with the "new plan", though.

[NatukiAdachi]

As for progress, I am attempting to import Dose and Plan, but I am getting errors in one of them. If I am able to successfully import, I would like to compare it to the original physical doses, but is it possible to convert the doses without having to re-plan? 2024年8月6日(火) 17:42 Niklas Wahl ***@***.***>:

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Regarding BED optimization, this is now on the dev branch: https://github.com/e0404/matRad/tree/dev I don't understand the problem with the "new plan", though. — Reply to this email directly, view it on GitHub <#741 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJIIKGUGYNNOBUFXFCSAAZDZQCEAPAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMRVGEZTCNI> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[wahln]

It would be best if you could point me to the dataset in the TCIA, then I could try importing myself.

When you import the RTDose you will have it available in matRad. However, recalculation of the RTPlan is difficult, because you need the correct machine data of that. I don't know which machine was used for these plans.

[NatukiAdachi]

Head-Neck Cetuximab | Head-Neck Cetuximab I am planning to use this dataset 2024年8月6日(火) 17:56 Niklas Wahl ***@***.***>:

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It would be best if you could point me to the dataset in the TCIA, then I could try importing myself. When you import the RTDose you will have it available in matRad. However, recalculation of the RTPlan is difficult, because you need the correct machine data of that. I don't know which machine was used for these plans. — Reply to this email directly, view it on GitHub <#741 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJIIKGV4KAHBWN5V5LOGUCDZQCFVXAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMRVGE2DMOI> . You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[NatukiAdachi]

If I can import RT-Dose, can I convert BED based on RT-Dose without Plan? I thought I could not. 2024年8月6日(火) 18:17 足立夏基 ***@***.***>:

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Head-Neck Cetuximab | Head-Neck Cetuximab I am planning to use this dataset 2024年8月6日(火) 17:56 Niklas Wahl ***@***.***>: > It would be best if you could point me to the dataset in the TCIA, then I > could try importing myself. > > When you import the RTDose you will have it available in matRad. However, > recalculation of the RTPlan is difficult, because you need the correct > machine data of that. I don't know which machine was used for these plans. > > — > Reply to this email directly, view it on GitHub > <#741 (reply in thread)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/BJIIKGV4KAHBWN5V5LOGUCDZQCFVXAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTAMRVGE2DMOI> > . > You are receiving this because you modified the open/close state.Message > ID: ***@***.***> >

[edwardwang1]

Hi @NatukiAdachi,

Could you clarify what you want to do? Do you already have a RTDose (dose estimiation) file that you generated through some other means, and then want to use matRad to optimize a new plan based on the dose estimation?

[NatukiAdachi]

What I would like to do is import the physical dose produced by another treatment planning device into matRad and convert that dose to BED. 2024年8月22日(木) 2:10 edwardwang1 ***@***.***>:

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Hi @NatukiAdachi <https://github.com/NatukiAdachi>, Could you clarify what you want to do? Do you already have a RTDose (dose estimiation) file that you generated through some other means, and then want to use matRad to optimize a new plan based on the dose estimation? — Reply to this email directly, view it on GitHub <#741 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJIIKGTOXAECFQGVRNJQ6RDZSTC2FAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBRGA3TENI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[edwardwang1]

Ah ok I don't have any first-hand experience with this, but I think it should be doable.

Once you load in your physical dose, you should have a resultGUI object. You can access the 3D dose matrix using resultGUI.physicalDose, and then you should be able to use element-wise matrix operations to convert that to BED.

