Medical Image Processing: X and Y coordinates switched around after using find and ind2sub?

I am trying to extract the non-zero points from a mask made from a medical image. These points will be used for an orthogonal projection onto a plane.

I will describe my problem below.

The mask consists of a matrix of zeros (undesired pixels) and ones (desired pixels). The mask can be visualised with for example sliceViewer or orthosliceViewer. I show you orthosliceViewer in Figure 1. The attached .mat file contains one of these masks.

You can observe that the middle of the mask is more or less

X = 239

Y = 207

Z = 85

In the next step I want to extract the coordinates of all the non-zero points (white on Figure 1). I use the following code:

index = find(mask);
[ori_x, ori_y, ori_z] = ind2sub([size(mask,1),size(mask,2),size(mask,3)], index);

This code makes sense to me. Next, I check the range of values in ori_x, ori_y, ori_z with the unique function.

This function show me that :

• X values vary between 199 and 215
• Y values vary between 233 and 248
• Z values vary between 77 and 93

When we compare these values to the "middle point of the mask" above. It seems that the Z value is fine, but the X and Y value seems to be switched.

I confirmed this suspision by extracting the centroid and bounding box of the mask using bwlabeln and regionprops3.

I know the quick fix would be to switch the X and Y value back, but I want to know what fundamental mistake I'm making. Can somebody help me?

Thanks in advance for your advice!

Sam

[Roger J]

Sam,

This is a common misunderstanding.

Please see if this link answers your question:

https://www.mathworks.com/matlabcentral/answers/225447-how-to-match-plot-and-image-coordinates#answer_184116

[Sam Donche]

Thank you for your answer.

This helps me out a lot.

Maybe you should post it as an answer?

Answer 1

[Roger J]

Sam,

This is a common misunderstanding.

Please see if this link answers your question:

https://www.mathworks.com/matlabcentral/answers/225447-how-to-match-plot-and-image-coordinates#answer_184116

If this is helpful, please mark as the answer.

Answer 2

[Image Analyst]

ind2sub gives [row, column, slice], which is [y, x, z].

It does not give [ori_x, ori_y, ori_z] = ind2sub(...) like you had. Try

[ori_y, ori_x, ori_z] = ind2sub(....