The purpose of this page is just to serve as todo or scratch pad for the development project and to list and share some ideas.

After making changes to the code and/or documentation, this page should remain on the wiki as a reminder of what was done and how it was done. However, there is no guarantee that this page is updated in the end to reflect the final state of the project

So chances are that this page is considerably outdated and irrelevant.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.

Mouse EEG - channel and source analysis

Introduction

This tutorial describes how to deal with mouse EEG in the aspect of preprocessing, time-frequency analysis, and visualization layout and how to apply the coregistration steps for making volume conduction model. If you are interested in how to measure mouse EEG prior to main process, you can check the nice video tutorialhttp://www.jove.com/video/2562/high-density-eeg-recordings-freely-moving-mice-using-polyimide-based. You can also find information about how to stimulate mouse brain by optical fiber <link*>. If you want to learn how to process EEG data conventionally, check the tutorial on Preprocessing of EEG data and computing ERPs.

Goals

  • improve channel level analysis
    • preprocessing and re-referencing
    • visualisation
    • statistics
    • coregistration of data over different animals
  • improve source level analysis
    • provide template volume conduction model
    • provide template electrode specification
    • coregistration/scaling/warping of template to actual animal dimensions
  • evaluation of data analysis methods

Procedure

We will do the following

  • define trials
  • preprocessing
  • checking for artifacts
  • rereferencing
  • time-locked averaging
  • making a channel layout, deal with animal size
  • visualizing ERPs
  • time-frequency analysis
  • visualizing TFRs
  • read the anatomical MRI data
  • coregister it
  • read the atlas data
  • coregister it
  • make segmentation of tissue inside skull
  • make mesh of brain-skull boundary
  • inflate segmentation using imdilate
  • make mesh of skull-skin boundary
  • make BEM volume conduction model
  • make source model
  • align electrodes with BEM model, deal with animal size
  • do source reconstruction
  • visualize source reconstruction
  • look up source reconstruction results in atlas

Background on the dataset

The purpose of the study in which the data that is demonstrated here is to use EEG with Optogenetic Stimulation (opto-EEG) for studying sensorymotor integration.

Sensorymotor integration is a neurological process dealing with somatosensation inputs into motor outputs in an effective way. Numerous studies have shown the direct signal pathways within somatosensor-motor circuits, however little is known how the tactile sensations with different stimulation frequency are processed from somatosensory to motor cortex in order to react appropriately to different types of stimulation. In present study, we mimicked the peripheral sensation by direct stimulation of S1, S2, M1 and sensory thalamus using optogenetic method and concurrently recorded the frequency dependent responses (1, 10, 20, 30, 40 and 50 Hz) with a depth electrode in the region of the optode (i.e. S1, S2, M1 and thalamus), and recording the EEG using the surface micro electrode array.

Subject and Experiment

In the study applied here, we used the transgenic mice (Thy1-ChR2-EYFP, B6 mice, 12 weeks; body weight 27 g, malehttp://jaxmice.jax.org/strain/007615.html). For implantation of electrodes on the skull and sensory thalamus (VPM; 1.82 mm posterior, 1.5 mm lateral and 3.7 mm ventral to bregma), mice were anesthetized (ketamine/xylazine cocktail, 120 and 6 mg/kg, respectively) and then positioned in a stereotaxic apparatus. Location of electrode placement is going to describe in section ?. We allocated two electrodes in the most anterior region as reference and ground electrodes. The brain signals are recorded by both high-density electrode array (EEG-38 channels + ground and reference-2 channels) and local field potential (single channel). The EEGs were acquired with an analog amplifier (Synamp, Neuroscan, USA) with a sampling frequency of 2000 Hz.

Optogenetic Stimulation

For optogenetic stimulation, we used a semiconductor laser (USA & BCL-040-445; 445 nm wavelength and 40 mW/mm2 maximum output power; CrystaLaser LLC., Reno, NV, USA) that was gated using a pulse generator (575 digital delay, Berkeley Nucleonics Corp., Berkeley, CA, USA). Blue light from the laser was guided to the brain using an optic fiber with clad/core diameters of 125 mm and 3.4 mm, respectively (P1-405A-FC-5; Thorlabs Inc., Newton, NJ, USA). The light intensity from the tip of optical fiber was approximately 2 mW/mm2 measured by integrating sphere coupled to spectrometer (BLUE-Wave-VIS2/IC2/IRRAD-CAL, Stellar-Net Inc., Tampa, FL, USA). Various pulse trains with a 20 ms pulse width were delivered in four different cortical regions (somatosensory cortices, primary motor cortex, and sensory thalamus marked as S1, S2, M1, and VPM in below figure, respectively).

mouse stimulation sites

Preprocessing

define trials

Using the FieldTrip function ft_definetrial you can define the pieces of data that will be read in for preprocessing. Trials are defined by their begin and end sample in the data file and each trial has an offset that defines where the relative t=0 point (usually the point of the optogenetic stimulus-trigger) is for that trial. The ft_definetrial and ft_preprocessing functions require the original EEG dataset acquiring from Synamp system, which is available at this link <cnt file link>.

