The purpose of this page is just to serve as a scratch pad for the new version of a tutorial site.

There is no guarantee that this page is updated in the end to reflect the final state of the tutorial site. So chances are that this page is considerably outdated and irrelevant. The notes here might not reflect the current state of the code, and you should not use this as serious documentation.

Source reconstruction of event-related fields using minimum-norm estimate

In this tutorial you can find information about how to do source-analysis with minimum-norm estimate on the event-related fields (MEG) of a single subject. We will working on the dataset described in the preprocessing tutorials (Trigger-based trial selection, Event related averaging and planar gradient), and we will use also the anatomical images that belong to the same subject. We will repeat code to select the trials and preprocess the data as described in the Event related averaging and planar gradient tutorial. We assume that preprocessing and event-related averaging is already clear for the reader. To preprocess the anatomical data, we will use two other software packages (FreeSurfer and MNE Suite).

This tutorial will not show how to do group-averaging and statistics on the source-level. It will also not describe how to do source-localization of oscillatory activation. You can check the Localizing oscillatory sources using beamformer techniques tutorial if you are interested in the latter.

In the Event related averaging and planar gradient tutorial time-locked averages of event related fields of three conditions have been computed and the Cluster-based permutation tests on event related fields tutorial showed that there was a significant difference among two conditions. The topographical distribution of the ERFs belonging to each conditions and ERFs belonging to those differences have been plotted. The aim of this tutorial is to calculate a distributed representation of the underlying neuronal activity that resulted in the brain activity observed at the sensor level.

To calculate distributed neuronal activation we will use the minimum-norm estimate. This approach is favored for analyzing evoked responses and for tracking the wide-spread activation over time. It is a distributed inverse solution that discretizes the source space into locations on the cortical surface or in the brain volume using a large number of equivalent current dipoles. It estimates the amplitude of all modeled source locations simultaneously and recovers a source distribution with minimum overall energy that produces data consistent with the measurement 1) 2). The reference for the implemented method is Dale et al. (2000).

Figure 1. shows the bigger steps in the calculation of the minimum-norm estimate. It shows that the computation of the inverse solution is based on the outputs of two independent processing steps: the processing of the anatomical images that leads to the forward solution and the processing of the MEG data. Creating the source model requires the use of two additional software packages, FreeSurfer and MNE Suite.

Figure 1. An overview of the bigger steps in the calculation of the minimum-norm estimate
Figure 1. An overview of the bigger steps in the calculation of the minimum-norm estimate

To compute the distributed neuronal activation using minimum-norm estimate we will perform the following steps:


The following will use the anatomical MRI belonging to Subject01. The file can be obtained from ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/Subject01.zip. The functions described in this part of the tutorial are using toolboxes that are under the fieldtrip/external folder. You do not have to add these toolboxes yourself, but it is important that you set up your matlab path properly. You can read about how to set up your matlab path here.

addpath <path to fieldtrip directory>;
ft_defaults;

Preprocessing of the anatomical MRI


The following figure shows the steps of the preprocessing and of the rest of the anatomical processing (volume conduction and source-model).

Figure 2. Pipeline for processing of the anatomical data
The anatomical preprocessing is done in Matlab with FieldTrip. At the end, a segmented mri is created for the volume conduction model, and an anatomical volume with and without brainmask is created in a Freesurfer compatible format for the source-space. The preprocessing involves the following steps:

  • read in the anatomical images into Matlab with ft_read_mri
  • (if your mri images are not in the CTF-coordinatesystem, you should realign them with the ft_volumerealign function. If you do not know which coordinate system the images are aligned to, you can check it with the ft_determine_coordsys function.)
  • reslice the volume with ft_volumereslice in order to have a uniform thickness for each slice
  • realign the resliced volume to the MNI space
  • save the CTF and also the MNI-aligned volume (we will need the field 'transform' of these later)
  • obtain a skull-stripped anatomy and a brain mask from the MNI-aligned mri volume using ft_volumesegment
  • save the MNI-aligned anatomy and the segmented anatomy in Freesurfer compatible format, using ft_volumewrite. These two will be used for creating the source model.

The input of the preprocessing is the anatomical MRI. We will create four outputs that will be necessary for the subsequent processing: 2 files in .mgz format that will be used for creating the source space, a matlab structure called “seg” that will be used for creating the volume conduction model, and a transformation matrix that will help us later to transform the volume conductor and the source-model to CTF space later.


