Overview

  • SimNIBS 2.1.1 has been tested in Ubuntu 16.04, Ubuntu 18.04, CentOS 6, CentOS 7, MacOS 10.13, Windows 7 and Windows 10. A 64-bit computer and 8 GB memory are recommended. The visualization of the meshes and results in Gmsh benefits from a fast graphics card, even though modern built-in graphics often works well.
  • Before you can start installation, you need to download the corresponding file
  • SimNIBS now has two programs to create individual head models from MRI data, the old mri2mesh (not available on Windows) or alternatively the new headreco. To use them, you have to additionally install
    • for mri2mesh: FreeSurfer (version 5.3.0 or newer) and FSL (version 5.0.9 or newer).
    • for headreco: MATLAB. As of version 2.1.1, SimNIBS ships with SPM12 and CAT12, therefore the installation of both is no longer required.
  • To create conductivity tensor maps from diffusion MRI data, SimNIBS needs FSL (version 5.0.9 or newer).


Windows

Linux

  • uncompress folder
tar -zxvf simnibs-X.X.X-Linux64.tar.gz
  • Go to simnibs-2.1.1-Linux64 folder
cd simnibs-2.1.1-Linux64
  • Execute the automated installation script
./install_simnibs.sh
  • The script will install a Miniconda instance in the installation folder. SimNIBS python dependencies (numpy, scipy, pyqt, pyopengl, nibabel) are installed in this local python instance.
  • The installation script will also modify the ~/.bashrc file to set-up the SimNIBS environment whenever a new terminal window starts.
  • Open a new terminal window or tab, a message should appear
setting up paths for SimNIBS 2.1.1
SIMNIBSDIR /path/to/simnibs
  • You can check the installation by opening the GUI
simnibs_gui

Troubleshooting

If the message

setting up paths for SimNIBS 2.1.1
SIMNIBSDIR /path/to/simnibs

Does not appear when opening a new terminal window, please ensure that you are using a bash terminal (and not tcsh)

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

CentOS 6

The Gmsh and GetDP binaries distributed with SimNIBS do not support CentOS 6.

You can download compatible versions of Gmsh and GetDP and substitute the binaries in $SIMNIBSDIR/bin

Uninstalling SimNIBS

Execute in the command line

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

MacOSX

  • Uncompress folder
tar -zxvf simnibs-2.1.1-MacOSX.tar.gz
  • Go to simnibs-2.1.1-MacOSX folder
cd simnibs-2.1.1-MacOSX
  • Execute the automated installation script
./install_simnibs.sh
  • The script will install a Miniconda instance in the installation folder. SimNIBS python dependencies (numpy, scipy, pyqt, pyopengl, nibabel) are installed in this local python instance.
  • The installation script will also modify the ~/.bash_profile file to set-up the SimNIBS environment whenever a new terminal window starts.
  • Now, open a new terminal window or tab, amessage should appear
setting up paths for SimNIBS 2.1.1
SIMNIBSDIR /path/to/simnibs
  • You can check the installation by opening the GUI
simnibs_gui

Install Gmsh

Install Gmsh and open “.msh” files by double clicking

Troubleshooting

If the message

setting up paths for SimNIBS 2.1.1
SIMNIBSDIR /path/to/simnibs

Does not appear when opening a new terminal window, please ensure that you are using a bash terminal (and not tcsh)

If you are getting segmentation fault errors or “xcrun: error: invalid active developer path”, install Xcode command line tools

xcode-select --install

Uninstalling SimNIBS

Execute in the command line

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

Optional Resources for Linux/MacOSX

MATLAB

To run the head reconstruction code headreco, MATLAB has to be callable from the command line by typing

matlab

If MATLAB is not set-up this way in your system, you can create a link to the matlab binary in your $PATH.

Linux

For a default MATLAB install in Linux, this can be done with (requires sudo)

sudo ln -s /usr/local/MATLAB/R<VERSION>/bin/matlab /usr/local/bin/matlab

substitute <VERSION> with your MATLAB version.

MacOSX

In a default MacOSX, installation, you can use the command

sudo ln -s /Applications/MATLAB_R<VERSION>.app/bin/matlab /usr/local/bin/matlab

substitute <VERSION> with your MATLAB version.

Other MATLAB Locations

For non-default installations, you can find your MATLAB installation by typing in a MATLAB terminal

matlabroot

FSL

FSL is needed to run the head segmentation script mri2mesh and the DWI to conductivity tensors script dwi2cond

Follow the instructions on this link

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)

FreeSurfer

FreeSurfer is needed to run the head segmentation script mri2mesh

Follow the instructions on this link

Make sure that you have a registration file, and set the path in the ~/.bashrc (Linux) or ~/.bash_profile (MacOSX)

Contact

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

 
 
version21/installation.txt · Last modified: 2018/09/19 10:38 by guilherme
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