Actually, example dataset has not digital trigger information. To mark stimulation timing in the file, they use analog input (41th channel) as trigger information. Since FieldTrip can offer to support customized function by using cfg.trialfun, this tutorial shows how to make trial-based dataset. This results in a cfg.trl = 'mousetrialfun' in which the beginning, the trigger offset and the end of each trial relative to the beginning of the raw data is defined.

function trl = mousetrialfun(cfg)

% this function requires the following fields to be specified
% cfg.dataset
% cfg.trialdef.threshold
% cfg.trialdef.prestim
% cfg.trialdef.poststim

hdr   = ft_read_header(cfg.dataset);
trigchan = find(strcmp(hdr.label, 'HL1'));
trigger_data = ft_read_data(cfg.dataset, 'chanindx', trigchan);
trigger_data = trigger_data - median(trigger_data);

if isfield(cfg, 'trialdef') && isfield(cfg.trialdef, 'threshold')
  trigger_threshold = cfg.trialdef.threshold;
else
  trigger_threshold = 0.5*max(trigger_data);
end

figure
plot(trigger_data, 'b')
hold on
plot(trigger_threshold*ones(size(trigger_data)), 'r')

trl = [];

stim_duration = cfg.trialdef.prestim  * hdr.Fs;% number of samples
rest_duration = cfg.trialdef.poststim * hdr.Fs;% number of samples

% extracts, trigger timing ------------------------------------------------
data1 = find(abs(trigger_data) > trigger_threshold);% exceed threshold
data2 = find(data1-[0,data1(1,1:end-1)] > rest_duration);% exceed 'rest_duration'
idx = data1(data2);
clear data1 data2

trigger_event(1,:) = idx;
clear idx

plot(trigger_event(1,:),0,'go')

% extracts, trigger contents ----------------------------------------------
for tr = 1:size(trigger_event,2)
  temp_data = abs(trigger_data(trigger_event(1,tr):trigger_event(1,tr)+stim_duration-1));
  idx = find_cross(temp_data, trigger_threshold, 'down'); clear temp_data
  trigger_event(2,tr) = size(find(idx == 1),2) / (stim_duration / hdr.Fs); clear idx
end; clear tr

trl       = [trigger_event(1, :) - stim_duration+1; trigger_event(1, :) + rest_duration]';
trl(:, 3) = zeros(size(trl, 1), 1);

function idx = find_cross(data, thr, type)
% find peaks.
% data = 1 by n vector.
% thr = the crossing point.
% type = 'both', 'up', 'down'.
% default type: 'both'.

if size(data,1) > 1
  data = data.';
  if size(data,2) > 1
    error('data must be vector form')
  end
end

% up crossing
tidx1 = zeros(1,size(data,2)-1);
tidx2 = zeros(1,size(data,2)-1);
idx1 = zeros(1,size(data,2)-1);
tidx1(find(data(1,1:end-1) <= thr)) = 1;
tidx2(find(data(1,2:end) > thr)) = 1;
idx1(find(tidx1 + tidx2 == 2)) = 1; clear tidx1 tidx2

% down crossing
tidx1 = zeros(1,size(data,2)-1);
tidx2 = zeros(1,size(data,2)-1);
idx2 = zeros(1,size(data,2)-1);
tidx1(find(data(1,1:end-1) >= thr)) = 1;
tidx2(find(data(1,2:end) < thr)) = 1;
idx2(find(tidx1 + tidx2 == 2)) = 1; clear tidx1 tidx2

% both
idx0 = zeros(1,size(data,2)-1);
idx0(find(idx1 + idx2 > 0)) = 1;

if nargin == 2
  idx = idx0;
elseif nargin == 3
  if strcmpi(type,'both')
    idx = idx0;
  elseif strcmpi(type,'up')
    idx = idx1;
  elseif strcmpi(type,'down')
    idx = idx2;
  end
end

Using this trial function, we can call ft_definetrial to find the trials, or segments of interest.

cfg = [];
cfg.dataset  = 'S1s_10Hz.cnt'; 
cfg.trialfun = 'mousetrialfun'; % ft_definetrial will call your function and pass on the cfg
cfg.trialdef.eventtype  = '?';
cfg.trialdef.eventvalue = 40000;
cfg.trialdef.prestim    = 1; % in seconds
cfg.trialdef.poststim   = 2; % in seconds
cfg = ft_definetrial(cfg);

You will see that the trial function produces a figure, which can be used to check whether the threshold was at the appropriate level and whether the onset of stimulation is properly detected.

FIXME insert figure (1 data loading)

The segments of interest are specified by their begin- and end-sample and by the offset that specifies the timing relative to the data segment. The offset is zero here indicating that the first sample is interpreted as time t=0.

>> cfg.trl

ans =

        7447       13446           0
       17447       23446           0
       27447       33446           0
       37447       43446           0
       47446       53445           0
       57445       63444           0
       67445       73444           0
...

preprocessing

After the segments of interest have been added to the configuration structure, we read them from the raw data file into memory. At this spet we also add the other preprocessing options to the configuration, such as the filter settings.

cfg.channel   = 'all';
cfg.baseline  = [-0.30, -0.05];
cfg.demean    = 'yes';
cfg.bsfilter  = 'yes';
cfg.bsfreq    = [59 61]
cfg.lpfilter  = 'yes';
cfg.lpfreq    = 100;
data          = ft_preprocessing(cfg);

The output of ft_preprocessing is a structure which has the following fields:

data = 
 
           hdr: [1x1 struct]
         label: {39x1 cell}
          time: {1x88 cell}
         trial: {1x88 cell}
       fsample: 2000
    sampleinfo: [88x2 double]
           cfg: [1x1 struct]

In the data.sampleinfo you can find the begin and endsample of each trial. The offset has been used to make an individual time axis for each trial.

