Installation

  • SimNIBS 2.1.0 has been tested in Ubuntu 16.04, Ubuntu 18.04, CentOS 6, CentOS 7 and MacOS 10.13. 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 also modern built-in graphics mostly works well.
  • Before you can start installation, you need to download the tarball archive.
  • SimNIBS has two programs to create individual head models from MRI data, the old mri2mesh and 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 and SPM12. The accuracy of the brain segmentations can be greatly improved by installing CAT12 version r1278. SimNIBS will NOT work with other CAT12 versions
  • To create conductivity tensor maps from diffusion MRI data, SimNIBS needs FSL (version 5.0.9 or newer).
  • SimNIBS does not support Windows.


Install 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, pyqt, pyopengl, nibabel, scikit-image) 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 2.1.0
SIMNIBSDIR /path/to/simnibs

You can check the installation by opening the GUI

simnibs_gui

Install Gmsh (Required in MacOS)

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

Install FSL (Optional)

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)

Install FreeSurfer (Optional)

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)

Install SPM12 (Optional)

SPM12 is needed to run the head segmentation scrip headreco

Follow the instructions on this link

Install CAT12 (Optional)

CAT12 can be used to improve the results of the head segmentation scrip headreco

Download version r1278 from the link uncompress the folder and move it to your

spm12/toolbox

folder

SimNIBS does not work with CAT12 versions other than r1278

Set-up MATLAB (Optional)

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.

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

or, in MacOS

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

substitute <VERSION> with your MATLAB version.

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

matlabroot

Troubleshooting

If the message

setting up paths for SimNIBS 2.1.0
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)

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

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

MacOS

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

xcode-select --install

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

 
 
version21/installation.txt · Last modified: 2018/06/30 22:36 by axel
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