Install MNE-C

Some advanced functionality is provided by the MNE-C command-line tools. It is not strictly necessary to have the MNE-C tools installed to use MNE-Python, but it can be helpful.

The MNE Unix commands can be downloaded at:

C API Reference gives an overview of the command line tools provided with MNE.

System requirements

The MNE Unix commands runs on Mac OSX and LINUX operating systems. The hardware and software requirements are:

  • Mac OSX version 10.5 (Leopard) or later.
  • LINUX kernel 2.6.9 or later
  • On both LINUX and Mac OSX 32-bit and 64-bit Intel platforms are supported. PowerPC version on Mac OSX can be provided upon request.
  • At least 2 GB of memory, 4 GB or more recommended.
  • Disk space required for the MNE software: 80 MB
  • Additional open source software on Mac OSX, see Additional software.

Installation

The MNE software is distributed as a compressed tar archive (Mac OSX and LINUX) or a Mac OSX disk image (dmg).

The file names follow the convention:

MNE-* <version>*- <rev> -* <Operating system>*-* <Processor>*.* <ext>*

The present version number is 2.7.0. The <rev> field is the SVN revision number at the time this package was created. The <Operating system> field is either Linux or MacOSX. The <processor> field is either i386 or x86_64. The <ext> field is ‘gz’ for compressed tar archive files and ‘dmg’ for Mac OSX disk images.

Installing from a compressed tar archive

Go to the directory where you want the software to be installed:

$ cd <dir>

Unpack the tar archive:

$ tar zxvf <software package>

The name of the software directory under <dir> will be the same as the package file without the .gz extension.

Installing from a Mac OSX disk image

  • Double click on the disk image file. A window opens with the installer package ( <name> .pkg) inside.
  • Double click the the package file. The installer starts.
  • Follow the instructions in the installer.

Note

The software will be installed to /Applications/ <name> by default. If you want another location, select Choose Folder... on the Select a Destination screen in the installer.

Setting up MNE Unix commands environment

The system-dependent location of the MNE Software will be here referred to by the environment variable MNE_ROOT. There are two scripts for setting up user environment so that the software can be used conveniently:

$ $MNE_ROOT/bin/mne_setup_sh

and

$ $MNE_ROOT/bin/mne_setup

compatible with the POSIX and csh/tcsh shells, respectively. Since the scripts set environment variables they should be ‘sourced’ to the present shell. You can find which type of a shell you are using by saying

$ echo $SHELL

If the output indicates a POSIX shell (bash or sh) you should issue the three commands:

$ export MNE_ROOT=<MNE>
$ export MATLAB_ROOT=<Matlab>
$ . $MNE_ROOT/bin/mne_setup_sh

with <MNE> replaced by the directory where you have installed the MNE software and <Matlab> is the directory where Matlab is installed. If you do not have Matlab, leave MATLAB_ROOT undefined. If Matlab is not available, the utilities mne_convert_mne_data, mne_epochs2mat, mne_raw2mat, nd mne_simu will not work.

For csh/tcsh the corresponding commands are:

$ setenv MNE_ROOT <MNE>
$ setenv MATLAB_ROOT <Matlab>
$ source $MNE_ROOT/bin/mne_setup

For BEM mesh generation using the watershed algorithm or on the basis of multi-echo FLASH MRI data (see Creating the BEM meshes) and for accessing the tkmedit program from mne_analyze, see Working with the MRI viewer, the MNE software needs access to a FreeSurfer license and software. Therefore, to use these features it is mandatory that you set up the FreeSurfer environment as described in the FreeSurfer documentation.

The environment variables relevant to the MNE software are listed in Environment variables.

Environment variables
Name of the variable Description
MNE_ROOT Location of the MNE software, see above.
FREESURFER_HOME Location of the FreeSurfer software. Needed during FreeSurfer reconstruction and if the FreeSurfer MRI viewer is used with mne_analyze, see Working with the MRI viewer.
SUBJECTS_DIR Location of the MRI data.
SUBJECT Name of the current subject.
MNE_TRIGGER_CH_NAME Name of the trigger channel in raw data, see mne_process_raw.
MNE_TRIGGER_CH_MASK Mask to be applied to the trigger channel values, see mne_process_raw.

Additional software

MNE uses the Netpbm package to create image files in formats other than tif and rgb from mne_analyze and mne_browse_raw. This package is usually present on LINUX systems. On Mac OSX, you need to install the netpbm package. The recommended way to do this is to use the MacPorts Project tools, see http://www.macports.org/:

  • If you have not installed the MacPorts software, goto http://www.macports.org/install.php and follow the instructions to install MacPorts.
  • Install the netpbm package by saying: sudo port install netpbm

MacPorts requires that you have the XCode developer tools and X11 windowing environment installed. X11 is also needed by MNE. For Mac OSX Leopard, we recommend using XQuartz (http://xquartz.macosforge.org/). As of this writing, XQuartz does not yet exist for SnowLeopard; the X11 included with the operating system is sufficient.

Testing the performance of your OpenGL graphics

The graphics performance of mne_analyze depends on your graphics software and hardware configuration. You get the best performance if you are using mne_analyze locally on a computer and the hardware acceleration capabilities are in use. You can check the On GLX... item in the help menu of mne_analyze to see whether the hardware acceleration is in effect. If the dialog popping up says Direct rendering context , you are using hardware acceleration. If this dialog indicates Nondirect rendering context , you are either using software emulation locally, rendering to a remote display, or employing VNC connection. If you are rendering to a local display and get an indication of Nondirect rendering context , software emulation is in effect and you should contact your local computer support to enable hardware acceleration for GLX. In some cases, this may require acquiring a new graphics display card. Fortunately, relatively high-performance OpenGL-capable graphics cards are not expensive.

There is also an utility mne_opengl_test to assess the graphics performance more quantitatively. This utility renders an inflated brain surface repeatedly, rotating it by 5 degrees around the z axis between redraws. At each revolution, the time spent for the full revolution is reported on the terminal window where mne_opengl_test was started from. The program renders the surface until the interrupt key (usually control-c) is pressed on the terminal window.

mne_opengl_test is located in the bin directory and is thus started as:

$ $MNE_ROOT/bin/mne_opengl_test

On the fastest graphics cards, the time per revolution is well below 1 second. If this time longer than 10 seconds either the graphics hardware acceleration is not in effect or you need a faster graphics adapter.

Obtain FreeSurfer

The MNE software relies on the FreeSurfer software for cortical surface reconstruction and other MRI-related tasks. Please consult the FreeSurfer home page.