Plotting signal of a region of interest

Hi,

I have 3D data [114,114,55] = [x, y , time]. I also have a binary mask with 0 background and 1s the pixels correspong to lung. I would like to plot the Signal versus time for the lung region.

I did the following:

dim=mask;
  SignalROI = zeros(1,1, size(dim,3));
  lung = lungdata.*mask;
  for i=0, size(dim,3)
       SignalROI(:,:,i) = mean(lung(:,:,i));
  end
plot(SignalROI)

But I get the following error:

"Subscript indices must either be real positive integers or logicals."

Could you please help?

Answer 1

[Steve Eddins]

A possible explanation is that you have a variable called "size" or "mean" in your workspace. For example, if you have a variable called "size" in your workspace, then size(dim,3) is an indexing expression into that variable rather than a call to the size function.

Here are a couple of other notes about the code:

• The for-loop syntax is incorrect. Indexing should start at 1, and the syntax should be for i = 1:size(dim,3). (Starting the index at 0 would also produce the error message you received.)
• mean(lung(:,:,i)) doesn't return a scalar. It returns a vector containing the mean of each column of lung(:,:,i). If you have R2018b or later, use this instead: mean(lung(:,:,i),'all'). Otherwise, use mean(mean(lung(:,:,i))).

[DM]

SignalROI = zeros(1,1, 26);
lung = lungdata.*mask;
  for i=0:26
       SignalROI(:,:,i) = mean(mean(lung(:,:,i)));
  end
 plot(SignalROI)

Hi Steve,

I made the corrections you suggested but I still get the same error. I removed the size and I just put a number. I am using Matlab R2017b. Any idea?

[Steve Eddins]

Dimitra, indexing should start at 1, not 0. I edited my answer above to show that.

[DM]

Sorry I didn't noticed that. I corrected the code as you suggested but then I has another error:

"Error using plot

Data cannot have more than 2 dimensions."

SignalROI = zeros(1,1, 26);
lung = lungdata.*mask;
  for i=1:26
       SignalROI(:,:,i) = mean(mean(lung(:,:,i)));
  end
 plot(SignalROI)

So I wrote the above code like this:

SignalROI = zeros(26);
lung = lungdata.*mask;
  for i=1:26
       SignalROI(i) = mean(mean(lung(:,:,i)));
  end
 plot(SignalROI)

Is the above correct?

[Steve Eddins]

Almost. zeros(26) makes a 26x26 matrix. Use zeros(26,1) or zeros(1,26) instead, depending on whether you want a column or a row vector.