bbelaoucha / openmeeg

A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG.

OpenMEEG: forward problems solver in the field of EEG and MEG

The OpenMEEG software is a C++ package for solving the forward problems of electroencephalography (EEG) and magnetoencephalography (MEG).

OpenMEEG is distributed under the French opensource license CeCILL-B. It is intended to give users the freedom to modify and redistribute the software. It is therefore compatible with popular opensource licenses such as the GPL and BSD licenses. The CeCILL-B license imposes to anybody distributing a software incorporating OpenMEEG the obligation to give credits (by citing the appropriate publications), in order for all contributions to be properly identified and acknowledged.

Cite this software

The references to be acknowledged are

Gramfort et al. OpenMEEG: opensource software for quasistatic
bioelectromagnetics. Biomedical engineering online (2010) vol. 9 (1) pp. 45

Kybic et al. Generalized head models for MEG/EEG: boundary element method
beyond nested volumes. Phys. Med. Biol. (2006) vol. 51 pp. 1333-1346

Install precompiled binaries

On Mac if you use Homebrew you can just do:

$ brew tap homebrew/science  # to get access to science packages
$ brew install openmeeg

Binaries for Linux/Mac/Windows are available at Download precompiled binaries.

On Ubuntu/Debian GNU Linux you may be able use the http://neuro.debian.net package repository.

Build OpenMEEG from source

Unix (Linux & Mac OS X)

On Debian/Ubuntu you will need to install the dependencies with:

sudo apt-get install git-core gcc g++ make cmake libopenblas-dev liblapacke-dev

optionally:

sudo apt-get install libhdf5-serial-dev libmatio-dev python-dev python-numpy swig libvtk6-dev doxygen libcgal-dev

On Fedora and Centos:

sudo yum install git-core gcc make cmake wget perl openblas-devel

optionally:

sudo yum install hdf5-devel matio-devel python-devel python2-numpy swig vtk-devel doxygen cgal-devel

On Mac OS X, you'll need CMake. We recommend you install it with Homebrew using:

$ brew install cmake

To configure your environment with Homebrew install the following packages with the brew command:

$ brew tap homebrew/science
$ brew update && brew upgrade

*optionally* but recommended::

$ brew install libmatio
$ brew install openblas && brew link openblas --force

*optionally*::

$ brew tap homebrew/python  # to have Python bindings
$ brew install vtk  # to have support for VTK file format
$ brew install --with-qt5 cgal  # to use CGAL meshing tools
$ brew install Doxygen  # to build the documentation

Then from a terminal:

$ git clone git://github.com/openmeeg/openmeeg.git

or if it does not work try:

$ git clone https://github.com/openmeeg/openmeeg.git

then:

$ cd openmeeg
$ mkdir build
$ cd build
$ cmake -DBUILD_TESTING=ON -DCMAKE_BUILD_TYPE=Release -DUSE_PROGRESSBAR=ON ..
$ make

OpenMEEG will download and compile the zlib, (optional vtk), hdf5, and matio by default. In case your system already provides these libraries (see optional packages), you should specify the following variables to the cmake command line: "-DUSE_SYSTEM_zlib=ON -DUSE_SYSTEM_hdf5=ON -DUSE_SYSTEM_matio=ON".

You will need to define more CMake variables if you want the support for:

• Parallel computation with OpenMP, add "-DUSE_OMP=ON". Then you can set the number of threads you want to run in parallel by setting the OMP_NUM_THREADS environment variable. On a Unix system if you want to run 4 threads in parallel do (before running OpenMEEG):

  $ export OMP_NUM_THREADS=4
  

• Python wrapping, add "-DENABLE_PYTHON=ON".

• VTK file format, add "-DUSE_VTK=ON".

• CGAL meshing tools, add "-DUSE_CGAL=ON".

Then you can run the full test suite with:

$ make check

or if you just want to run the tests for OpenMEEG:

$ make test-OpenMEEG

If no test is failing you can install with:

$ make install

You should now be able to run the om_assemble command and see something like this:

$ om_assemble
om_assemble version 2.3.2 compiled at May 24 2017 11:43:33

om_assemble [-option] [filepaths...]

option :
   -HeadMat, -HM, -hm :
       Compute Head Matrix for Symmetric BEM (left-hand side of linear system).
       ...

In some Linux distributions (AMD64/X86_64) you may see some errors like this:

Error while loading shared libraries: libOpenMEEG.so.1: cannot open shared object file: No such file or directory

OpenMEEG puts its libraries in "/usr/local/lib64", which is not included in your loader's search path. If so, run this command as root:

# echo '/usr/local/lib64/' >> /etc/ld.so.conf && ldconfig

Now you can try to run the om_assemble again.

You can now give a try to OpenMEEG on the sample dataset.

Windows

You will need to install visual studio, CMake. Then download the source from github, load the CMake.exe GUI, set the proper option and generate the visual studio project. You can then open it and build the project.

Supported Blas-Lapack Implementations

• on Linux: Intel MKL , OpenBLAS, Atlas, Lapack
• on Mac OS X: Intel MKL , OpenBLAS, vecLib
• on Windows: Intel MKL , OpenBLAS, Clapack

Using OpenMEEG

Have a look into data/README.rst for defining your geometry. and/or specify to cmake "-DBUILD_TUTORIALS=ON", and read the tutorials in pdf.

CeCILL-B full license

This software is governed by the CeCILL-B license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL-B license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".

As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's authors, the holders of the economic rights, and the successive licensors have only limited liability.

In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security.

The fact that you are presently reading this means that you have had knowledge of the CeCILL-B license and that you accept its terms.