resample

Resample a chest CT volume to a target voxel size, without changing the spatial limits in the patient coordinate system. This can be useful to standardize the voxel spacing in a data set of scans acquired using different settings.

The CT volume is saved as a directory of DICOM files. The volume is part of a data set containing three CT scans. The size of the entire data set is approximately 81 MB. Download the data set from the MathWorks® website, then unzip the folder.

zipFile = matlab.internal.examples.downloadSupportFile("medical","MedicalVolumeDICOMData.zip");
filepath = fileparts(zipFile);
unzip(zipFile,filepath)

Specify the directory of DICOM files for the first CT volume in the data set.

dataFolder = fullfile(filepath,"MedicalVolumeDICOMData","LungCT01");

Create a medical volume object, medVol, for the CT volume. The voxel size is 0.7285-by-0.7825-by-2.5 mm.

medVol = medicalVolume(dataFolder);
medVol.VoxelSpacing

ans = 1×3

    0.7285    0.7285    2.5000

Resample medVol so that it has a voxel size of 0.5-by-0.5-by-1.25 mm. First, calculate the ratio between the original voxel size and the target voxel size, in millimeters, in each dimension.

targetVoxelSize = [0.5 0.5 1.25];
ratios = targetVoxelSize ./ medVol.VoxelSpacing;

Calculate the target dimensions, in voxels, of the resampled volume.

origSize = size(medVol.Voxels);
newSize = round(origSize ./ ratios);

Define the spatial referencing for the resampled volume. First, get the mapping between the intrinsic and patient coordinate systems of medVol by using the intrinsicToWorldMapping object function. The output, origMapping, is an affinetform3d object that contains a transformation matrix in its A property.

origRef = medVol.VolumeGeometry;
origMapping = intrinsicToWorldMapping(origRef);
tform = origMapping.A;

Transform the matrix tform so that it corresponds to the target voxel size. Create an affinetform3d object, newMapping, that contains the transformed matrix.

newMapping4by4 = tform.* [ratios([2 1 3]) 1];
newMapping = affinetform3d(newMapping4by4);

Create a medicalref3d object that describes the target spatial referencing for the resampled volume.

newRef = medicalref3d(newSize,newMapping);

To maintain the mapping between the patient coordinate axes and the anatomical planes, use the orient object function to set the PatientCoordinateSystem property of newRef to match origRef.

newRef = orient(newRef,origRef.PatientCoordinateSystem);

Resample medVol by using the resample object function. The voxel size of the new medical volume matches the target size.

newVol = resample(medVol,newRef)

newVol = 
  medicalVolume with properties:

                 Voxels: [746×746×176 int16]
         VolumeGeometry: [1×1 medicalref3d]
           SpatialUnits: "unknown"
            Orientation: "transverse"
           VoxelSpacing: [0.5000 0.5000 1.2500]
           NormalVector: [0 0 1]
       NumCoronalSlices: 746
      NumSagittalSlices: 746
    NumTransverseSlices: 176
           PlaneMapping: ["sagittal"    "coronal"    "transverse"]
               Modality: "unknown"
          WindowCenters: []
           WindowWidths: []