How to divide the brain segmented slices in left and right compartments (halves)?

Question

Gopichandh Danala 2018-5-9

0
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/399949-how-to-divide-the-brain-segmented-slices-in-left-and-right-compartments-halves

回答： Anton Semechko 2018-5-31

samples.zip

Hi. I have a series of brain CT images, the goal is to segment brain followed by separating brain into left and right halves to compute brain area and blood area in each half.

I am attaching a zip file of 7 sample segmented brain images selected from a sequence (not continuous slices just slices that may cover all types of slices).

For this question, I am trying to divide the brain into left and right compartments.

I have been using to find left and right start indexes of the image to split into half. But this didn't give accurate results to divide into left and right halves.

My approach so far:

img_dir = pwd;
fileList = dir(img_dir);
fileList = fileList(~ismember({fileList.name},{'.','..'}));
num_of_slices = length(fileList);
for idx = 1: num_of_slices
    fileName = fileList(idx).name;
    img_slice_path = fullfile(img_dir,fileName);
    imgs{idx} = imread(img_slice_path);
    figure(1), imshow(imgs{idx},[]);
    pause(0.5);
end

seperate left and right based on midpoint of left_idx and right_idx

[nrow, ncol] = size(imgs{1});
[leftBrain_imgs,rightBrain_imgs] = deal(cell(1,length(imgs)));
for val = 1: length(imgs)
    tempImg = imgs{val};
      columnsWithAllZeros = all(tempImg == 0);
      left_idx = find(~columnsWithAllZeros,1,'first');
      right_idx = find(~columnsWithAllZeros,1,'last');
      cent_idx = floor(mean([left_idx,right_idx]));
      rightImg_idxs = 1:cent_idx; % right side is shown left
      leftImg_idxs = cent_idx+1:ncol; % left side is shown right
      [leftBrain_img,rightBrain_img]  = deal(zeros(nrow, ncol));
      rightBrain_img(:,rightImg_idxs) = tempImg(:,rightImg_idxs);
      leftBrain_img(:,leftImg_idxs) = tempImg(:,leftImg_idxs);
      leftBrain_imgs{val} = leftBrain_img;
      rightBrain_imgs{val} = rightBrain_img;
      figure(2),
      subplot(121), imshow(rightBrain_imgs{val},[]), title('right brain');
      subplot(122), imshow(leftBrain_imgs{val},[]), title('left brain');
      pause(0.5)
end

Note: The brain may be slightly tilted slightly to the left or right.

Any ideas on how to do this?

Thanks, Gopi

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Alina tom 2018-5-30

I have downloaded you sample images its just black image .. can you check your fine again

Gopichandh Danala 2018-5-30

在 MATLAB Online 中打开

This images are actually correct, maybe you are not using full display range.

imshow(imgs{idx},[]);

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Answer 1

Anton Semechko 2018-5-31

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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/399949-how-to-divide-the-brain-segmented-slices-in-left-and-right-compartments-halves#answer_322587

The simplest way to approach your problem is to

(1) Aggregate all (segmented) slices from a given 3D image to form a volume that represents your object of interest (i.e., brain).

(2) Compute either inertia-tensor-based or minimum volume bounding box (BB) of the object. Directions of the BB edges form an object-based anatomical reference frame.

(3) Partition object using the plane that passes trough the BB centroid and has normal corresponding to the anatomical direction of interest.

My guess is that this approach will only give a rough estimate of what you are looking for. However, this estimate can be used to initialize search for a plane of (reflectional) symmetry, that should give a more accurate partition.