1. Preprocessing of the anatomical MRI: read in MRI data


mri = ft_read_mri('Subject01.mri');

2. Preprocessing of the anatomical MRI: realign to CTF


The volume conduction model describes the geometry and the electrical (conductive) properties of the head. The volume conduction model (or headmodel) requires a geometrical description of the head. In this tutorial we have an anatomical MRI of the subject from which we can construct the head model. Here, you can read more about the coordinate systems. And here, you can read more about the headmodel.

In this example, we are using an MRI which has been already processed to contain a transformation matrix that corresponds to the CTF convention. Therefore, it does not need to be realigned.

I THINK THAT THE SECTION BELOW (UNTIL THE END OF THIS SECTION) SHOULD BE MADE INTO A SEPARATELY LINK. OTHERWISE, IT IS CONFUSING WHEN YOU SAY THAT YOU DON'T NEED TO REALIGN AND THEN SHOW THE CODE ANYWAY. FURTHERMORE, IF IT IS A TUTORIAL, THEN THE IMMEDIATE CODE BELOW WON'T WORK BECAUSE THERE IS NO VARIABLE mri_other THAT CAN BE USED AS AN INPUT ARGUMENT. ALSO IF MADE INTO A SEPARATE LINK.

But if you are not sure of the coordinate system of your mri, you can use the following function to check it:

mri_other = ft_determine_coordsys(mri_other, 'interactive', 'yes');

If it worked well, you will see the coordinate system specified in the mri structure in the mri.coordsys field. If 'coordsys' is not 'ctf', you will need to align your mri to the fiducial points (LPA, RPA and nasion) with the ft_volumerealign function. This function does not change the anatomical data, instead it creates a transformation matrix that aligns the anatomical data to the intended coordinate system (in this case CTF).

cfg        = [];
cfg.method = 'interactive';
mri        = ft_volumerealign(cfg, mri_other);

3. Preprocessing of the anatomical MRI: reslicing


This steps reslices the anatomical volume in a way that each slice will be equaly thick. We use 1 mm thick slices and we specify the dimension as 256X256X256, because this is the format which FreeSurfer works with.

cfg            = [];
cfg.resolution = 1;
cfg.dim        = [256 256 256];
mrirs          = ft_volumereslice(cfg, mri);
save mrirs;

4. Preprocessing of the anatomical MRI: Re-align to MNI

The creation of the source-space for the minimum-norm estimate will happen with the help of two additional software packages, FreeSurfer and the MNE Suite. Before using this software the anatomical MRI has to be preprocessed in FieldTrip which involves the creation of a brainmask, and coregistering the MRI to a coordinate frame that Freesurfer understands (e.g., the Talairach or MNI coordinate system).

You will use ft_volumerealign to navigate through the anatomical volume, and identify the landmarks which define the Talairach coordinate system. This means that you need to identify the anterior commissure, the posterior commissure, and an interhemispheric point (which defines the XZ-plane), also referred to as landmarks. You can navigate through the slices (at each of the 3 dimensions x, y, and z) with the arrow keys on the keyboard (??).

When you have identified the landmarks you can stored their voxel coordinates (location) by pressing the keys on the keyboard that correspond to the first letter in the name of the landmark ('a', 'p', and 'z' at the right locations. When all landmarks have been identified, press the 'q' key (for quit), the transformation matrix is updated to reflect the transformation from voxel space into Talairach space.

For a detail guide on identifying landmarks in the anatomical volume see this link: page moved and edited text for this link

Importantly, the implicit assumption is that the original transformation matrix correctly describes a right-handed coordinate system (otherwise left and right may become mixed up). In this example, we are using an MRI which has been already processed to contain a correct transformation matrix (in this case corresponding to the CTF convention, which is also a right-handed coordinate system). If you are processing MRI scans in the native file format without explicit orientation information, the previous step may lead to a left/right flip. I THINK THIS LEFT/RIGHT FLIP NEEDS TO BE EXPLAINED MORE. DO YOU MEAN THAT THE LEFT HEMISPHERE BECOMES THE RIGHT, AND THE RIGHT BECOMES THE LEFT? IS THAT THE SAME/DIFF AS SEEING THE REFLECTION OF THE BRAIN??


load mrirs;
cfg        = [];
cfg.method = 'interactive';
mri_mni    = ft_volumerealign(cfg, mrirs);
save mri_mni mri_mni                  %we will need this structure at 
                                      %later stages (save to disk)

5. Preprocessing of the anatomical MRI: segmentation


This step uses a segmentation of the anatomy, where gray, white and the cerebro-spinal fluid compartments are differentiated, to create a skull-stripped anatomy and a brainmask. The brainmask is a binary mask of the inner skull. The function ft_volumesegment will produce the required output.