We can simply plot all channels in a single trial using standard MATLAB code:

plot(data.time{1}, data.trial{1});
legend(data.label);
grid on

FIXME insert figure (2 single trial plot )

checking for artifacts

Using ft_databrowser we can do a quick visual inspection of the data and check whether there are artefacts.

cfg = [];
cfg = ft_databrowser(cfg, data);

FIXME insert figure (3 datatrial browser)

The HL1 channel contains the analog representation of the stimulus, which is of much larger amplitude than all other channels. We can exclude it in the guy (click “channel” button) or using the following:

cfg = [];
cfg.viewmode = 'vertical';
cfg.channel = {'all', '-HL1'};
cfg = ft_databrowser(cfg, data);

We see that some channels show a much lower noise level than others (e.g. AF8). This might be due to differences in electrode-skull impedance.

FIXME insert figure (4 check the impedance and report it here)

rereferencing

The two most frontal electrodes in the grid were used as ground and reference during acquisition. These two electrodes are placed just anterior of the Fp1 and the Fp2 electrode.

This section shows a technique known as common average referencing (CAR) to generate a simple re-referencing method for array-type electrode recordings. CAR is a computationally simple technique. CAR is commonly used in EEG, where it is necessary to identify small signal sources in very noisy recordings.

We hypothesize that CAR will improve neural recording quality with respect to 38 ch electrode references.

cfg            = [];
cfg.reref      = 'yes';
cfg.refchannel = {'FP1';'FP2';'AF3';'AF4';'AF7';'AF8';...
              'F1';'F2';'F5';'F6';'FC1';'FC2';'FC5';'FC6';...
              'C1';'C2';'C3';'C4';'C5';'C6';...
              'CP1';'CP2';'CP3';'CP4';'CP5';'CP6';...
              'P1';'P2';'P3';'P4';'P5';'P6';'PO3';'PO4';'PO7';'PO8';'O1';'O2'};
data_car       = ft_preprocessing(cfg, data);

If you want to see the improvement of CAR, re-run for ft_databrowser with different variable (data_car).

cfg            = [];
cfg.viewmode   = 'vertical';
cfg.channel    = {'all', '-HL1'};
cfg            = ft_databrowser(cfg, data_car);

FIXME insert figure (5 datatrial browser)

Channel level analysis - ERPs

making a channel layout and deal with animal size

In order to make layout of high-density electrode array (HD-array) on mouse skull, FieldTrip support layout files ('mouse_layout.mat') that gives you exact control of the 2-D position of the sensors for topoplotting, and of the per-channel local coordinate axes for the multiplotting. The mat-file containing various variables to draw outlines of the headshape within the name “lay”. Let us give you the information how to make customized layout for HD-array by using FieldTrip. This figure indicates an electrode arrangement of HD-array (this example photo is taken from Lee et al. (2011) Journal of Visualized Experiments (video, pdf).

You can specify cfg.image in ft_prepare_layout and subsequently click on the location of each electrode. After specifying each electrode location, you'll be asked to specify the outlines of the head (i.e. the circle around the head, the eyes, the nose and ears (dash lines) and optionally some lines representing other important landmarks: bold lines, bregma, and lambda) and to specify the mask for the topographic interpolation (green dash line). Find the bregma and lambda points on the skull, and record them with the stereotaxic ruler. The bregma and lambda points are located in the same anterio-posterior axis. The anterio-posterior axis of high-density electrode array (HD-array) matches the line between bregma and lambda points. The bregma point (0, 0) should be located at the middle of the 4th layer of the anterior of HD-array because we follow the Paxinos coordinate system. We implemented a mouse layout on fixed length (4.2 mm) of between bregma and lambda.

cfg         = [];
cfg.image   = 'mouse_skull_with_HDEEG.png';
lay         = ft_prepare_layout(cfg);

After creating the layout, you should manually assign the correct name of the channel labels in the lay.label cell-array. Channel arrangement in lay.label is followed click sequence during ft_prepare_layout process. You can use ft_layoutplot for a visual inspection of the complete layout.

cfg          = [];
cfg.layout   = lay;  
ft_layoutplot(cfg);

FIXME insert figure (6 layout plot)

If you think that some outlines (nose, eyes, head, whiskers and ears) are not necessary, you can pass without assigning any outline. Next step is zero point calibration for the bregma point. If you, however, use customized layout for single subject, you don’t need to carry out next step.

