I have a CT scan with a shape of (350, 512, 512) and a voxel size of (2, 1.13, 1.13). I would like to do an interpolation to get a new voxel size of (1,1,1) by using zoom from scipy. Here is the code I am using volume = np.stack([dcm.pixel_array for dcm in dicom_files]).astype(np.uint16) #3D volume with original data volume = volume * slope + intercept #convert to Hounsfield Units full_ct_spacing = [slice_thickness, pixel_spacing[0], pixel_spacing[1]] #shape of a voxel new_spacing = np.array([1,1,1]) #target spacing resize_factor = full_ct_spacing / new_spacing #resize factor volume = zoom(volume.astype(np.uint16), resize_factor, order=1, mode='reflect') #interpolated volume I get a new CT scan with a shape of (700, 580, 580) but when I dislay it the grey levels seem to be reversed. Air is white and bones are black. Is it due to the zoom function ? What is the best way to interpolate CT scan ? Continue reading...