% segmentation of the mri
load mri_mni;
cfg           = [];
cfg.coordsys  = 'spm';
cfg.output    = {'skullstrip' 'brain'};
seg           = ft_volumesegment(cfg, mri_mni);
save seg seg;

The seg structure will be used later for creating the volume conduction model. Also the skull-stripped anatomy will be later saved to disk in a Freesurfer compatible format, to facilitate the creation of the source model.

6. Preprocessing of the anatomical MRI: save to disk


load mri_mni;
load seg;


% save both the original anatomy, and the masked anatomy in a freesurfer compatible format
cfg             = [];
cfg.filename    = 'Subject01';
cfg.filetype    = 'mgz';
cfg.parameter   = 'anatomy';
ft_volumewrite(cfg, mri_mni);

cfg.filename    = 'Subject01masked';
ft_volumewrite(cfg, seg);
Importantly, the mgz-filetype can only be used on the Linux and Mac platforms (and on Windows running virtual box). When you are processing the anatomical information on one of these platforms it is OK to save as mgz (and useful too, because it compresses the files and uses less diskspace as a consequence). Note however that these files cannot be saved and read on a Windows PC. If you have your Matlab installed on Windows, you may try to save the volume as a nifti file, for example. For this, you have to use cfg.filetype = 'nifti'. And you can convert the nifti file to mgz using mri_convert with FreeSurfer.


The matlab-based preprocessing of the anatomical data is now finished. We created two .mgz files that will be used for creating the source model and a seg structure that will be used for creating the volume conduction model.

However, it is important that the anatomical MRI and the sensor positions are expressed in the same coordinate system. The MEG sensor positions are always defined relative to the fiducial coils. If we want to create a volume conduction model and a sourcemodel, the anatomical data must also be expressed relative to these points (i.e., in the CTF coordinate system). Therefore, we saved also the mri volume aligned to MNI and also CTF coordinates. We will use the transformation matrices of these volumes to transform the volume conduction model and the sourcespace to the CTF coordinate system.

Source model


Source model: Introduction


This part describes how to set up the source-space for the minimum norm estimate. This entails the creation of a triangulated cortical mesh, ideally consisting of a number of approximately equally sized triangles that form a topological sphere. The latter property is required to create an inflated cortex and to do intersubject realignment. The following uses Freesurfer to create a topologically correct description of the cortex. This typically yields a mesh with > 100000 vertices per hemisphere which is too much for a workable minimum norm estimate. Therefore, we use the MNE-suite to downsample the triangulated meshes. This step serves the purpose of retaining a topologically correct description of the surface, and keeping the variance in triangle size low. In contrast, Matlab's reducepatch function breaks the topology and leads to a bigger variance in triangle size.
The creation process of the source-space can be divided into 4 stages (after the preprocessing steps):

  1. Volumetric processing in Freesurfer.
  2. Surface based processing in Freesurfer.
  3. Creation of the mesh using MNE-suite.
  4. Coregistration of the source space to the sensor-based coordinate system with FieldTrip.

The volumetric and surface based processing (first and the second steps) takes 10 hours altogether. These steps will run on the computer for themselves. There is only one checkpoint between the volume and the surface based processing where an intermediate result can be checked interactively.

The input of the creation process of the source-space are mgz files that were created in the preprocessing. The output is the source model that is a matlab structure called 'sourcespace' in this tutorial.

The instructions about how to install and run Freesurfer and MNE Suite are aimed at users at the Center of Neuroimaging of the Donders Institute and at the MPI for Psycholinguistics in Nijmegen.

