JEMRIS  2.8.3
open-source MRI simulations

This section describes the installation procedures for building jemris from scratch. This is usually not necessary. Binary packages for Linux, Windows and Mac OS X, are available in the section Download.


JEMRIS relies on several libraries, which need to be downloaded and installed prior to its compilation:

  • CVODE variable time stepping ODE solver >=2.5
  • Xerces-C++ XML parser >=2.8
  • HDF5 a file format for storing and managing data >=1.8
  • CLN library for Numbers version >=1.2.X
  • GiNaC library for symbolic mathematics >=1.4.X

Some Linux distributions have the above packages prebuilt and included in their package management.



Should you want to exploit more than one CPU core, you will need an implementation of MPI. JEMRIS has been tested with MPICH2. JEMRIS on Mac OS X works well with the pre-compiled MPICH implementation available from Homebrew.

Boost C++

The boost C++ libraries are used for the evaluation of elliptical integration terms of the Biot-Savart law. JEMRIS is operational without the boost libraries while Biot-Savart-Loops behave like ideal coils.

Compiling JEMRIS

Note that all libraries above are mandatory for compiling JEMRIS (runtime and development versions need to be present)

Download the JEMRIS source package from Download and unpack the tar ball.

JEMRIS is built in a similiar way as many open source software packages.

Installation with cmake

  • "# cd jemris-X.X"
  • "# mkdir build; cd build; cmake .."
  • "# make"
  • "# ctest -V"
  • "# make install"

Installation with automake

  • "# cd jemris-X.X"
  • "# ./configure"
  • "# make"
  • "# make check"
  • "# make install"

The last step will only work if you have write access to /usr/local/bin and /usr/local/share. The binaries jemris and if available pjemris, matlab GUI files and examples are installed.

Now you may run the Matlab GUIs for sequence design and simulation (see Sequence development tool: JEMRIS_seq and MRI Simulation tool: JEMRIS_sim).

Here, you may start by loading one of the example sequences in the directory "/usr/local/share/jemris/exmaples".

-- last change 11.06.2019 | Tony Stoecker | Imprint | Data Protection --