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

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Sam Donche
Sam Donche 2020-7-29
回答： Image Analyst 2020-7-31
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

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采纳的回答

Roger J
Roger J 2020-7-30
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.

更多回答（1 个）

Image Analyst
Image Analyst 2020-7-31
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(....

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