1. Source model: Volumetric processing in Freesurfer


Freesurfer's anatomical processing pipeline consists of a series of automated steps, which essentially consist of:

  1. processing steps on a volumetric anatomical MRI (image intensity normalization, co-registration with Talairach space, skull stripping, automatic segmentation of sub-cortical structures, and finally segmentation)
  2. extraction of the cortical mesh
  3. processing of the surface meshes (smoothing, topology fixing, inflation, co-registration with a spherical template)

Here is a link to the different processing steps. Although the Freesurfer procedure can be invoked using only a few Freesurfer commands, below we will describe the (sub)commands that will achieve the same. These commands sequentially generate a series of files (volumetric, surface and transformation matrices). Each of the output files serves as input to the sequential analysis steps. A table of file dependencies can be found here.
There are a few analysis steps in Freesurfer, which are not guaranteed to give a nice result, and require some user interaction to get it right. Moreover, Freesurfer can be quite picky with respect to the exact format of the MRI-volumes. One step, which in our experience is notorious for not being very robust, is automatic skull-stripping. Therefore, we advocate a hybrid approach that uses SPM for an initial segmentation of the anatomical MRI during the preprocessing. With this segmentation, we created a brainmask that provides a robustly skull-stripped image, which is a prerequisite for a correct segmentation in Freesurfer. Although this approach may seem a bit convoluted (you may rightfully ask why we need to redo the segmentation in Freesurfer if we already did it in SPM), the interdependencies between different files generated along the Freesurfer pipeline make tapping into this pipeline at a random point quite complicated. For this reason a large part of the volumetric processing in Freesurfer needs to be done as well.


In order to be able to use Freesurfer, you need to have a working installation of the package. It can be downloaded from here. If you are working at the Center of Neuroimaging of the Donders Institute you can find more versions of Freesurfer under the /opt/FreesurferXXX directories. (If you are working at the MPI for Psycholinguistics, you should install the software yourself in your directory.) We recommend to use Freesurfer 5.1.0. You can run the commands below by just copying and pasting them into the terminal window of the Linux system (from where you use/initiate Matlab).

%% I totally skipped past the previous line and got confused with the code below, CAN WE KEEP THE PREVIOUS LINE IN BOLD?? I also added a comment above the first box of code below. ALSO FOR CLARITY, CAN WE INSERT A COMMENT IN THE FIRST CODE BOX THAT RETURNS/RESUMES TO BEING EXECUTED IN MATLAB?

To get started, you need to set up your environmental variables. (Pay attention to the (lack of) spaces.)

% run this code in linux
export FREESURFER_HOME=<path to Freesurfer>
export SUBJECTS_DIR=<Subject directory>

SUBJECTS_DIR is the directory where you will store all the Freesurfer-processed anatomical data of all your subjects. Then, type this command to set up Freesurfer:

source $FREESURFER_HOME/SetUpFreeSurfer.sh

It is useful to set up a subject-specific directory:

mksubjdirs $SUBJECTS_DIR/Subject01


Now, we are ready to start using Freesurfer. As a first step in the volumetric pipeline, we have to 'convert' the anatomical MRI once more, but now using a Freesurfer command. You can find now a new folder in the subject directory called “mri” into which you will copy both the masked and the original mgz files you created in the previous preprocessing steps in FieldTrip. All the Freesurfer commands will be called from the “mri” directory. (The first three lines of the following code is doing all of these for you.)

cp Subject01masked.mgz $SUBJECTS_DIR/Subject01/mri/Subject01masked.mgz
cp Subject01.mgz $SUBJECTS_DIR/Subject01/mri/Subject01.mgz
cd $SUBJECTS_DIR/Subject01/mri/
mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
mri_convert -c -oc 0 0 0 Subject01.mgz orig-nomask.mgz

We now have a 'brainmasked' anatomical volume in orig.mgz, which is the starting input volume to the following pipeline:

recon-all -talairach -subjid Subject01
recon-all -nuintensitycor -subjid Subject01
recon-all -normalization -subjid Subject01
cp T1.mgz brainmask.mgz
recon-all -gcareg -subjid Subject01
recon-all -canorm -subjid Subject01
recon-all -careg -subjid Subject01
recon-all -calabel -subjid Subject01
recon-all -normalization2 -subjid Subject01
recon-all -segmentation -subjid Subject01
recon-all -fill -subjid Subject01

This ends the part of the Freesurfer pipeline concerned with volumetric processing. At this stage you should have a file filled.mgz containing the segmentation of the cortical white matter (cerebellum is not included!). You can check how this looks using FieldTrip, by doing the following:

% go to the Subject01/mri directory
mri = ft_read_mri('filled.mgz');
cfg = [];
cfg.interactive = 'yes';
figure;ft_sourceplot(cfg, mri);

Figure 3. Filled mgz


Figure 3. Filled mgz created by Freesurfer. The two hemispheres have different colors (white and grey), cerebellum is not included.

