MATLAB: Convert pixel value to HU

dicom

How can I change a voxel value of a Micro CT image series to HU units ?

i need to change the voxel value and the header in dicom to use the new dicom in the treatment planning system

the linear equation i will be used to change the voxel is

y = 0.7966x-568.5

Best Answer

Hi Ahmad,

In order to convert the data found in CT data to Housefield Units you have to apply a linear transformation to the data.

The equation, which is used for converting into HouseField Units,

HU = pixel_value*slope +intercept

The tags are alse called as Rescale Slope and Rescale Intercept.

The slope and intercept are found in the DICOM file itself and you can read the DICOM image to MATLAB using “dicomread”.

Thanks & Regards,

Gouri Chennuru.

Related Solutions

MATLAB: How to use dicomwrite after modification

You are constructing file names for all the dcm files in the directory. You iterate over each one, displaying a file name appropriate for each. You the assign the undefined variable x to a variable indexed by the file number.

You are not presently reading any file. You are not presently collecting any dicom metadata. If you were collecting it, then which one would you want to collect, since you seem to be wanting to write a single output file? The single output file looks likely to want to be the adjusted value hu, which is a stack of images, but metadata for one file would not be appropriate for a stack of images in dicom. Perhaps you want to write just file #200 ? Why bother to read the other files then?

tmp11 = min(max (0.7966*crop -568.5, -1000),4096);

0.7966*crop -568.5 values that come out smaller than -1000 would be replaced with -1000 . Resulting values that are more than 4096 would be replaced with 4096. The resulting range of values would be -1000 to 4096.

hu = uint16(tmp11);

Minimum value of uint16 is 0, so all the values in the range -1000 to 0 would be replaced by 0 when doing the uint16 conversion. If that was the intention, then why not use max with 0 instead of -1000 ? Or code is not making sense.

crop=zeros(209,218,394);

You do that no matter how many files there are in the directory.

        crop(:,:,k)=x;

are you sure that the undefined variable or function x will return a result that is exactly 209 x 218 ?

MATLAB: I have a folder of .tif images that need to be converted to a different format for downstream analysis

Hi,

I think your input tif files are in single format whereas your output file format which is jpeg doesn't support single format while using imwrite (you can find using help imwrite in the 'fmt' of the file output section)

You can do this instead. either save them in a different file format let us say 'bmp', 'jp2' or 'png'. Else you can do the following thing by converting your input image from single format to unsigned integer 8 (uint8).

% Specify the folder where the files live.
myFolder = '/Users/masonlien/Desktop/PhD/Drone/2020/test';
% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isfolder(myFolder)
	errorMessage = sprintf('Error: The following folder does not exist:\n%s\nPlease select another folder.', myFolder);
	uiwait(warndlg(errorMessage));
	myFolder = uigetdir();
end
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.tif'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
numFiles = length(theFiles);
if numFiles == 0
	warningMessage = sprintf('Warning: no TIFF images found in the folder:\n%s', myFolder);
	uiwait(warnuser(warningMessage));
	return;
end
for k = 1 : numFiles
	baseFileName = theFiles(k).name;
	fullFileName = fullfile(myFolder, baseFileName);
	fprintf('Now reading %s (#%d of %d).\n', fullFileName, k, numFiles);
    % such as reading it in as an image array with imread()
    
    % Change made here 
	imageArray = uint8(imread((fullFileName)));
	imshow(imageArray);  % Display image.
	caption = sprintf('%s (#%d of %d)', fullFileName, k, numFiles);
	title(caption, 'FontSize', 14, 'Interpreter', 'none');
	drawnow; % Force display to update immediately.
	% Write it out as a PNG file.
	baseFileName = strrep(lower(baseFileName), '.tif', '.jpg');
	outputFileName = fullfile(myFolder, baseFileName);
	fprintf(1, 'Now writing %s\n', outputFileName);
 	imwrite(imageArray, outputFileName);
end

Best Answer

Related Solutions

MATLAB: How to use dicomwrite after modification

MATLAB: I have a folder of .tif images that need to be converted to a different format for downstream analysis

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