How can I obtain voxel coordinates and corresponding intensity value of all voxels in a MRI image?

Hi I have medical MRI images. I wish to obtain all voxel coordinates as 3 columns with the 4th column giving the corresponding intensity value.

1st column :- X coordinate

2nd column :- Y coordinate

3rd column :- Z coordinate

4th column :- corresponding intensity value

Is there any function that can automatically do that ? The file format is DICOM file. Your help is appreciated

Answer 1

[Image Analyst]

Yes, use meshgrid and (:). Something like (untested)

[x, y, z] = meshgrid(1:columns, 1:rows, 1:slices);
out4Column = [x,y,z, yourImage(:)];

[Sara Salimi]

Dear Image Analyst, Thanks for your answer. I'm a beginner in matlab. How can I load MRI image and how can apply this command for that image Voxels? I know we can load the image by dicomread() command. But I don know how can I apply those command to find the position and intensity of voxels? I need to extract coordinates and intensity for each voxel. I have attached one of the files. Could you please help me? Once again Thanks a lot for your help.

[Walter Roberson]

out4Column = [x,y,z, yourImage(:)]; should be

out4Column = [x(:), y(:), z(:), yourImage(:)];

[Walter Roberson]

There is an example of reading in a series of dicom images in this article

Once you have your 4D array, say X, then you can get the results you are looking for by:

idx = find(X);
[row, col, page] = ind2sub(size(X), idx);
out4Column = [col(:), row(:), page(:), X(idx)];

Notice that I used col and then row rather than row and then col. In MATLAB, the rows correspond to Y (height) and the columns correspond to X (across)

The above lists only the non-zero values. If you want to include the 0 values as well, that can be done without much trouble.

The coordinates that would be used here are pixel coordinates. If you need the values in real-world coordinates, it will be necessary to extract some header information from the dicom files to figure out how pixels corresponds to x and y and z.

[Sara Salimi]

Dear Walter, many thanks for your answer, I tried the code for a folder of MRI images and it was successful. It gave me out4Column with 4 columns. Could you please explain what is idx = find(X)? Is X(idx) the amount of intensity for the voxel? Is the first column as col number and second column as row number? Nevertheless I appreciate your help.

Thanks

[Walter Roberson]

http://www.mathworks.com/help/matlab/ref/find.html

"k = find(X) returns a vector containing the linear indices of each nonzero element in array X."

Linear indices are described at http://www.mathworks.com/help/matlab/ref/find.html#buf0c2r-8

I did code the first column of the output as column number (which corresponds to X), then the second as row number (which corresponds to Y), then the third as page number (which corresponds to Z), then the fourth as the intensity.

It is not common to create a table of values such as this: most of the time that you need this kind of information, it is easier to deal with it as separate variables then as a single matrix. Mostly a table like this is useful for writing the values out to a file.

Keep in mind that the size of the table might be up to 4 times larger than the size of the image array itself, if none of the values in the image are 0.

[Sara Salimi]

Dear Walter, Once again Thanks alot for your help.

I really appreciate it.

Regards

Sara

[Image Analyst]

Walter, thanks for the correction.

[Sara Salimi]

Hi again,

I changed the code for another folder which includes 22 dicom image; however, it gives this error "Subscripted assignment dimension mismatch.

Error in TempTest (line 10) X(:,:,1,p) = dicomread(filename); "

I also changed the image array size to 22 (number of images in the folder). Before I change the folder, it was working for dicom image downloaded from Dicom example files ,what is the problem? :(

Thanks for your help in advance

[Walter Roberson]

Some of your images are a different size. You should assign the result of dicomread() to a variable and then test the size() of the result to determine whether it fits into the array. See my code in http://uk.mathworks.com/matlabcentral/answers/258988-loading-mutiple-dicom-images#answer_202284

[Sara Salimi]

Dear Walter,

Many thanks for your help.

[Sara Salimi]

Hi Walter, I checked the size of files, you are absolutely right, It shows which of my images is corrupt. For the next step, what should I solve this issue and resize all dicom files with a same size?

I really appreciate your help :)

[Image Analyst]

Contact the manufacturer or person that made your images to find out why they're different sizes.

[Sara Salimi]

Thanks again

[Vasantha Lakshmi]

I need to get the voxel coordinates and intensity values of mri image which are of .mha format.How can I get it?

[Walter Roberson]

Look for read_mha in the File Exchange