2. Source model: Surface based processing in Freesurfer


The surface construction is done by the following sequence of commands (from the Subject01/mri directory):

recon-all -tessellate -subjid Subject01
recon-all -smooth1 -subjid Subject01
recon-all -inflate1 -subjid Subject01
recon-all -qsphere -subjid Subject01
recon-all -fix -subjid Subject01
cp brain.mgz brain.finalsurfs.mgz
recon-all -finalsurfs -subjid Subject01
recon-all -smooth2 -subjid Subject01
recon-all -inflate2 -subjid Subject01
recon-all -sphere -subjid Subject01
recon-all -surfreg -subjid Subject01

After these steps (which may take quite a while) you end up with a bunch of files in the Subject01/surf/ directory. We are going to use lh.white and rh.white to create the source space in the next step.

3. Source model: Creation of the mesh using MNE Suite


Just like with Freesurfer, we have to first take care that MNE-suite is installed, and that some environmental variables are correctly specified. If you are working at the Center of Neuroimaging of the Donders Institute, you can find the MNE Suite under the /opt/mne directory. At the MPI for Psycholinguistics, MNE Suite is installed under the /mnt/data1/mne directory.

export MNE_ROOT=<MNE directory>
cd $MNE_ROOT/bin
. ./mne_setup_sh
export SUBJECTS_DIR=<Subject directory>
export SUBJECT=Subject01

Now we can create the source space

mne_setup_source_space --ico -6

This step creates a bunch of files in <Subject directory>/Subject01/bem/, containing different representations of the source space. In subsequent steps, FieldTrip will use the Subject01-oct-6-src.fif file. We can already have a look in MATLAB at how the source space looks.

bnd = ft_read_headshape('Subject01-oct-6-src.fif', 'format', 'mne_source');
figure;ft_plot_mesh(bnd);

Figure 4. Source-space downsampled
Figure 4. The source-space downsampled by MNE Suite

4. Source model: Co-registration of the source space to the sensor-based head coordinate system


We have the source locations co-registered to the Talairach (MNI) coordinate system, so now we need to co-register the source space to the sensor-array (i.e., we have to express the positions of the sources in the same (CTF) coordinate system as the sensors). For this, we will use transformation matrices of the earlier re-aligned mri volumes. By combining the transformation matrix of the volume that is aligned to the CTF coordinates (from voxel space to CTF space) and the transformation of the volume that is aligned to the MNI coordinates (from voxel space to MNI space), we will get a matrix that transforms the data from CTF to MNI space. We will apply this transformation matrix to the source-points. Next to this, we will convert the units to cm.

load mrirs % mri volumed aligned to the CTF coordinate system (and resliced)
           % (see Preprocessing of the anatomical MRI,step 3)
load mri_mni % mri volume aligned to the Talairach (MNI) coordinate system 
             % (see Preprocessing of the anatomical MRI,step 4)

mrirs = ft_convert_units(mrirs, 'cm');
mri_mni = ft_convert_units(mri_mni, 'cm');
T   = mrirs.transform*inv(mri_mni.transform);

% go to the Subject01/bem directory
bnd  = ft_read_headshape('Subject01-oct-6-src.fif', 'format', 'mne_source');
sourcespace = ft_convert_units(bnd, 'cm');
sourcespace = ft_transform_geometry(T, sourcespace);
save sourcespace sourcespace;
save T T; %we will need the transformation matrix also in the next step

Volume conduction model


We create the volume conduction model from the segmented volume (see Preprocessing of the anatomical MRI, step 5). In order to get a volume conduction model that is aligned with the source space we will apply the same transformation matrix (T) on the volume conductor as the transformation matrix that we applied on the sourcespace.

load seg;
load T;


cfg = [];
vol = ft_prepare_singleshell(cfg,seg);
vol.bnd = ft_transform_geometry(T, vol.bnd);
save vol vol;

It is useful to check if the resulting sourcespace and the volume conductor are aligned. To plot, you can use this code:

% load vol                                       % volume conduction model
load sourcespace;
figure;hold on;
ft_plot_vol(vol, 'facecolor', 'none');alpha 0.5;
ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight 

If they are not aligned, it may be because vol is not expressed in CTF coordinates. You can check using ft_determine_coordsys.

