# Optional Dependencies¶

## MATLAB¶

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

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