Getting started

Installing pre-compiled packages

If you are using a Conda-like environment (e.g. Anaconda, Miniconda, Micromamba), a pre-built package is available on conda-forge: running conda install -c conda-forge dicomifier will install the latest stable version.

Compiling from source

If you need to compile Dicomifier from scratch, you will need

• A build environment with a C++11 compiler and Python ≥ 3.6

• CMake ≥ 3.5

• The Boost libraries ≥ 1.58

• Pybind11 ≥ 2.0.1

• Odil ≥ 0.12.2

• The dateutil, nibabel and numpy Python modules

If using Conda, all dependencies can be installed by conda install --yes -c conda-forge boost cmake nibabel numpy odil pkg-config pybind11 python-dateutil

The compilation process follows the usual CMake workflow:

• Specify which Python interpreter you use. It can be python, python3, or a more specific version, e.g. python3.10. Store it in an environment variable, e.g. export PYTHON_EXECUTABLE=$(which python3)

• Choose an install directory. It can be within the source directory, or in any other directory that you can write into. Store it in an environment variable, e.g. export DICOMIFIER=${HOME}/src/dicomifier/install

• Create a build directory in the source directory.

• From the source directory, run cmake -DPYTHON_EXECUTABLE="${PYTHON_EXECUTABLE}" -DCMAKE_INSTALL_PREFIX="${DICOMIFIER}" -S . -B build to configure the build environment.

• Run cmake --build build --parallel to build Dicomifier.

• Finally, run cmake --install build to install Dicomifier to your specified location.

You may need to adjust your environment (e.g. by modifying your .bashrc file) before you can use Dicomifier:

• From the build directory, run grep PYTHON_SITE_PACKAGES CMakeCache.txt | cut -d= -f2 to determine the path to the Python files within the install directory

• Modify the search paths so that they include the install directory. In the following code sample, the first line must match the install directory, and in the last line, the lib/python3.11/site-packages part must match the output of the previous command

  export DICOMIFIER=${HOME}/src/dicomifier/install
  export PATH="${DICOMIFIER}/bin:${PATH}"
  export LD_LIBRARY_PATH="${DICOMIFIER}/lib:${LD_LIBRARY_PATH}"
  export PYTHONPATH="${DICOMIFIER}/lib/python3.11/site-packages:${PYTHONPATH}"
  

You may also refer to the continuous integration scripts to see working examples.

Basic usage

Dicomifier has a single command line executable, called dicomifier, which accepts several commands:

• List convertible data in a directory: dicomifier list my_directory

• Convert Bruker data to DICOM: dicomifier to-dicom bruker_directory dicom_directory

• Convert Bruker or DICOM data to NIfTI: dicomifier to-nifti bruker_or_dicom_directory nifti_directory

To list all available commands, run dicomifier --help; to get help about a specific command, run dicomifier some-command --help.