MNE Class Notes

These notes describe the setup of the laptops used for the MNE class. These notes complement the notes for the MultiModal course, which describes a course setup more generally.

CentOS config

• Centos 5 x86_64 SMP

• laptops are named 'nmrclass<number>', where <number> is 7 - 21

• user account named 'mneclass', default shell is tcsh, with the default password (ask Nick or Help), where 'mneclass' user created this way:

useradd -d /home/mneclass -s /bin/tcsh mneclass

followed by:

passwd mneclass

• the 'mneclass' account .cshrc should contain this:

# exit if not an interactive shell
if ($?USER == 0 || $?prompt == 0) exit

alias dir "ls -alF"

# turn-off error beep
xset b off

#
# MATLAB
#
if ( -e /home/apps/matlab/bin ) then
  setenv PATH "/home/apps/matlab/bin":"$PATH"
  setenv MATLAB_ROOT /home/apps/matlab
  echo "MATLAB_ROOT       $MATLAB_ROOT"
endif

#
# MNE
#
if ( -e /home/apps/mne/current ) then
  setenv MNE_ROOT /home/apps/mne/current
  echo "MNE_ROOT       $MNE_ROOT"
  if ( -e /home/apps/mne/sample-data ) then
    setenv MNE_DATA /home/apps/mne/sample-data
    echo "MNE_DATA          $MNE_DATA"
    setenv SUBJECTS_DIR $MNE_DATA/subjects
    echo "SUBJECTS_DIR      $SUBJECTS_DIR"
    setenv SUBJECT sample
  endif
  source $MNE_ROOT/bin/mne_setup
endif

#
# Freesurfer and FS-FAST
#
if ( -e /home/apps/freesurfer/SetUpFreeSurfer.csh ) then
  setenv FREESURFER_HOME /home/apps/freesurfer
  setenv NO_FSFAST 1
  source $FREESURFER_HOME/SetUpFreeSurfer.csh
endif

Notes

• MNE v2.7.0 is installed in /home/apps/mne, and a symlink made to /home/apps/mne/current
• The file MNE-sample-data-2.5.tar.gz has been untarred to /home/apps/mne