claesnl/rtx2mnc_py

Converts an Dicom RTX struct to minc

rtx2mnc_py

Converts an Dicom RTX struct to minc

Authors

Rigshospitalet

• Claes Ladefoged [email protected]

Installation (under /opt/bin/rtx2mnc_py):

git clone https://github.com/claesnl/rtx2mnc_py.git
ln -s $HOME/rtx2mnc_py/rtx2mnc.py /opt/bin/rtx2mnc_py

Usage:

rtx2mnc_py < VOLUME.mnc > < RTx > < out_label.mnc > [ --verbose ] [ --visualize ]
      	   < VOLUME.mnc > is the file which the RTx was defined on.
      	   < RTx > is the RT struct in DICOM format.
      	   < out_label.mnc > is the resulting MINC file with the contours in the RT file set to 1. 
                             If more than one struct, out_label will be suffixed by a running number.
      	   --verbose turns on additional information
      	   --visualize shows individual slices for debugging

Requires/Dependencies:

• MINC tools
• pyminc
• DCMTK
• pydicom
• opencv2-python
• numpy

Installation of dependencies:

MINC tools:

git clone --recursive https://github.com/BIC-MNI/minc-toolkit-v2.git minc-toolkit-v2
cd minc-toolkit-v2 && mkdir build && cd build
ccmake .. -DMT_BUILD_SHARED_LIBS:BOOL=ON
make && sudo make install

pyminc:

git clone https://github.com/Mouse-Imaging-Centre/pyminc.git
cd pyminc
python setup.py install

DCMTK:

git clone https://github.com/commontk/DCMTK.git
cd DCMTK
./configure
make all
sudo make install-all

Python tools:

pip install pydicom opencv-python numpy

Version changes:

• 1.0.0 :: 2018-03-08 :: Added basic functionality working for one or more RT-files
• 1.0.1 :: 2018-03-08 :: Added RT-name in MNC header