Installing SimNIBS

  • SimNIBS has been tested under Ubuntu and Mac OS X. As FEM calculations are memory intensive, a 64-bit computed and 8 GB memory or more is recommended. The visualization of the meshes and results benefits from a fast graphics card.
  • Before you can start installation, you need to download the tarball archive (NOTE: users of version 1 will have to register again).
  • Installation for most Linux distributions as well as MacOSX is supported by an installation script
  • SimNIBS does not support Windows
  • In order to create head models, SimNIBS requires FreeSurfer (version 5.3.0 or newer) and FSL (version 5.0.5 or newer).
  • It is possible to run simulation in the example data set without FSL and FreeSurfer

Installation Script

Tested on Ubuntu 14.04 and 16.04, CentOS 6 and MacOSX 10.10, 10.11 and 10.12

Note: If you only want to use SimNIBS together with the example dataset, the installation of FSL and FreeSurfer is not needed. You can install them still later on in case you want to build your own head models.

Install FSL

Follow the instructions on http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux Remember to add “source /etc/fsl/5.0/fsl.sh” in the end of the ~/.bashrc (Linux) or ~/.bash_profile (MacOSX) file (assuming that fsl is installed as usually into /etc/fsl/5.0)

Install FreeSurfer

Follow the instructions on http://freesurfer.net/fswiki/DownloadAndInstall make sure that you registered the installation, and that you set the path in the ~/.bashrc (Linux) or ~/.bash_profile (MacOSX)

Installing SimNIBS

uncompress folder

tar -zxvf simnibs_X.X.X.tar.gz

Go to simnibsX.X.X folder

cd simnibsX.X.X

Execute the automated installation script

./install_simnibs.sh

The script will install a Miniconda instance in the installation folder. SimNIBS python dependencies (numpy., scipy, pyside, pyopengl, nibabel) are installed in this local python instance.

In order to set up the SimNIBS environment every time the terminal is open, the installation script will also modify the ~/.bashrc file on Linux, or the ~/.bash_profile file in MacOSX.

Now, open a new terminal window or tab

A message should appear

setting up paths for SimNIBS 2.0.1
SIMNIBSDIR /path/to/simnibs

You can check the installation by opening the GUI

simnibs_gui

Troubleshooting

Linux

If getting errors when installing with “sudo”, please try using the “-E” option in order to keep the environment variables

sudo -E ./install_simnibs.sh

MacOSX

If the GMSH toolbar is missing, try downloading it from http://gmsh.info/ and start GMSH from the launcher

If you are getting segmentation fault errors or “xcrun: error: invalid active developer path” try:

Install Xcode command line tools, if you haven't

xcode-select --install

Re-compile the binaries

cd $SIMNIBSDIR/fem_efield
make

Uninstalling SimNIBS

Linux

Execute in the command line

rm -r $SIMNIBSDIR
sed -i.bak '/SIMNIBS/d' ~/.bashrc

OSX

Execute in the command line

rm -r $SIMNIBSDIR
sed -i.bak '/SIMNIBS/d' ~/.bash_profile

Contact

For any questions about the installation, please contact support@simnibs.org

 
 
version2/installation.txt · Last modified: 2017/04/06 09:20 by guilherme
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