How to do skull stripping when the skull in the image is not complete?

How do I remove the skull (as well as others tissues that are not tumor, but have similar intensity) from the MRI images? I have seen methods including removing the largest blob (the skull), but the skull does not enclose the brain fully in the picture I attached here. Using imbinarize will also keep other tissues which have similar intensity as the tumor in the image.

I have tried to use imerode, but the skull is not removed entirely.

Any help is appreciated. Thanks!

[Umar]

Hi Eudora,

To address solution to your posted comments, you have to follow the following steps, load the MRI image into Matlab, convert the RGB image to grayscale for processing.Use Otsu's method (graythresh) to find an optimal threshold for binarization. Binarize the grayscale image using the threshold to create a binary mask of the tumor region.Eliminate small objects (noise) from the binary mask using bwareaopen.Invert the binary mask to retain the tumor region while excluding other tissues. You should be able to show the original MRI image alongside the extracted tumor region for visualization. Here is the snippet code to help you further,

% Read the MRI image

MRI = imread('MRI_image.jpg');

% Convert the image to grayscale

MRI_gray = rgb2gray(MRI);

% Threshold the image to create a binary mask of the tumor region

threshold = graythresh(MRI_gray);

binary_mask = imbinarize(MRI_gray, threshold);

% Remove small objects to exclude noise

binary_mask_cleaned = bwareaopen(binary_mask, 1000);

% Invert the binary mask to keep the tumor region

tumor_region = imcomplement(binary_mask_cleaned);

% Display the resulting image with only the tumor region

imshowpair(MRI, tumor_region, 'montage');

This code snippet should help you effectively remove non-tumor tissues, like the skull, from MRI images while preserving the tumor region for further analysis or processing. Please let me know if you have any further questions.