How to calculate the volume of tumor in logical image

Hi all

if i have logical image .mat as attached, how to calculate the volume of my tumor inside?

Answer 1

[Bjorn Gustavsson]

You can simply calculate how many cells (voxels?) in your labels-variable are 1:

Voxels = sum(labels(:)==1)

That is the number of elements in labels that are 1, if each cell corresponds to voxels of the same size you just need to scale that sum with the voxel-volume. If the voxel-volume varies you'd have to take that into account too:

VoxelVol = sum((labels==1).*dV,'all');

where you'd have to supply a 3-D array dV of the same size as labels with the volume of the individual voxels.

HTH

[mohd akmal masud]

sir, what is dV?

[Bjorn Gustavsson]

If you have varying size of the voxels, for example if the voxels in the first and last slices are larger than the ones in the centre, then you have to take that into account. For example if the size varies as:

[x,y,z] = meshgrid(1:130,1:130,1:36);
dV = 1 + 4/36^2*(z-18.5).^2;

then you would have spacing between the slices in the z-direction that grows quadratically from the middle. This should be reasonably simple to correct for (or completely impossible, if you don't have the information)...

[mohd akmal masud]

TQ very much sir @Bjorn Gustavsson

[mohd akmal masud]

Hi @Bjorn Gustavsson, do you know how to extract the pixel value of tumor in uint16 .mat file as attached.

means, I have data uint16 .mat. then I label it into tumor and background, and save it into logical .mat. Means the background is 0, tumor is 1.

how to extract the pixel value of tumor in uint16 .mat?

[Bjorn Gustavsson]

To just extract the tumor-flagged voxels from your imstack3-variable you can do just this:

Tumor_vals = imstack3(labels(:));

If you need to find the location/indices of the tumors you can do:

[idx1] = find(labels(:));                                     
[i1,i2,i3] = ind2sub(size(labels),idx1);
slice(double(imstack3),63,60,7),shading flat                
hold on
plot3(i2,i1,i3,'r.')

HTH

[mohd akmal masud]

tq sir @Bjorn Gustavsson

[Bjorn Gustavsson]

You're welcome!