Optional Dependencies

MATLAB

Required by: headreco head segmentation pipeline

For headreco, MATLAB needs to be configured such that typing matlab on a terminal window will start it.

This is already the case in most Windows installations. However, on Linux and MacOSX you might need to create a link to the matlab executable somewhere in your system $PATH. This can be done with the commands

  • Linux

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

  • MacOSX

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

If MATLAB is not installed in the default location, you can find out where it is installed by typing in a MATLAB terminal

matlabroot

SimNIBS also has a MATLAB API, available in the matlab/ subfolder of the SimNIBS installation directory.

FSL

Required by: mri2mesh head segmentation pipeline and dwi2cond conductivity tensor reconstruction pipeline

  1. Follow the instructions on this link

  2. 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

Required by: mri2mesh head segmentation pipeline

  1. Follow the instructions here

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