In the aspect of mouse anatomy, the bregma point is located in the middle of the 4th layer of the anterior of HD-array that it should be set (0, 0) because we follow the Paxinos coordinate system. To calibrate layout position, we just subtract the value of bregma on acquired layout from previous step.

xy_shift         = [382, 280];
lay.pos          = lay.pos – repmat(xy_shift, size(lay.pos, 1), 1);
lay.mask{1, 1}   =  lay.mask{1, 1}- repmat(xy_shift, size(lay.mask{1, 1}, 1), 1);
for i =1:1:size(lay.outline, 2)
    lay.outline{1, i}= lay.outline{1, i}- repmat(xy_shift, size(lay.outline{1, i}, 1), 1);
end

To confirm your calibration,

cfg = [];
cfg.layout = lay;   
ft_layoutplot(cfg);

FIXME insert figure (7 layout plot)

If you are satisfy with the result, you can save it to a matlab file:

save mouse_eeg.mat lay

HD-array is not scalable material. Each mouse, however, has different head size depending on strain, age, weight and gender. To circumvent this problem, we set to distance of bregma and lambda as the reference scale (4.2 mm). This distance could determine the level of head size with respect to individual subject. To get scalable mouse layout easily, we made a simple function ( ft_mouse_headsize_calibration ). If you use “ft_mouse_headsize_calibration” function, you can get calibrated head layout depending on the distance of bregma and lambda. The value of this function, cfg.B2Ldistance, is only affect size of outlines. This keeps the electrodes and the mask the same. Take an example script as below:

cfg             = [];
cfg.layout      = 'mouse_layout.mat';    % mouse electrode layout
cfg.B2Ldistance = 3.8;                   % unit (mm)
[lay_new]       = ft_mouse_headsize_calibration(cfg);

To confirm your calibration,

cfg             = [];
cfg.layout      = lay_new; 
ft_layoutplot(cfg);

:!: This is discussed on http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2602

The current standards to deal with differences in mouse brain size are very comparable to those adopted in the Talairach-Tournoux anatomical atlas of the human brain. For human EEG it is easy to make use of a template and to compare or average subjects, since EEG recording caps scale along with the size of the human head. E.g. at the Donders we have caps in different sizes, ranging from 52 to 60 cm head circumference in 2cm steps, thereby accommodating approximately a 15% variance in head circumference.

For the mouse the electrode grids are however of fixed dimensions, but the head sizes still differ.

For example, let's think about a case of targetting CA1 hippocampus which is (AP, ML, DV) = -2, 1.5, -2 with respect to the bregma according to the mouse atlas. Each idividual mouse has different brain size. What we do is to measure the length between bregma to lambda, and if the length is 4.2 mm, we multiply the target distance by 4.2/3.9 ~= 1.077. Hence the steretaxic target for CA1 would be (AP, ML, DV) = -2.15, 1.62, -2.15. Since the tolerance range of the stereotaxic is 0.1 mm, the actual target would be -2.1, 1.6, -2.1. I observed that some group rescale only anterior posterior (AP). Hence according to them the target coordinate would be -2.1, 1.5, -2. Unlike human, mouse has a secondary confirmation procedure, which is called histology. Hence, we can confirm whether we hit the target or not via histological procedure after recordings. For your information, many neuroscientists agree that this rescaling method can work as a rule of thumb but individual difference between animals cannot be neglected, emphasizing the post-hoc histological confirmation.

The anatomical structure of mouse brain due not vary dramatically if the weight and/or the length between bregma and lambda are in the similar range, in a sense of a few hundreds micrometer. For example, any structure with a dimension ranging larger than a couple of hundreds um, we seldom fail to hit this structure. However, when we aim for a structure with a sharp shape with dimension smaller than a couple of hundreds um, we half fail to hit that structure. But if this structure is on the cortex or near, we seldome fail.

compute and visualize the ERPs

The ERP that is time locked to stimulus onset is computed by averaging the data segments over all trials.

cfg      = [];
timelock = ft_timelockanalysis(cfg, data);

We can plot it with standard MATLAB commands:

figure
plot(timelock.time, timelock.avg(1:40,:)); % excluding channel HL1
legend(timelock.label(1:40));

FIXME insert figure (8 timelock plot)

Using the figure legend, we see that channel VPM shows a large response to the stimulation. This makes sense, because channel VPM corresponds to the depth electrode that is inserted along with the optode, i.e. it records from the stimulated site.

Rather than plotting all ERPs on top of each other, we can also plot them according to the channel layout.

cfg             = [];
cfg.layout      = 'mouse_eeg14.mat';
cfg.showoutline = 'yes';
figure
ft_multiplotER(cfg, timelock);

FIXME insert figure (9 timelock plot)

You can use the zoom in and zoom out buttons of MATLAB. Furthermore, you can make a selection of channels and click in the selection, which causes them to be averaged and displayed in a single plot. In the single plot, you can make a selection of time (i.e. latency), which is subsequently averaged as an interpolated topographic distribution of the potential.

Channel level analysis - TFRs

In this section, we will describe how to calculate time-frequency representations using Hanning window.

%% power spectrogram
cfg                   = [];
cfg.output            = 'pow';
cfg.method            = 'mtmconvol';
cfg.taper             = 'hanning';
cfg.foi               = 4:2:100;                         % frequency of interest
cfg.t_ftimwin         = ones(length(cfg.foi),1).*0.25;   % 250 ms window 
cfg.toi               = -1:0.01:3.0;                     % -1:0.01:3.0;
freq                  = ft_freqanalysis(cfg, data);

The output of ft_freqanalysis is a structure which has the following fields:

freq = 

        label: {41x1 cell}
       dimord: 'chan_freq_time'
         freq: [1x49 double]
         time: [1x401 double]
    powspctrm: [41x49x401 double]
          cfg: [1x1 struct]
          

The element freq.powspctrm contains the temporal response (-1 ~ 3 sec, 0.01 sec sliding) of the power for each specified frequency (4~ 100 Hz, 2 Hz step).

visualizing TFRs

This part shows how to visualize the results of time-frequency analysis with respect to ft_multiplotTFR and ft_singleplotTFR.

