Resources

From MEGwiki

Contents 1 Software for Data Analysis 2 How to obtain Elekta Neuromag software for your Linux computer 3 How to get MNE Software to run properly on a x86_64 Linux machine 4 Useful References 5 Tips for Using HP UNIX 6 Links 6.1 Some Other Neuromag Sites

Software for Data Analysis

Follow the links for manuals, and instructions for obtaining and installing these programs. For more details about each software package, their capabilities/limitations, and requirements: check out these slides.

Native
Elekta Neuromag Software: SSS, offline averaging, dipole modeling, Minimum Current Estimate (MCE)

Freeware
FreeSurfer and MNE-Suite: reads fiff, runs in Mac or Linux, offline averageing, MNE, dSPM, sLORETA, automatic segmentation of coretex, good visualizations
Field Trip: links to EEGLAB, runs on MatLab in Linux and Windows, need FiffAccess, distributed L2 modeling, dipole modeling, beamformers (DICS), get it here

Commercial
BESA: reads fiff files, runs in Windows, offline averaging, MNE, dipole fitting
ASA: runs in Windows, get it here
Curry: by Neuroscan, runs in Windows, source modeling, does L1 and L2 norms

How to obtain Elekta Neuromag software for your Linux computer

1. Email the CABMSI director (Anto Bagic) for Elekta representative contact information
2. From your Linux command prompt, collect the outputs to these commands:
   • uname -a
   • hostname
   • /sbin/ifconfig
3. Email the outputs from the previous commands to the Elekta representative, also specifying the software you would like to install. The main software suite (DANA) is available, as well as MaxFilter. The representative will reply with an FTP link to download the software, along with license information to copy into a file along with the installation.
4. Download the files and read the installation instruction PDF. Start with the DANA software if you are installing that. Otherwise, install MaxFilter with the special instructions on how to install if DANA does not exist on your system. You will need root access to install the software.
5. You may need to download and install Open Motif (libXm.so.3 is required). You can search online for an RPM containing this software.
6. If you are using an x86_64 Linux system (type "uname -m" to find out) you will need to execute the following commands after installation:
   • cp -r /neuro/bin/util/i686-pc-linux-gnu /neuro/bin/util/x86_64-pc-linux-gnu
   • cp -r /neuro/bin/X11/i686-pc-linux-gnu /neuro/bin/X11/x86_64-pc-linux-gnu
7. If you are using MaxFilter, email the CABMSI director for the calibration files specific for our MEG system. The files (named below) should be copied to the appropriate directories:
   • /neuro/databases/sss/sss_cal.dat
   • /neuro/databases/ctc/ct_sparse.fif
8. Ensure you have copied the license information from the Elekta representative into /neuro/setup/licenses.neuromag
9. In order to run Cliplab, MRIlab, or Seglab, you will need an additional license file. You can get this file (/neuro/setup/LICENSES) by emailing the output of the following command to the Elekta representative: /neuro/bin/admin/license_probe
10. Run your software!

• Available Elekta Neuromag software:
  • Graph [HP-UNIX only]
  • MaxFilter [Linux & HP-UNIX]
    • Tested on Linux by Mwcole (2008-03-04) [Linux version: openSUSE 10.2 x86_64]
      • Notes: Applied to two sets of data; filters quite well. Worked with data that crashed on HP-UNIX machine at CABMSI.
  • Xplotter [Linux & HP-UNIX]
    • Tested on Linux by Mwcole (2008-03-04) [Linux version: openSUSE 10.2 x86_64]
      • Notes: Will run.
  • Xfit [Linux & HP-UNIX]
    • Tested on Linux by Mwcole (2008-03-04) [Linux version: openSUSE 10.2 x86_64]
      • Notes: Will run. Beta version (not for clinical use).
  • Seglab [Linux & HP-UNIX]
    • Tested on Linux by Mwcole (2008-03-04) [Linux version: openSUSE 10.2 x86_64]
      • Notes: Will run.
  • MRIlab [Linux & HP-UNIX]
    • Tested on Linux by Mwcole (2008-03-04) [Linux version: openSUSE 10.2 x86_64]
      • Notes: Will run. Beta version (not for clinical use).
  • DicomAccess [Linux & HP-UNIX; not tested]
  • Cliplab [Linux & HP-UNIX]
    • Tested on Linux by Mwcole (2008-03-04) [Linux version: openSUSE 10.2 x86_64]
      • Notes: Will run.

Mwcole 10:32, March 6, 2008 (EST)

How to get MNE Software to run properly on a x86_64 Linux machine

• The current version of MNE Software (2.5.2) cannot compute the inverse operator on x86_64 Linux machines
• Solution:
  • Email Matti Hamalainen (msh@nmr.mgh.harvard.edu), creator of MNE, for the file mne-lapack-fix.tar.gz
  • Unpack this file in $MNE_ROOT
• Note: According to Dr. Hamalainen, this should be fixed in version 2.6

Useful References

The Basics of MEG
Acquisition and Filtering
Source Localization Papers
Color picture of the Vectorveiw Sensor Array

Tips for Using HP UNIX

• Run the bash shell (command "bash" at the prompt) or the tcsh shell (command "tcsh") to enable the following features:

1) Press 'tab' to autocomplete filenames and commands
2) Press the up arrow to show the previously typed command

• How to create UNIX shell scripts:

Unix Shells

Links

Elekta Neuromag

Some Other Neuromag Sites

Martinos Center at Harvard University
BioMag Laboratory Helsinki, FI
Low Temperature Laboratory Helsinki, FI
CBU at Cambridge (with their own MEG wiki)
University of California, San Diego (UCSD)
Oxford
Max Planck Institute for Human Cognitive and Brain Sciences
University of Utah
University of New Mexico

Erika 09:38, 2 May 2007 (PDT)