Figure 5. Source-space with volume conductor
Figure 5. The final version of the source-space aligned and plotted together with the volume conductor


The following will use the MEG data belonging to Subject01. The file can be obtained from ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/Subject01.zip. For both preprocessing and averaging, we will follow the steps that have been written in the Event related averaging and planar gradient tutorial. We will use trials belonging to two conditions (FC and FIC) and we will calculate their difference.

Preprocessing of MEG data

Reading the FC data

The ft_definetrial and ft_preprocessing functions require the original MEG dataset, which is available from ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/Subject01.zip.

% find the interesting segments of data
cfg = [];                                           % empty configuration
cfg.dataset                 = 'Subject01.ds';       % name of CTF dataset  
cfg.trialdef.eventtype      = 'backpanel trigger';
cfg.trialdef.prestim        = 1;
cfg.trialdef.poststim       = 2;
cfg.trialdef.eventvalue     = 9;                    % trigger value for fully congruent (FC)
cfg = ft_definetrial(cfg);            

% remove the trials that have artifacts from the trl
cfg.trl([2, 3, 4, 30, 39, 40, 41, 45, 46, 47, 51, 53, 59, 77, 85],:) = []; 

% preprocess the data
cfg.channel    = {'MEG', '-MLP31', '-MLO12'};       % read all MEG channels except MLP31 and MLO12
cfg.demean     = 'yes';
cfg.baselinewindow  = [-0.2 0];
cfg.lpfilter   = 'yes';                              % apply lowpass filter
cfg.lpfreq     = 35;                                 % lowpass at 35 Hz.

dataFC_LP = ft_preprocessing(cfg);                      

These data have been cleaned from artifacts by removing several trials and two sensors; see the visual artifact rejection tutorial.

Subsequently you can save the data to disk.

save dataFC_LP dataFC_LP
2009/03/11 13:50

Reading the FIC data

The ft_definetrial and ft_preprocessing functions require the original MEG dataset, which is available from ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/Subject01.zip.

% find the interesting segments of data
cfg = [];                                           % empty configuration
cfg.dataset                 = 'Subject01.ds';       % name of CTF dataset  
cfg.trialdef.eventtype      = 'backpanel trigger';
cfg.trialdef.prestim        = 1;
cfg.trialdef.poststim       = 2;
cfg.trialdef.eventvalue     = 3;                    % trigger value for fully incongruent (FIC)
cfg = ft_definetrial(cfg);            

% remove the trials that have artifacts from the trl
cfg.trl([15, 36, 39, 42, 43, 49, 50, 81, 82, 84],:) = []; 

% preprocess the data
cfg.channel    = {'MEG', '-MLP31', '-MLO12'};        % read all MEG channels except MLP31 and MLO12
cfg.demean     = 'yes';
cfg.baselinewindow  = [-0.2 0];
cfg.lpfilter   = 'yes';                              % apply lowpass filter
cfg.lpfreq     = 35;                                 % lowpass at 35 Hz.

dataFIC_LP = ft_preprocessing(cfg);                      

These data have been cleaned from artifacts by removing several trials and two sensors; see the visual artifact rejection tutorial.

Subsequently you can save the data to disk.

save dataFIC_LP dataFIC_LP
2009/03/11 13:47

Averaging and noise-covariance estimation

The function ft_timelockanalysis makes averages of all the trials in a data structure and also estimates the noise-covariance. For a correct noise-covariance estimation it is important that you used the cfg.demean = 'yes' option when the function ft_preprocessing was applied.

The trials belonging to one condition will now be averaged with the onset of the stimulus time aligned to the zero-time point (the onset of the last word in the sentence). This is done with the function ft_timelockanalysis. The input to this procedure is the dataFC_LP structure generated by ft_preprocessing. At the same time, we need to compute the noise-covariance matrix, therefore cfg.covariance = 'yes' has to be specified as well as the time window where the noise-covariance will be estimated. Here, we use the baseline where there is no signal of interest yet.

  load dataFC_LP;
  load dataFIC_LP;
  cfg = [];
  cfg.covariance = 'yes';
  cfg.covariancewindow = [-inf 0]; %it will calculate the covariance matrix 
                                   % on the timepoints that are  
                                   % before the zero-time point in the trials
  tlckFC = ft_timelockanalysis(cfg, dataFC_LP);
  tlckFIC = ft_timelockanalysis(cfg, dataFIC_LP);
  save tlck tlckFC tlckFIC;

