Note: This library was developed for a historic version of Geant4. It is not developed anymore. If anyone wants to continue the work, I will be most happy to pass it over.

g4application-dicom

DICOM plugin for g4application (see https://github.com/janpipek/g4application), based on GDCM.

MIT License (see LICENSE file).

The plugin is in an EARLY stage of development. Currently working only with geant9 branch of g4application due to massive API changes.

Requirements:

• g4application
• Geant4
• GDCM
• boost
• json-cpp (for reading material settings)
• C++11 capable compiler (gcc 4.8 tested)

Features

• Loading DICOM files (Note: tested for CT images with standard orientation and one slice per file, others may cause problems)
• Construction of voxel geometry
• Translation and rotation of the geometry
• Tools for creating materials (defined in external JSON)

Macro commands

• /dicom/loadFiles - specify DICOM files to load (using glob syntax). Can be used multiple times.
• /dicom/readFiles - force reading of files. Not necessary because geometry building does this automatically.
• /dicom/loadMaterials - load materials from a JSON file (path relative to current working directory)
• /dicom/crop - select only a rectangular subset of voxels. Provide 6 values (xmin, xmax, ymin, ymax, zmin, zmax) as voxel indices, 0 meaning no limit. Zero-based indexing, upper limit is not inclusive.
• /dicom/autoCrop - crop the volume to the smallest rectangular box that contains all voxels with Hounsfield value larger than the limit (though in most cases manual setting seems better)
• /dicom/rotateX - rotate current setup around X axis
• /dicom/rotateY - rotate current setup around Y axis
• /dicom/rotateZ - rotate current setup around Z axis
• /dicom/resetRotation - reset rotation to the default setting

Note: The rotation commands rotate the volume itself, not the coordinate frames as standard G4PVPlacement.

Configuration values

• dicom.phantom_center_x (in mm)
• dicom.phantom_center_y (in mm)
• dicom.phantom_center_z (in mm)
• dicom.materials.hu_step - step in HU units when generating table of materials
• dicom.vis.showVoxels - whether to visualize individual voxels. Otherwise, only the surrounding box is displayed.
• dicom.phantom_rotation_theta - Euler angle theta (in deg)
• dicom.phantom_rotation_phi - Euler angle phi (in deg)
• dicom.phantom_rotation_psi - Euler angle psi (in deg)
• dicom.parallel - (bool) Whether to build voxel volume in a parallel world

Important Classes

• DicomReader - utility that reads DICOM files using GDCM
• DicomSlice - data from one particular DICOM file (independent of GDCM)
• DicomData - a set of slices with included sorting and validation
• DicomPlugin - the plugin class for g4application
• (V)DicomMaterialDatabase - (abstract) class that provides material info for each pixel
• DicomGeometryBuilder - class that builds the voxel geometry for g4application
• VoxelParameterisation - G4VNestedParameterisation for the voxel phantom

Inspiration

• https://github.com/christopherpoole/G4VoxelData by Christopher Poole
• the official Geant4 DICOM extended example.

Contact

I'd be happy to accept feature requests, cooperation, questions, bug reports... Please write to jan.pipek AT gmail.com