[NatukiAdachi]

Thank you. But this way, would the same alpha/beta be applied to both Target and OAR? If I want to change the alpha/beta freely like the BED optimization tool now available on GITHUB, do I need to be more creative? 2024年8月22日(木) 8:43 edwardwang1 ***@***.***>:

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Ah ok I don't have any first-hand experience with this, but I think it should be doable. Once you load in your physical dose, you should have a resultGUI object. You can access the 3D dose matrix using resultGUI.physicalDose, and then you should be able to use element-wise matrix operations to convert that to BED. — Reply to this email directly, view it on GitHub <#741 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJIIKGU4J6BH6BI2ORJBPSTZSUQ3JAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBRGM2DAOI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[NatukiAdachi]

I am sure Struct info is stored in cst. So I think that by tying ResultGUI to cst, I can assign alpha/beta according to Struct. how do I tie it? 2024年8月22日(木) 13:46 足立夏基 ***@***.***>:

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Thank you. But this way, would the same alpha/beta be applied to both Target and OAR? If I want to change the alpha/beta freely like the BED optimization tool now available on GITHUB, do I need to be more creative? 2024年8月22日(木) 8:43 edwardwang1 ***@***.***>: > Ah ok I don't have any first-hand experience with this, but I think it > should be doable. > > Once you load in your physical dose, you should have a resultGUI object. > You can access the 3D dose matrix using resultGUI.physicalDose, and then > you should be able to use element-wise matrix operations to convert that to > BED. > > — > Reply to this email directly, view it on GitHub > <#741 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/BJIIKGU4J6BH6BI2ORJBPSTZSUQ3JAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBRGM2DAOI> > . > You are receiving this because you were mentioned.Message ID: > ***@***.***> >

[wahln]

For each contour, there are stored index lists (i.e., which voxels they belong to, in the cst. In the 5th column, it stores the parameters. So here's some code draft (did not test it myself) on how to calculate the LQM survival organ-by-organ that you can build on:

%ct scenario (in case of 4D cts)
ctScen = 1;

%resulting survival cube
survival = zeros(size(resultGUI.physicalDose));

%take care of volume overlap according to what is written in cst(:,5).Priority
cstOverlap = matRad_setOverlapPriorities(cst);

%Loop over all 
for i = 1:size(cstOverlap,1)
  %Get alpha and beta from cstOverlap
  alpha = cstOverlap{i,5}.alphaX;
  beta = cstOverlap{i,5}.betaX;
  
  %Voxel indices of structure
  volIx = cstOverlap{i,4}{ctScen};

  %dose in volume
  volDose = resultGUI.physicalDose(volIx);
  
  %survival in volume voxels
  volSurvival = exp(-alpha*volDose - beta*volDose.^2);
  
  %Write survival in volume to cube
  survival(volIx) = volSurvival;
end

%add to resultGUI to make available in GUI
resultGUI.survival = survival;

[wahln]

Using the physical dose makes, in my opinion, sense for photons only.
If you work with particles, especially heavier than protons, you should probably use the RBE-weighted doses (or use alpha & beta distributions instead of fixed values per dose).

[NatukiAdachi]

Thank you. I am going to use the photon dataset. I have tried BED conversion %データのロード load 2-1.mat %ct scenario (in case of 4D cts) ctScen = 1; %resulting survival cube BED = zeros(size(resultGUI.physicalDose)); %take care of volume overlap according to what is written in cst(:,5).Priority cstOverlap = matRad_setOverlapPriorities(cst); %Loop over all for i = 1:size(cstOverlap,1) %Get alpha and beta from cstOverlap alpha = cstOverlap{i,5}.alphaX; beta = cstOverlap{i,5}.betaX; % Get number of fractions numOfFractions = 1; % cstの行数を取得してnumCstEntriesに設定する numCstEntries = size(cst, 1); % cstをループで回して、条件に一致する場合にPriorityとalphaXを変更 for i = 1:numCstEntries if strcmp(cst{i, 3}, 'TARGET') cst{i, 5}.Priority = 1; % Targetに対するPriorityの設定 1or2 cst{i, 5}.alphaX = 0.5; % Targetに対するalphaXの設定 変えない elseif strcmp(cst{i, 3}, 'OAR') cst{i, 5}.Priority = 2; % OARに対するPriorityの設定 1or2 cst{i, 5}.alphaX = 0.1; % OARに対するalphaXの設定 0.1or0.25 end end %Voxel indices of structure volIx = cstOverlap{i,4}{ctScen}; %dose in volume volDose = resultGUI.physicalDose(volIx); %survival in volume voxels volBED = numOfFractions .* volDose .* (1 + volDose./(alpha/beta)); %Write survival in volume to cube BED(volIx) = volBED; end %add to resultGUI to make available in GUI resultGUI.BED = BED; matRadGUI Then I got the following error . 次を使用中のエラー: caxis (行 33) The range must be a two-element vector of increasing numbers. エラー: matRad_plotColorbar (行 38) caxis(window); エラー: matRadGUI>UpdatePlot (行 1088) handles.cBarHandel = matRad_plotColorbar(handles.axesFig,doseMap,handles.dispWindow{selectIx,1},'fontsize',defaultFontSize); エラー: matRadGUI>popupDisplayOption_Callback (行 1826) UpdatePlot(handles); エラー: gui_mainfcn (行 95) feval(varargin{:}); エラー: matRadGUI (行 88) gui_mainfcn(gui_State, varargin{:}); エラー: matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)matRadGUI('popupDisplayOption_Callback',hObject,eventdata,guidata(hObject)) Is there a solution? It worked fine if I did not change anything in cst. 2024年8月22日(木) 17:08 Niklas Wahl ***@***.***>:

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Using the physical dose makes, in my opinion, sense for photons only. If you work with particles, especially heavier than protons, you should probably use the RBE-weighted doses (or use alpha & beta distributions instead of fixed values per dose). — Reply to this email directly, view it on GitHub <#741 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJIIKGQLWPJJIFK6ZFWG2Z3ZSWL6JAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBRGYZTGOA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[wahln]

The part below should be directly run after loading:

% cstをループで回して、条件に一致する場合にPriorityとalphaXを変更
for i = 1:numCstEntries
  if strcmp(cst{i, 3}, 'TARGET')
    cst{i, 5}.Priority = 1; % Targetに対するPriorityの設定 1or2
    cst{i, 5}.alphaX = 0.5; % Targetに対するalphaXの設定 変えない
  elseif strcmp(cst{i, 3}, 'OAR')
    cst{i, 5}.Priority = 2; % OARに対するPriorityの設定 1or2
    cst{i, 5}.alphaX = 0.1; % OARに対するalphaXの設定 0.1or0.25
  end
end

Otherwise the changes are not applied before extracting the information and applying the overlap.

Also try to update to the latest dev branch (now contains all changes to dev_varRBErobOpt), a few days ago we fixed a bug related to display.

You can also try to manually plot slices from the BED to check if the conersion worked:

figure;
imagesc(resultGUI.BED(:,:,sliceNum));
colorbar;

[NatukiAdachi]

Thank you. Solved it successfully, I will try the latest dev branch as well. 2024年8月22日(木) 19:48 Niklas Wahl ***@***.***>:

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The part below should be directly run after loading: % cstをループで回して、条件に一致する場合にPriorityとalphaXを変更for i = 1:numCstEntries if strcmp(cst{i, 3}, 'TARGET') cst{i, 5}.Priority = 1; % Targetに対するPriorityの設定 1or2 cst{i, 5}.alphaX = 0.5; % Targetに対するalphaXの設定 変えない elseif strcmp(cst{i, 3}, 'OAR') cst{i, 5}.Priority = 2; % OARに対するPriorityの設定 1or2 cst{i, 5}.alphaX = 0.1; % OARに対するalphaXの設定 0.1or0.25 endend Otherwise the changes are not applied before extracting the information and applying the overlap. Also try to update to the latest dev branch (now contains all changes to dev_varRBErobOpt), a few days ago we fixed a bug related to display. You can also try to manually plot slices from the BED to check if the conersion worked: figure; imagesc(resultGUI.BED(:,:,sliceNum));colorbar; — Reply to this email directly, view it on GitHub <#741 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJIIKGUCJBERZYQZN5TOMLLZSW6WNAVCNFSM6AAAAABKE22SKGVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTANBRG44DCMQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>