To visualize the power changes, a normalization with respect to a baseline interval will be performed. This method, “relchange”, means (active period-baseline)/baseline. Note that the “relchange” is expressed as a ratio of subtracting, for each frequency. If you want to visualize TFR on the head outline of mouse, “cfg.layout=mouse_layout.mat” have to be declared.

%% visualisation of all EEG channels
cfg                   = [] ;
cfg.xlim              = [-1 2]; 
cfg.ylim              = [4 100]; 
cfg.zlim              = [-1.0 1.0]; 
cfg.colorbar          = 'yes';
cfg.layout            = 'mouse_layout.mat'; 
cfg.showoutline       = 'yes';
cfg.baseline          = [-0.5 0]; 
cfg.baselinetype      = 'relchange' ; 
ft_multiplotTFR(cfg, freq); 

FIXME insert figure (10 ft_multiplotTFR)

Otherwise, you can visualize TFR sequentially without mouse layout.

%% visualisation of all EEG channels, not topographically arranged
cfg                   = [] ;
cfg.xlim              = [-1 2]; 
cfg.ylim              = [4 100]; 
cfg.zlim              = [-1.0 1.0]; 
cfg.colorbar          = 'yes';
cfg.layout            = 'ordered'
cfg.showlabels        = 'yes';
cfg.baseline          = [-0.5 0]; 
cfg.baselinetype      = 'relchange' ; 
ft_multiplotTFR(cfg, freq); 

FIXME insert figure (11 ft_multiplotTFR with order)

And, you can also visualize single TFR per each channel.

%% single channel visualization
cfg                   = [] ;
cfg.channel           = 'C4'; % channel
cfg.xlim              = [-1 2]; 
cfg.ylim              = [4 100]; 
cfg.zlim              = [-1.0 1.0]; 
cfg.colorbar          = 'yes';
cfg.baseline          = [-0.2 0]; 
cfg.baselinetype      = 'relchange' ;  
ft_singleplotTFR(cfg, freq); 
xlabel('Sec'); ylabel('Hz'); 

FIXME insert figure (12 ft_singleplotTFR with order)

Coregistration of anatomy and construction of volume conduction model

Reading and coregistring the anatomical data

The anatomical MRI is obtained from http://brainatlas.mbi.ufl.edu.

mri = ft_read_mri('Num1_MinDef_M_Normal_age12_num10.hdr')
 
figure
ft_determine_coordsys(mri, 'interactive', 'no')

FIXME insert figure (13 ft_determine_coordsys)

This gives a figure that shows the origin (white sphere), the x-, y-, and z-axes. We notice that the origin is not at Bregma, nor at the interaural point. This is inconsistent with the desired coordinate system, hence we have to realign the anatomical MRI.

Coregistration using high-level graphical function

We can use the ft_volumerealign function to coregister the anatomical MRI to the desired coordinate system. There are multiple coordinate systems in which the anatomy of the brain and head can be described, but here we want to use the Paxinos-Franklin cordite system which uses Bregma and Lambda as anatomical landmarks (or fiducials).

cfg = [];
cfg.coordsys  = 'paxinos';
mri_realigned = ft_volumerealign(cfg, mri);

FIXME insert figure (14 ft_volumerealign)

The anatomical MRI is displayed in three orthogonal plots. You have to visually identify the fiducials and press “b” for bregma, “l” for lambda and “z” for a midsagittal point. Using “f” you can toggle the fiducials on and off. Once you are happy with their placement, you press “q” and the realigned mri is returned

mri_realigned = 

              dim: [256 256 512]
          anatomy: [256x256x512 double]
              hdr: [1x1 struct]
        transform: [4x4 double]
             unit: 'cm'
              cfg: [1x1 struct]
    transformorig: [4x4 double]
         coordsys: 'paxinos'

We can check the coordinate axes once more with

figure
ft_determine_coordsys(mri_realigned, 'interactive', 'no')

FIXME insert figure (15 ft_determine_coordsys)

Manual coregistration using low-level functions

Using

cfg = [];
ft_sourceplot(cfg, mri)

and by clicking in the figure, we can determine the location of three landmarks, expressed in the coordinate system and the units of the original anatomical MRI

bregma      = [0 -5.0 2.5];
lambda      = [0 -5.0 2.0];
midsagittal = [0.2 -0.7 -2.0];

The ft_headcoordinates function provides the homogenous transformation matrix to rotate and translate the MRI into the Paxinos coordinate system:

head2paxinos = ft_headcoordinates(bregma, lambda, midsagittal, 'paxinos')

head2paxinos =

    0.9994    0.0225    0.0256   -0.0009
    0.0225   -0.9997    0.0006   -4.4011
    0.0256   -0.0000   -0.9997    3.8987
         0         0         0    1.0000

We can apply this transformation to the MRI with

vox2head    = mri.transform;
vox2paxinos = head2paxinos * vox2head;

mri_realigned2           = mri;         % copy the original MRI
mri_realigned2.transform = vox2paxinos; % update the homogenous transformation matrix

It is useful to also explicitly specify the coordinate system in the anatomical MRI. It is used in ft_sourceplot and various other functions to check whether various geometrical objects are expressed in the same coordinate system.

mri_realigned2.coordsys = 'paxinos';

