= Preparing an MNE Analysis =

In order to use MNE, you have to run the setup command:
{{{
mne_setup_2.6.0, mne_setup_2.7.1_32bit, or mne_setup_2.7.3_32bit}}}
for Versions 2.6, 2.7.1. or 2.7.3, respectively. 

You can also use the 64 bit equivalents:
{{{
mne_setup_2.7.0_64bit, or mne_setup_2.7.3_64bit}}}
for Versions 2.7.0 or 2.7.3. The 64 bit versions still have limited functionality compared to the 32 bit equivalents.

You can actually see al these options by typing 'alias' into your terminal window. It will show all aliases currently active, including all mne_setup variations.


For most operations, MNE expects that the environment variable SUBJECTS_DIR is set, e.g.
{{{
setenv SUBJECTS_DIR /mydatadirectory/MRIs
}}}

and in some cases also the SUBJECT variable:

{{{
setenv SUBJECT /mydatadirectory/Subject1
}}}

You shouldn't mix MNE versions (unless you know what you are doing, but who does?). If you are starting an MNE analysis now, the latest version is 2.7.3 (and Freesurfer 5.1.0).

= MNE Version 2.6 =

If you want to use the '''MNE Matlab toolbox''' on a regular basis, you should add the line

    ''run /imaging/local/linux/mne_2.6.0/mne/matlab/toolbox/mne_setup_toolbox.m''

to your startup.m file. 

If you run mne_setup_2.6.0 before starting Matlab, it will automatically add the paths to the MNE tools.

= MNE Version 2.7.x =

Add the following to your Matlab startup.m file:
{{{
%---------------------- MNE --------------------------%
mnehome = getenv('MNE_ROOT');
mnematlab = sprintf('%s/share/matlab',mnehome);
if (exist(mnematlab) == 7)
    path(path,mnematlab);
end
clear mnehome mnematlab;
%-----------------------------------------------------%
}}}

If you run the MNE setup script before starting Matlab, it will automatically add the paths to the MNE tools.