How to determine whether the tumour present in brain is malign or benign using MATLAB.

The project is on BRAIN TUMOUR EXTRACTION USING MRI IMAGES using MATLAB and further determining whether the extracted tumour is MALIGN or BENIGN.

The project has been completed upto the point of brain tumour extraction.

The problem arising now is how to determine as to in which category this extracted tumour falls... MALIGN or BENIGN.

What should be its coding and how is it implemented in MATLAB is the required area of concern.

The MRI scanned images being used by me for this project can be seen at http://www.flickr.com/photos/77172895@N08/?saved=1

The code written by me so far for the extraction of tumour is given below. It shows the output on a graphical user interface.

function varargout = PROJECT(varargin)
% PROJECT M-file for PROJECT.fig
%      PROJECT, by itself, creates a new PROJECT or raises the existing
%      singleton*.
%
%      H = PROJECT returns the handle to a new PROJECT or the handle to
%      the existing singleton*.
%
%      PROJECT('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in PROJECT.M with the given input arguments.
%
%      PROJECT('Property','Value',...) creates a new PROJECT or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before PROJECT_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to PROJECT_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help PROJECT

% Last Modified by GUIDE v2.5 09-Apr-2012 15:06:22

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @PROJECT_OpeningFcn, ...
                   'gui_OutputFcn',  @PROJECT_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT

% --- Executes just before PROJECT is made visible.
function PROJECT_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to PROJECT (see VARARGIN)

% Choose default command line output for PROJECT
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes PROJECT wait for user response (see UIRESUME)
% uiwait(handles.figure1);

% --- Outputs from this function are returned to the command line.
function varargout = PROJECT_OutputFcn(hObject, eventdata, handles) 
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;

% --- Executes on button press in pushbutton1.
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 img;
global bw;
global img_gray;

img_gray=rgb2gray(img);
axes(handles.axes2);
imshow(img_gray);
[r c]=size(img_gray);

b=zeros(r,c);

hp_fil=[-1 2 -1;0 0 0;1 -2 1];
b=imfilter(img_gray,hp_fil);
axes(handles.axes4);
imshow(b);
c=b+img_gray+25;
medfilt2(c);
axes(handles.axes6);
imshow(c); 

T = graythresh(c);
bw = im2bw(c,T+0.3);

% --- Executes on slider movement.
function slider1_Callback(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

% --- Executes during object creation, after setting all properties.
function slider1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
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 img;
global bw;
global bw5;
global img_gray;
global bw3;

fs = get(0,'ScreenSize');
figure('Position',[0 0 fs(3)/2 fs(4)])
SE = strel('disk',0);

bw1 = imerode(bw,SE);
subplot(3,2,1);
imshow(bw1);

SE = strel('disk',0);
bw1 = imdilate(bw1,SE);
subplot(3,2,2);
imshow(bw1);

SE2 = strel('disk',1);
bw2 = imerode(bw1,SE2);
subplot(3,2,3);
imshow(bw2)

SE2 = strel('disk',1);
bw2 = imerode(bw2,SE2);
subplot(3,2,4);
imshow(bw2)

SE3 = strel('disk',6);
bw3 = imerode(bw2,SE3);
subplot(3,2,5);
imshow(bw3)

SE3 = strel('disk',6);
bw3 = imdilate(bw3,SE3);
subplot(3,2,6);
imshow(bw3)

% --- Executes on button press in pushbutton3.
function pushbutton3_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global img;
global bw;
global bw5;
global img_gray;
global bw3;
fs = get(0,'ScreenSize');
figure('Position',[round(fs(3)/2) 0 fs(3)/2 fs(4)])

[r2 c2]=size(bw3);

for i=1:1:r2
    for j=1:1:c2
        if bw3(i,j)==1
            img_gray(i,j)=255;
        else
            img_gray(i,j)=img_gray(i,j)*0.3;
        end;
    end;
end;
subplot(2,1,1);
imshow(img);
subplot(2,1,2);
imshow(img_gray);

% --- Executes on slider movement.
function slider3_Callback(hObject, eventdata, handles)
% hObject    handle to slider3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
ts=get(handles.slider3,'value');
global img;

if (ts==.05) 
    img=imread('img3.jpg');
end
if (ts== .1)
    img= imread('img5.jpg')
end
if (ts== .15)
    img= imread('img6.jpg')
end
if (ts== .2)
    img= imread('img8.jpg')
end
if (ts== .25)
    img= imread('img9.jpg')
end
if (ts== .3)
    img= imread('img10.jpg')
end
if (ts== .35)
    img= imread('img14.jpg')
end

axes(handles.axes1);
imshow(img);

% --- Executes during object creation, after setting all properties.
function slider3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

% --- Executes on button press in pushbutton5.
function pushbutton5_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton5 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global e;

fs = get(0,'ScreenSize');
figure('Position',[0 0 fs(3)/2 fs(4)])
[Lo_D,Hi_D,Lo_R,Hi_R] = wfilters('db2'); 

[LL1,HL1,LH1,HH1] = dwt2(e,Lo_D,Hi_D);
[LL,HL,LH,HH] = dwt2(LL1,Lo_D,Hi_D);

subplot(2,2,1)
imshow(LL/1000)
title('Approximate image')

subplot(2,2,2)
imshow(HL/1000)
title('Horizontal detail')

subplot(2,2,3)
imshow(LH/1000)
title('Vertical detail')

subplot(2,2,4)
imshow(HH/1000);
title('Diagonal detail')

% --- Executes on button press in pushbutton6.
function pushbutton6_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton6 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global img;
global I1;
global e;

I1=rgb2gray(img);

x=adapthisteq(I1);

se=strel('disk',35);
a=imopen(x,se);

se1=strel('disk',25);
b=imerode(a,se1);
axes(handles.axes2)
imshow(b)

c = fspecial('gaussian', [3 3], .5);
d=imfilter(b,c);
axes(handles.axes4)
imshow(d);

e=d+I1;
axes(handles.axes6)
imshow(e);

[Walter Roberson]

Note: In our research work, we have found that the question of whether a tumor is present or not, what stage it is at, and whether it is benign or not, are better handled by MRS (Magnetic Resonance Spectroscopy) rather than MRI (Magnetic Resonance Imaging.) The chemical signatures (MRS) are more distinct than the optical shapes (MRI).

This won't affect your project, as your project is about MRI specifically; it is just a point of science.

[tarun Advani]

Mr Walter. thnx for the knowledge point regarding the MRS thing.

Regarding the project.. i am still in waiting for a genuine solution and i am in quick need of it as the submission dates are nearing by.

[Walter Roberson]

There is no meaningful solution when you are training with only 5 images, each of unknown class.

Answer 1

[fatom fafa]

Its a good question, same problem faces my in my project brain tumor have many types and categories please if you find the solution please contact with me and tell me how did you overcome such problem.