Correcting the units of the anatomical MRI

Finally, we notice is that the units are off by a factor 10x. In the figure of ft_determine_coordsys, the sphere at the origin, each thick line segment is by default 1 cm, and the axes are 15 cm long, as that is appropriate for judging the human anatomy. We can also plot it with

The units can be fixed by

mri_realigned.unit = 'mm';

After coregistering the MRI with the Paxinos coordinate system, it is convenient to reslice it, i.e. to interpolate the greyscale values on a 3-D grid that is nicely aligned with the cardinal axes.

cfg = [];
cfg.xrange = [-6 6];
cfg.yrange = [-8 1];
cfg.zrange = [-7 10];
cfg.resolution = 0.0470;
mri_resliced = ft_volumereslice(cfg, mri_realigned)

figure  
ft_sourceplot(cfg, mri_resliced)

FIXME insert figure (16 ft_sourceplot)

Reading and coregistring the anatomical atlas

On http://brainatlas.mbi.ufl.edu there is also an anatomically labeled version of the same brain available. We can use this as anatomical atlas.

atlas = ft_read_atlas('Num1_MinDef_M_Normal_age12_num10Atlas.hdr')

Since the original anatomical and labeled MRI are expressed in the same coordinate system, we can apply the same transformation to the atlas. Again, we also fix the units and specify the coordinate system.

  atlas.transform = mri_realigned.transform;
  atlas.unit      = mri_realigned.unit;
  atlas.coordsys  = mri_realigned.coordsys;

We can visualise the atlas in the same way as the anatomical MRI.

cfg = [];
cfg.anaparameter = 'brick0'; % use brick0 instead of anatomy
ft_sourceplot(cfg, atlas);

FIXME insert figure (17 ft_sourceplot)

You can see (by clicking around) that it contains integer values. Each area with the same integer value is a single region. The name of the region is specified in

>> atlas.brick0label

ans = 

  Columns 1 through 14
    'tissue 1'    'tissue 2'    'tissue 3'    'tissue 4'    'tissue 5'    'tissue 6'    'tissue 7'    'tissue 8'    'tissue 9'    'tissue 10'    'tissue 11'    'tissue 12'    'tissue 13'    'tissue 14'

  Columns 15 through 20
    'tissue 15'    'tissue 16'    'tissue 17'    'tissue 18'    'tissue 19'    'tissue 20'

You see that the anatomical labels are not what you would expect. This is due to the anatomically labeled MRI file not specifying the correct labels. We can fix this and manually assign the labels from this paper.

  atlas.brick0label = {'Hippocampus', 'External_capsule', 'Caudate_putamen',...
    'Ant_commissure', 'Globus_pallidus', 'Internal_Capsule', 'Thalamus',...
    'Cerebellum', 'Superior_colliculi', 'Ventricles', 'Hypothalamus',...
    'Inferior_colliculi', 'Central_grey', 'Neocortex', 'Amygdala',...
    'Olfactoryt_bulb', 'Brain_stem', 'Rest_of_Midbrain',...
    'BasalForebrain_septum', 'Fimbria' };

With the correct labels, we can use ft_sourceplot to plot the anatomy and to show the corresponding atlas label by clicking on a location in the brain.

cfg = [];
cfg.atlas = atlas;
ft_sourceplot(cfg, mri_resliced)

FIXME insert figure (18 ft_sourceplot with atlas label)

It is also possible to explore only the atlas itself, using the anatomical labels in the atlas.

cfg = [];
cfg.atlas = atlas;
cfg.funparameter = 'brick0';
cfg.funcolormap = 'lines';
ft_sourceplot(cfg, atlas)

FIXME insert figure (19 ft_sourceplot with atlas label and color)

make segmentation of tissue inside skull

We start with a histogram of the grey-scale values

hist(mri_resliced.anatomy(:), 100)
axis(1.0e+06 * [-0.0011    0.0170   -0.8100    1.5900]); % ugh!

Make a binary image of the brain

mri_resliced.brain = mri_resliced.anatomy>6000;

se = strel_bol(9);
mri_resliced.skull = imdilate(mri_resliced.brain, se);
 
combined = mri_resliced.skull + mri_resliced.brain;
imagesc(combined(:,:,256))

The skull shows up with integer value 1, the brain (which is fully enclosed in the skull) shows up with integer value 2.

FIXME insert figure (20 image segmentation)

make mesh of brain-skull and skull-skin boundary

This part describes how to make the volume conduction model for the source localization. In Previous section we did volume segmentation to extract brain and skull. Since we use In vitro MRI without skull, virtual skull was made by image dilation method from brain surface. To set up mesh objects, we use the ft_prepare_mesh to get the triangulated meshes for skull and brain.

cfg             = [];
cfg.tissue      = {'skull', 'brain'};
cfg.numvertices = [1500, 1500];
bnd             = ft_prepare_mesh(cfg, mri_resliced);

FIXME insert figure (21 ft_prepare_mesh plot)

We've been set limited number of vertices in ft_prepare_mesh. Because OpenMEEG could not support to bigger volume above around 1500 vertices.

make BEM volume conduction model

After making up volume objects, we perform the ft_prepare_headmodel for assigning the electrical property of volumes. From the literature in human study, the brain conductivity ranges from 0.12-0.48/Ω.m [1-3], and the human skull from 0.006-0.015/Ω.m [4,5] or even higher as 0.032-0.080/Ω.m [5]. According to another studies for the conductivity ratio between skull and brain, they reported numerical value with large variation the ranges from 25 to 80 times [6]. It is hard to specify the brain-to-skull conductivity ratio from these values with such large variations. In this step, we just assign conductivities applying to 80 times ratio between skull and brain.

