how to calculate maximum, minimum dose in some specific region.

Dear All

i want to make GUI it will work as we contoure some region of interest in the patient CT in Pinnacle treatment planning system and then calculate the dose and find mean maximum dose in that region.

But i have a image file and a dose file. i want to use these to calculate the maximum, minimum, and mean doses inside the contour region. i want to make contoure in the image and use that in dose to find the dose in that region and calculate maximum, minimum, and mean dose in that region.

till now, i made a GUI i can open a image (there are 55 image Slices, i can open one at a time) on the axis then i can contour by imfreehand. i thoght if i have the all x,y cooridnates inside the region then i will find these coordinate in the dose file which is in excel for the same slice to calculate the mean maximum doses but it vain. please find some time and help me.

regards Muhammad

Answer 1

[Image Analyst]

Once you draw the mask and use .CreateMask to get your binary image, you can get the x,y coordinates from find()

[rows, columns] = find(binaryImage);  % [y,x], not (x,y) because rows = y.

Then call xlsread() to read in the x,y coordinates from your workbook and find the max.

[Muhammad]

yes, i reached to find the excel sheet which contains [y,x]. now i want to use these coordinates in the dose matrix to find the dose at every pixel. i have a excel sheet which contains the dose of this image. i need to caculate the dose at every pixel using this dose excel file and then will find the maximum, minu=imum , median dose in that region.

[Image Analyst]

So what does the worksheet look like? Is is a long list of (x,y,dose) values in 3 columns and thousands of rows?

[Muhammad]

the dose excel file contains 127 rows and lot of columns. but image file which i created using Find(binary) contans a lot of rows and 2 columns.

[Muhammad]

Dose excel file contains 127 rows and 127 Columns.

[Image Analyst]

OK so read it in as a 2D array of numbers, called dose. Then convert your binary image to dose like this:

doseImage = zeros(size(binaryImage)); % Preallocate dose image.
doseImage(binaryImage) = dose(binaryImage);

This assumes that your dose array in the workbook corresponds column for column and row for row with your image.

[Muhammad]

Dear Dr. i ma new in MATLAB envirment but trying to learn this. i want to clear more so that it will be better understandable. i upload image on Axis GUI then i zoom the image and contoure some part and created a excel sheet. that contains [y,x] values. i want to calculate the dose of these [y,x]values using the another excel file which is dose file of the same image and have 127 rows and 127 columns and contains dose at every coordinate. i think now this will be more understandable. the code i used is given below.

if true

 function Contourpushbutton_Callback(hObject, eventdata, handles)
% imfreehand
h=imfreehand(gca,'closed',0);
% waitfor(h);
pos = getPosition(h);
% sz = size(handles.listbox1);
handles.output = hObject;
index = get(handles.listbox1,'value');
sz = size(handles.I{index});
handles.maskedImage = poly2mask(pos(:,1), pos(:,2), sz(1), sz(2));
guidata(hObject, handles); %use this line to save the handles structure during callbacks
  end

if true

   [x, y] = find(handles.maskedImage ~= 0);
[FileName,PathName] = uiputfile('*.xls','Save data to spreadsheet');
Data=[x,y];
xlswrite([PathName '/' FileName],Data);

end

[Image Analyst]

You can use the .createMask method to create a binary image directly, instead of using poly2mask, as shown in the attached demo below.

But I'm not sure how the image and the mask you draw on it is related to the table of dose numbers in the workbook, and what you want as a final output.