The source space, the volume conduction model and the position of the sensors are necessary inputs for creating the leadfield (forward solution) with the ft_prepare_leadfield function. The sensor positions are contained in the grad field of the averaged data. However, the grad field contains the positions of all channels, therefore, the used channels have to be also specified.

load tlck;
load sourcespace;
load vol;

cfg = [];
cfg.grad = tlckFC.grad;                      % sensor positions
cfg.channel = {'MEG', '-MLP31', '-MLO12'};   % the used channels
cfg.grid.pos = sourcespace.pnt;              % source points
cfg.grid.inside = 1:size(sourcespace.pnt,1); % all source points are inside of the brain
cfg.vol = vol;                               % volume conduction model
leadfield = ft_prepare_leadfield(cfg);

save leadfield leadfield;

FIXME
The ft_sourceanalysis function calculates the inverse solution. The method used (minimum-norm estimation) has to be specified with the cfg.method option. The averaged functional data, the forward solution (the output of the ft_prepare_leadfield function), the volume conduction model (in this case, the output of the ft_prepare_singleshell function) and the noise-covariance matrix (the cov field of the output of the ft_timelockanalysis function) has to be provided.

The lambda value is a scaling factor that is responsible for scaling the noise-covariance matrix. If it is zero the noise-covariance estimation will be not taken into account during the computation of the inverse solution. Noise-covariance is estimated in each trial separately and then averaged, while the functional data (of which we calculate the source-analysis) is simply averaged across all the trials. Therefore, the higher the number of trials the lower the noise is in the averaged, functional data, but the number trials is not reducing the noise in the noise-covariance estimation. This is the reason while it is useful to use a scaling factor for the noise-covariance matrix if we want to estimate more realistically the amount of noise.

You do not have to specify of the noise-covariance matrix separatly, because it is in the tlckFC.cov and in the tlckFIC.cov fields, and ft_sourceanalysis will take it into account automatically.

load tlck;
load leadfield;
load vol;

cfg=[];
cfg.method = 'mne';
cfg.grid = leadfield;
cfg.vol = vol;
cfg.lambda = 1e8;
sourceFC = ft_sourceanalysis(cfg,tlckFC);
sourceFIC = ft_sourceanalysis(cfg, tlckFIC);

save source sourceFC sourceFIC;

You can plot the inverse solution onto the source-space at a specific time-point with the ft_plot_mesh function.

load sourceFIC;
load sourcespace;

bnd.pnt = sourcespace.pnt;
bnd.tri = sourcespace.tri;
m=sourceFIC.avg.pow(:,450); % plotting the result at the 450th time-point that is 
                         % 500 ms after the zero time-point
ft_plot_mesh(bnd, 'vertexcolor', m);

Figure 6. The source reconstruction at 500 ms
Figure 6. The result of the source-reconstruction of the FIC condition plotted onto the source-space at 500 ms after the 0 time-point

But we would like to know where the difference between the conditions can be localized. Therefore, we calculate the difference of the two conditions, and we use ft_sourcemovie to visualize the results.

cfg = [];
cfg.projectmom = 'yes';
sdFC = ft_sourcedescriptives(cfg,sourceFC);
sdFIC = ft_sourcedescriptives(cfg, sourceFIC);

sdDIFF = sdIC;
sdDIFF.avg.pow = sdFIC.avg.pow - sdFC.avg.pow;
sdDIFF.tri = sourcepspace.tri;

save sd sdFC sdFIC sdDIFF;

cfg = [];
cfg.mask = 'avg.pow';
ft_sourcemovie(cfg,sdDIFF);

Figure 7. One frame from ft_sourcemovie
Figure 7. One frame from the movie that shows the differences of the two source-reconstructions

In this tutorial we showed how to do MNE source reconstruction method on a single subject data. We compared the averaged ERF in two conditions and we reconstructed the sources and we calculated the difference of the two source-reconstruction. We showed also how you can visualize the results.

Functions and tutorial pages that show how to average, and how to analyze statistically source-reconstructions across subjects or how to compare those to a template brain are still under development.

1)
Ou, W., Hamalainen, M., Golland, P., 2008, A Distributed Spatio-temporal EEG/MEG Inverse Solver
2)
Jensen, O., Hesse, C., 2010, Estimating distributed representation of evoked responses and oscillatory brain activity, In: MEG: An Introduction to Methods, ed. by Hansen, P., Kringelbach, M., Salmelin, R., doi:10.1093/acprof:oso/9780195307238.001.0001