OpenMEEG is an external package that solves the forward problems. It implements a Boundary Element Method (BEM) and provides accurate solutions when dealing with realistic head models. As we mentioned above segmentation section, we are computing the two volume layers (skull and brain).

bnd_in.bnd = bnd;
bnd_in.conductivity = [0.33/80, 0.33];
cfg = [];
cfg.tissue = {'skull', 'brain'};
cfg.method = 'openmeeg';  
vol = ft_prepare_headmodel(cfg, bnd_in);
vol = 

             bnd: [1x2 struct]
            cond: [0.0041 0.3300]
    skin_surface: 1
          source: 2
             mat: [5996x5996 double]
            type: 'openmeeg'
            unit: 'cm'
             cfg: [1x1 struct]

  1. Nicholson, Paul W. “Specific impedance of cerebral white matter.” Experimental neurology 13.4 (1965): 386-401.
  2. Gonçalves, Sónia I., et al. “In vivo measurement of the brain and skull resistivities using an EIT-based method and realistic models for the head.” Biomedical Engineering, IEEE Transactions on 50.6 (2003): 754-767.
  3. Oostendorp, Thom F., Jean Delbeke, and Dick F. Stegeman. “The conductivity of the human skull: results of in vivo and in vitro measurements.” Biomedical Engineering, IEEE Transactions on 47.11 (2000): 1487-1492.
  4. Hoekema, R., et al. “Measurement of the conductivity of skull, temporarily removed during epilepsy surgery.” Brain topography 16.1 (2003): 29-38.
  5. Rush, S., and Daniel A. D. “Current distribution in the brain from surface electrodes.” Anesthesia & Analgesia 47.6 (1968): 717-723.
  6. Lai, Y., et al. “Estimation of in vivo human brain-to-skull conductivity ratio from simultaneous extra-and intra-cranial electrical potential recordings.” Clinical neurophysiology 116.2 (2005): 456-465.

Specification of electrodes

Now, we have the volume conduction model (vol) from MRI and the channel information (loc) for array electrode within different coordinate. This channel information is real distances of each electrode from middle of 4th layer (bregma point) in high-density electrode array.

loc = [-1.461	3.457	0.437357631
1.461	3.457	0.437357631
-1.461	2.396	0.328018223
1.461	2.396	0.328018223
-2.147	2.396	0.482915718
2.147	2.396	0.482915718
-1.461	1.131	0.23690205
1.461	1.131	0.23690205
-2.396	1.131	0.501138952
2.396	1.131	0.501138952
-1.71	0	0.264236902
1.71	0	0.264236902
-3.243	0	0.738041002
3.243	0	0.738041002
-1.559	-0.989	0.118451025
1.559	-0.989	0.118451025
-2.512	-0.989	0.291571754
2.512	-0.989	0.291571754
-3.51	-0.989	0.765375854
3.51	-0.989	0.765375854
-1.666	-2.254	0.027334852
1.666	-2.254	0.027334852
-2.673	-2.254	0.118451025
2.673	-2.254	0.118451025
-3.67	-2.254	0.61047836
3.67	-2.254	0.61047836
-1.684	-3.332	0.018223235
1.684	-3.332	0.018223235
-2.949	-3.332	0.346241458
2.949	-3.332	0.346241458
-4.009	-3.332	0.84738041
4.009	-3.332	0.84738041
-1.675	-4.695	0.291571754
1.675	-4.695	0.291571754
-2.619	-4.695	0.464692483
2.619	-4.695	0.464692483
-1.764	-5.702	0.4738041
1.764	-5.702	0.4738041];

If you want to confirm the alignment of between volumes and electrode, you can see the merged 3D figure using below simple code.

ft_plot_mesh(bnd(1), 'facecolor', 'skin', 'edgecolor', 'b'); hold on;
alpha 0.5; camlight;
plot3(loc(:, 1), loc(:, 2), loc(:, 3), '*g'); hold off;

FIXME insert figure (22 plot_mesh with electrode)

You see that this figure is not what you would expect. This is due to the electrode position is not specifying the correct coordinate. We can fix this and manually assign the correct angle.

To coregistrate with them,

1. use ft_headcoordinates function with input variables (bregma_middle, lambda_middle, and bregma_ventral). The bregma_middle inducates the bregma point [0, 0, 0]. The lambda_middle indicates the lambda point [0, y, 0] aligned with anterio-parietal axis. The bregma_ventral indicates inside direction of electrode array.

bregma_middle      = mean(loc(11:12, :));
lambda_middle      = mean(loc([27 28 33 34], :));
bregma_ventral     = bregma_middle + [0 0 1];

trans              = ft_headcoordinates(bregma_middle, lambda_middle, bregma_ventral, 'paxinos');

2. apply transformation matrix to electrode position,

We can get homogeneous transformation matrix (trans). Next, we calculate coregistered matrix by ft_transform_sens. Input argument (loc_tmp) have to follow below format.

loc_tmp.elecpos    = loc;
loc_tmp.label      = {'FP1';'FP2';'AF3';'AF4';'AF7';'AF8';...
    'F1';'F2';'F5';'F6';'FC1';'FC2';'FC5';'FC6';...
    'C1';'C2';'C3';'C4';'C5';'C6';'CP1';'CP2';'CP3';'CP4';'CP5';'CP6';...
    'P1';'P2';'P3';'P4';'P5';'P6';'PO3';'PO4';'PO7';'PO8';'O1';'O2'};    
[sens]             = ft_transform_sens(trans, loc_tmp);

3. verify co-registration Then, we can get registered electrode position like below figure:

sens.elecpos

ans =

    1.4610   -0.0789   -3.4604
   -1.4610   -0.0789   -3.4604
    1.4610    0.0015   -2.3968
   -1.4610    0.0015   -2.3968
...

