DICOM to HDF5 Converter

created by: Hunter Stephens

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.

DCMTK
BOOST
HDF5
OpenCV
CMake

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

Installation

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

Usage

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

Example

cd /path/to/dicom
dcm2hdf $PWD 2

Result is a plan.hdf5 file within DICOM directory.

HDF5 Structure

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