How to ADD DICOM slices into Voxel 3d grid

[Yahia Walid]

Hi , I need to load slices (almost 500 dcm image file ) in to a grid of voxels , how do I do that using Field3D???

[Magnus Wrenninge]

Hi, 

I'm not personally familiar with the DICOM API, but this is roughly the way you'd set up the Field3D data structure:

int xDim = [dicom slice x resolution];

int yDim = [dicom slice y resolution];

int zDim = [number of dicom slices];

DenseField<float>::Ptr dense(new DenseField<float>);

DenseField<float> *rawPtr = dense.get();

dense->name = "dicom_data";

dense->attribute = "density";

dense->setSize(Imath::V3i(xDim, yDim, zDim));

Then, you would traverse each slice and copy each pixel value into a voxel:

for (int k = 0; k < zDim; ++k) {

  for (int j = 0; j < yDim; ++j) {

    for (int i = 0; i < xDim; ++i) {

      rawPtr->fastValue(i, j, k) = dicomSlices[z].pixel(i, j);

    }

  }

}

Finally, to write the data to disk:

Field3DOutputFile out;

out.create("filename.f3d");

out.writeScalarLayer<float>(dense);

I hope that helps,

Magnus

On Thu, Dec 26, 2013 at 6:34 AM, Yahia Walid <geek.k...@gmail.com> wrote:

Hi , I need to load slices (almost 500 dcm image file ) in to a grid of voxels , how do I do that using Field3D???

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[Yahia Walid]

Le jeudi 26 décembre 2013 15:34:43 UTC+1, Yahia Walid a écrit :

Hi , I need to load slices (almost 500 dcm image file ) in to a grid of voxels , how do I do that using Field3D???

 what about opacity man? and how do I specify the path of my numerous slices automaticly , i have like 500 of them which means i can't do it manuelly , and thanks for the reply man . 

[Magnus Wrenninge]

Opacity would be no different, just store it directly, but change dense->attribute = "opacity" to be explicit about what's being stored. 

As far as indexing your slices, I don't know enough about your file naming and the DICOM API, but I imagine it would be something like this:

for (int k = 0; k < zDim; ++k) {

  std::stringstream filename;

  filename << "/my/root/path/slice." << k << ".dicom";

  dicomSlices[k] = readDicomFile(filename.str());

}

Magnus

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