CODEWITHSUNDEEP
c++opencvdcmtk
rvimieiro
rvimieiro

Reputation: 1145

Read a 3D Dicom image with DCMTK and convert it to OpenCV Mat

I have a dicom 3D image which is [512,512,5] (rows, cols, slices). I want to read it with DCMTK toolkit and convert it to a OpenCV Mat object. The image is 16 bits unsigned int.

My question is: Does anyone know the correct way to convert this dicom image into a Mat object? How to properly read all the slices with the method getOutputData?

Upvotes: 0

Views: 1335

Answers (1)

rvimieiro
rvimieiro

Reputation: 1145

Based on the comments of @Alan Birtles, there is the possibility to specify the frame you want to read on the getOutputData method. After reading each frame, you simply merge the Mat objects into a single Mat.

I wrote this code to get the whole volume:

DicomImage *image = new DicomImage(file);

// Get the information
unsigned int nRows = image->getHeight();
unsigned int nCols = image->getWidth();
unsigned int nImgs = image->getFrameCount();

vector <Mat> slices(nImgs);

// Loop for each slice
for(int k = 0; k<nImgs; k++){

    (Uint16 *) pixelData = (Uint16 *)(image->getOutputData(16 /* bits */,k /* slice */));

    slices[k] = Mat(nRows, nCols, CV_16U, pixelData).clone();

}

Mat img;

// Merge the slices in a single img
merge(slices,img);

cout << img.size() << endl;
cout << img.channels() << endl;

// Output:
// [512 x 512]
// 5

Upvotes: 2

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