DICOM to HDF5 Converter

Converts a DICOM directory into an HDF5 data file with CT volume and ROI volume masks.

Pre-installation

dcm2hdf requires a few prerequiste toolkits to be installed and visible to cmake.

note: sometimes dcmtk needs to be built from source for the cmake config file to be properly installed

dcm2hdf is built using cmake.

Windows users please consult relevant documentation to install prequiste libraries so that cmake can find the libraries. Alternatively, add all libraries and source to VisualStudio and build

Linux/Mac users

mkdir build
cmake ..
make
sudo ln -s /path/to/dcm2hdf /usr/local/bin

dcm2hdf [/path/to/dicom] [scale factor]

Example

cd /path/to/dicom
dcm2hdf $PWD 2

Result is a plan.hdf5 file within DICOM directory.

\CT  [CT stack volume]
\x   [x coordinates]
\y   [y coordinates]
\z   [z coordinates]
\ROI_name [3D structore mask]
    ...