DICOM series: Reading, Manipulation and Visualization

Specific Domains Biology, Health, and Medicine
1

I have a DICOM image series generated from Micro CT scanning. How does one read the series, store the intensity values in a 3D matrix so that data manipulation is possible?

var = dcmdir_parse(“/path/to/dicom/folder/”);
The above command reads the series and stores in the variable var.

What functions are available to process the data further?

2

You can search the tag you want with var[tag"TagName"]
Several examples with a RT dose DICOM file:

using DICOM
rt_dose = dcm_parse(rt_dose_path)
slice_thickness = rt_dose[tag"SliceThickness"]
pixel_spacing = rt_dose[tag"PixelSpacing"]
image_position = rt_dose[tag"ImagePositionPatient"]
dose_grid_scaling = rt_dose[tag"DoseGridScaling"]
pixel_array = float.(rt_dose[tag"PixelData"])

and for sub-tag :

beam_number = rt_dose[tag"ReferencedRTPlanSequence"][1][tag"ReferencedFractionGroupSequence"][1][tag"ReferencedBeamSequence"][1][tag"ReferencedBeamNumber"]
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