Filling up the outer surface holes/gaps

Hello Matlab experts,

I want to fill up the gaps or open spaces in the the brown layer(skin). What would be the best way to do so?

Morophological operations like dilation is not feasible as it takes spaces from other voxels like yellow layer(bones).

I have shared the file in nifti format here: google drive link which can be read as

lab = niftiread('lab_superior.nii.gz');

Thanks.

Answer 1

[darova]

HEre is a start:

h = strel('disk',5);
I1 = imdilate(yellow,h);        % imdilate yellow part (bone)
I2 = I1 & ~yellow;              % select outside region/area only
I = I2 & skin;

[banikr]

Hi darova,

I understand there will be two layers from this operation and taking the outmost layer as skin solves the issue. Take a look at the images below:

How would you do that?

lab_superior = niftiread('lab_superior.nii.gz');
h = strel('disk', 5);
bone1 = imdilate((lab_superior==4), h); % bone1 is binary
boneExt = bone1&(lab_superior~=4); % select only dilated parts of the bones
% boneExt = bone1 - (lab_superior==4); % same as previous line
skin1 = boneExt&(lab_superior==10); % 10 is the skin label
volumeViewer(skin1);

[darova]

What should i see in those images?

[banikr]

if I can take only the peripheral/outer layer then I can add it as skin layer.

But how do I remove the inner layers/contours?

[darova]

Can you make a sketch or something?

I don't understand your question

[banikr]

The dilation and subtraction generates two layers of skin. I only need the outer one(yellow - left below). I want to remove the inner ones since there can't be skin under/inside bones.

[darova]

Why bwlabel doesn't work? The region look pretty separate

Am i wrong?

[banikr]

Hi,

bwlabeln works for images having no connected regions. For example, the 3D binary label has connected components(yellow marked in the image).

So it doesn't work.

[darova]

What about this?

I0 = imread('im.png');
I1 = ~im2bw(I0);
I2 = I1*0;
for j = 1:size(I1,2)
    i = find(I1(:,j),1,'first');
    if ~isempty(i)
        I2(i,j) = true;
    end
end
imshowpair(I1,I2,'montage')