Array indices must be positive integers or logical values Error

rgb = inp(:,:,[1 1 1]);
red = rgb(:,:,1);
red(tumorOutline)= 255;
green = rgb(:,:,2);
green(tumorOutline)= 0;
blue = rgb(:,:,3);
blue(tumorOutline)= 0;

tumorOutlineInserted(:,:,1) = red;
tumorOutlineInserted(:,:,2) = green;
tumorOutlineInserted(:,:,3) = blue;

axes(handles.axes6);
imshow(tumorOutlineInserted);
Why this code give error that array in

dices must be positive integers or logical values

Error in line 3

[Star Strider]

... because ‘TumorOutline’ is not a logical index or a positive integer.

It is not obvious what it is.

[Jan]

Please post the complete error message. I would reveal, which line is falling. Either Star Strider's idea is the problem, or this line, if you have redefined "axes" as a local variable:

axes(handles.axes6);

[Shindujah Arudchelvan]

function pushbutton1_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global brainImg
[filename, pathname] = uigetfile({'*.jpg'; '*.bmp'; '*.tif'; '*.gif'; '*.png'; '*.jpeg'}, 'Load Image File');
if isequal(filename,0)||isequal(pathname,0)
    warndlg('Press OK to continue', 'Warning');
else
brainImg = imread([pathname filename]);
axes(handles.axes1);
imshow(brainImg);
axis off
helpdlg(' Image loaded successfully ', 'Alert'); 
end
[m n c] = size(brainImg);
if c == 3
    brainImg  = rgb2gray(brainImg);
end


% --- Executes on button press in pushbutton2.
function pushbutton2_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global brainImg inp
num_iter = 10;
delta_t = 1/7;
kappa = 15;
option = 2;

inp = anisodiff(brainImg,num_iter,delta_t,kappa,option);
inp = uint8(inp);

inp=imresize(inp,[256,256]);
if size(inp,3)>1
    inp=rgb2gray(inp);
end
axes(handles.axes2);
imshow(inp);


% --- Executes on button press in pushbutton3.
function pushbutton3_Callback(hObject, eventdata, handles)
global  inp h tumor_label tumor
%% thresholding
sout=imresize(inp,[256,256]);
t0=60;
th=t0+((max(inp(:))+min(inp(:)))./2);
for i=1:1:size(inp,1)
    for j=1:1:size(inp,2)
        if inp(i,j)>th
            sout(i,j)=1;
        else
            sout(i,j)=0;
        end
    end
end
%% Morphological Operation

label=bwlabel(sout);
stats=regionprops(logical(sout),'Solidity','Area','BoundingBox');
density=[stats.Solidity];
area=[stats.Area];
high_dense_area=density>0.6;
max_area=max(area(high_dense_area));
tumor_label=find(area==max_area);
tumor=ismember(label,tumor_label);

if max_area>100
   axes(handles.axes3);
imshow(tumor);
else
    h = msgbox('No Tumor!!','status');
    %disp('No tumor');
    return;
end
%% Bounding box

box = stats(tumor_label);
wantedBox = box.BoundingBox;
axes(handles.axes4);
imshow(inp);
hold on;
rectangle('Position',wantedBox,'EdgeColor','y');
hold off;

           
% --- Executes on button press in pushbutton4.
function pushbutton4_Callback(hObject, eventdata, handles)
global erodedImage tumor inp

dilationAmount = 5;
rad = floor(dilationAmount);
[r,c] = size(tumor);
filledImage = imfill(tumor, 'holes');

for i=1:r
   for j=1:c
       x1=i-rad;
       x2=i+rad;
       y1=j-rad;
       y2=j+rad;
       if x1<1
           x1=1;
       end
       if x2>r
           x2=r;
       end
       if y1<1
           y1=1;
       end
       if y2>c
           y2=c;
       end
       erodedImage(i,j) = min(min(filledImage(x1:x2,y1:y2)));
   end
end
%figure
%imshow(erodedImage);
%title('eroded image','FontSize',20);

tumorOutline (erodedImage)=0;   // error line

axes(handles.axes5);
imshow(tumorOutline);

rgb = inp(:,:,[1 1 1]);
red = rgb(:,:,1);
red(tumorOutline)= 255;   //error line
green = rgb(:,:,2);
green(tumorOutline)= 0;
blue = rgb(:,:,3);
blue(tumorOutline)= 0;

tumorOutlineInserted(:,:,1) = red;
tumorOutlineInserted(:,:,2) = green;
tumorOutlineInserted(:,:,3) = blue;

axes(handles.axes6);
imshow(tumorOutlineInserted);

% --- Executes on button press in pushbutton5.
function pushbutton5_Callback(hObject, eventdata, handles)

Answer 1

[Image Analyst]

A thorough discussion of the error is in the FAQ:

https://matlab.fandom.com/wiki/FAQ#.22Subscript_indices_must_either_be_real_positive_integers_or_logicals..22

Answer 2

[Image Analyst]

You can't assign certain locations of tumorOutline to be zero when you haven't defined the array.

tumorOutline (erodedImage)=0;   // error line

Assuming erodedImage is a logical image of true and false, you're saying that you want the true parts of erodedImage to be black in tumorOutline. Essentially you want tumorOutline to be black where erodedImage is not black. However is the first element is at, say (30, 50) what is it supposed to do with the prios elements, and where is (30,50) in the image? It has not seen tumorOutline before so it has no idea how many rows or columns it has. To fix that particular error, you can declare it somehow, like

tumorOutline = true(size(erodedImage)); % Declare in advance so it knows the size of tumorOutline.
tumorOutline (erodedImage)=0;   % No error now;

However there may be other errors and it still may not do what you want due to errors in your algorithm.