Getting started with Neuromag data

All data recorded with an Elekta-Neuromag system is stored in *.fif files, see support for Neuromag and/or Elekta meg data.

To load the data into Matlab you need the MNE toolbox from Matti Hämäläinen, see MNE software. Then (in matlab) you need to add the paths where the FieldTrip and MNE toolboxes can be found.

To get started, you should add the FieldTrip main directory to your path, and execute the fieldtripdefs function, which sets the defaults and configures up the minimal required path settings (see the faq):

addpath <full_path_to_fieldtrip>
fieldtripdefs

The first step is to see if you can read in the data using both the toolboxes by typing the following in the command window:

>> hdr = ft_read_header(filename); %your fif-filename
>> hdr

hdr = 

          label: {317x1 cell}
         nChans: 317
             Fs: 1000
           grad: [1x1 struct]
           unit: {1x317 cell}
       nSamples: 396000
    nSamplesPre: 0
        nTrials: 1
           orig: [1x1 struct]

The header contains a lot of information about the measurement parameters. In this example 317 channels were recorded, the sampling frequency was a 1000 Hz and in the field hdr.grad you can find information about the sensor-locations, for example. The field 'hdr.orig' contains all the original header information.

>> dat = ft_read_data(filename);
>> size(dat)

ans =

         317      396000

The variable 'dat' contains all the data for 317 channels for all samples. This is a recording of 396 seconds sampled at 1000 Hz.

When this works you are sure that fieldtrip can handle your dataset and you can start to analyse your data as described here.

• Reading .fif mri-data with fieldtrip and making a single shell headmodel (example script can be found here).

Not yet documented or fixed but encountered:

• read_trigger, this function assumes that event_values below 5 are noise. In the new system (Elekta Neuromag VectorView 306) this is not always the case.