JEMRIS  2.8.2
open-source MRI simulations


JEMRIS Version 2.8.2
Copyright (C) 2006-2018 Tony Stöcker, Kaveh Vahedipour, Daniel Pflugfelder
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA


We finally opened a discussion group on Google. Please ask all questions related to JEMRIS there.


JEMRIS is developed and maintained by ...

Tony Stöcker, project founder (tony.stoecker(at)
Framework design, sequence and solver implementation, package maintenance.

Daniel Pflugfelder (d.pflugfelder(at)
MPI parallelization, performance debugging, code optimization, Temporal variations, Diffusion.

Kaveh Vahedipour (kaveh (at)
Framework design, parallel TX/RX, supercomputer implementation.


Over the years JEMRIS improved a lot through feedback and bug reports from the user community. Thanks a lot for your contributions!

A major contribution to JEMRIS is the Pulseq integration, which allows you to run JEMRIS sequences on real MR scanners. Thanks a lot to the Pulseq developer team!
Check the section Exporting a Sequence to an MRI Scanner to learn how to export Pulseq files from JEMRIS. Read this paper for more information:
Layton, K. J., Kroboth, S., Jia, F., Littin, S., Yu, H., Leupold, J., Nielsen, J.F., Stöcker T, & Zaitsev, M. (2017). Pulseq: A rapid and hardware-independent pulse sequence prototyping framework. Magnetic Resonance in Medicine, 77(4), 1544–1552. DOI

Thanks to Alexandre Fortin et al, JEMRIS now supports flow simulation in arbitrary complex geometries (since version 2.8.2). Flow simulation examples can be found in "/usr/local/share/jemris/angio_simu" of your local JEMRIS installation. Read this paper for more information:
Fortin, A., Baruthio, J., Delbany, M., & Durand, E. (2018). Flow MRI simulation in complex 3D geometries : Application to the cerebral venous network. Magnetic Resonance in Medicine. [early view] DOI

Main Reference

If you use JEMRIS for research publications, please cite this paper:
Stöcker, T., Vahedipour, K., Pflugfelder, D., & Shah, N. J. (2010). High-performance computing MRI simulations. Magnetic Resonance in Medicine, 64(1), 186–93. DOI

-- last change 24.05.2018 | Tony Stoecker | Imprint | Data Protection --