Analysis of MEG Data in SPM5
Many of us here use SPM for EEG and/or MEG analysis. The main reason is that SPM is freeware (requiring only Matlab), and thus modifiable and relatively easily understandable (if you have basic knowledge of a procedural computer language, given that Matlab is fairly high level). Several of us are actively extending SPM for our own purposes, particularly in relation to the Neuromag type of MEG data.
For specific demo using data from our Neuromag MEG machine, see SpmDemo
For a fuller demo of other EEG/MEG analysis in SPM5 (though from a different MEG machine), including more general features (e.g, time-freq analysis, 3D statistical maps), with proper step-by-step instructions via the GUI, see: http://www.fil.ion.ucl.ac.uk/spm/data/mmfaces.html
- For a more theoretical introduction to source localisation in SPM5, see these slides: attachment:henson-SPM-Grad08-4-meeg.ppt
Here are some relevant papers:
Summary of localisation approach using ReML for evoked and induced responses (mathematical; cites earlier development papers too): attachment:FristonEtAl_hbm_06.pdf
Basic considerations for Group Analyses (though using individual meshes): attachment:HensonEtAl_NI_07.pdf
Use of inverse-normalised canonical meshes: attachment:MattoutEtAl_JCIN_07.pdf
New method of Multiple Sparse Priors (MSP): attachment:FristonEtAl_NI_08_MSP.pdf
Additional SPM5 functions:
If you are not using the version of SPM5 installed on the CBU network (ie do not have */spm5/cbu_updates on your Matlab path) - eg are an external collaborator - you will need to download the latest versions of some site-specific SPM5 functions in order to read the FIF format data files from our MEG scanner. These SPM functions can be downloaded from here: http://imaging.mrc-cbu.cam.ac.uk/svn/spm5_cbu_updates/devel (see also http://www.mrc-cbu.cam.ac.uk/~rh01/fif2spm.html).
Miscellaneous helpful SPM/Matlab functions we've written can be found here: http://imaging.mrc-cbu.cam.ac.uk/svn/meg_misc/devel/ For permission to contribute to or edit this repository, contact Ian Nimmo-Smith.
A meta-toolbox of functions that allow you to apply EEGLAB functions (eg. ICA, plot raw data, plot ERFimage) to SPM-format MEG data can be found here: http://imaging.mrc-cbu.cam.ac.uk/svn/spmeeglab/devel/ For further information, contact Jason Taylor. Help on artefact correction using ICA is forthcoming...
This page describes the procedure for creating a 3D SensorSpm (topography x time).
First you will probably want to run your raw data through the [:Maxfilter:Maxfilter utility], particularly if you 1) used Active Shielding during acquisition, 2) if you want to apply SSS to remove noise, 3) if you used continuous HPI. Max Filter can also downsample (eg from 1000Hz to 200Hz) and convert the data into different datatypes (e.g, short), which will help reduce filesize and processing time.
- Next you will need to convert your *.FIF files into Matlab and SPM format. For those using SPM5 at the CBU, this is now an option on the SPM5 GUI "convert" button (when in "EEG" mode) (which utilises the function spm_eeg_rdata_FIF.m). Then you can perform averaging, filtering and other preprocessing in SPM, as well as distributed source localisation.