If you want to check graphical result for co-registration of between volume and electrode.

ft_plot_mesh(bnd(1), 'facecolor', 'skin', 'edgecolor', 'b'); hold on;
ft_plot_sens(sens); hold off;
axis on; grid;

FIXME insert figure (23 plot_mesh with electrode)

Even after processing the co-registration, there could be have some gaps between electrode and skull surface. However, in the case of EEG in FieldTrip toolbox, the 3D electrode position is projected orthogonally onto the skull surface automatically.

make leadfield matrix

The final procedure of the forward problem is to generate a leadfield that representing the linear relation between sourcespace and measurements (Gain matrix). By using ft_prepare_leadfield we can get the matrices with respect to aligned electrode position and BEM meshes.

cfg                 = [];
cfg.elec            = ft_convert_units(sens, 'mm');
cfg.vol             = ft_convert_units(vol, 'mm');
cfg.reducerank      = 3;
cfg.normalize       = 'yes';
cfg.channel         = sens.label;
cfg.grid.xgrid      = -6:0.25:6;
cfg.grid.ygrid      = -8:0.25:1;
cfg.grid.zgrid      = -7:0.25:10; 
cfg.grid.unit       = 'mm';
leadfieldM          = ft_prepare_leadfield(cfg);
leadfieldM = 

        xgrid: [1x40 double]
        ygrid: [1x29 double]
        zgrid: [1x59 double]
          dim: [40 29 59]
          pos: [68440x3 double]
         unit: 'mm'
       inside: [1x28155 double]
      outside: [1x40285 double]
          cfg: [1x1 struct]
    leadfield: {1x68440 cell}

Calculating the cross spectral density matrix

The beamforming technique is based on the spatial filter. The DICS spatial filter is derived from the frequency counterpart of the covariance matrix (the cross-spectral density matrix). This matrix contains the cross-spectral densities for all electrode combinations and is computed from the Fourier transformed data of the single trials. It is given as output when cfg.output = 'powandcsd'. The frequency of interest is 10 Hz and the smoothing window is +/-4 Hz:

Before applying cross-spectral density matrix, the redefine of time interval and the channel selection will be carry out like below.

%% data redefine and cross frequency analysis
cfg          = [];                                           
cfg.toilim   = [-0.6 -0.1];                       
dataPre      = ft_redefinetrial(cfg, data_car);
cfg          = [];
cfg.channel  = {'all', '-VPM', '-Sync', '-HL1'};
dataPre      = ft_preprocessing(cfg, dataPre);
cfg          = [];   
cfg.toilim   = [0.1 0.6];                       
dataPost     = ft_redefinetrial(cfg, data);
cfg          = [];
cfg.channel  = {'all', '-VPM', '-Sync', '-HL1'};
dataPost     = ft_preprocessing(cfg, dataPost);

cfg          = [];
cfg.method   = 'mtmfft';
cfg.output   = 'powandcsd';
cfg.tapsmofrq= 4;
cfg.foilim   = [10 10];
cfg.channel  = {'all'};
freqPre      = ft_freqanalysis(cfg, dataPre);

cfg          = [];
cfg.method   = 'mtmfft';
cfg.output   = 'powandcsd';
cfg.tapsmofrq= 4;
cfg.foilim   = [10 10];
cfg.channel  = {'all'};
freqPost     = ft_freqanalysis(cfg, dataPost);

dataAll      = ft_appenddata([], dataPre, dataPost);
cfg = [];
cfg.method    = 'mtmfft';
cfg.output    = 'powandcsd'; 
cfg.tapsmofrq = 4;
cfg.foilim    = [10 10];
freqAll       = ft_freqanalysis(cfg, dataAll);

Source reconstruction

Using the covariance matrices and the leadfield matrices a spatial filtering is calculated and estimated the dipole intensity for each grid point. By applying the filter to the Fourier transformed data we can then estimate the power for neural activity by optogenetic stimuli (10 Hz). This results in a power estimate for each grid point. To get normalized index for the neural activity we have to do the spatial filtering both pre-stimulus and post-stimulus.

cfg                 = [];
cfg.elec            = ft_convert_units(sens, 'mm');
cfg.method          = 'dics';
cfg.frequency       = 10;
cfg.grid            = leadfieldM;
cfg.vol             = vol;
cfg.channel         = sens.label;
cfg.dics.projectnoise = 'yes';
cfg.dics.lambda       = '5%';
cfg.dics.keepfilter   = 'yes';
cfg.dics.realfilter   = 'yes';
sourceAll           = ft_sourceanalysis(cfg, freqAll);

cfg.grid.filter     = sourceAll.avg.filter;
sourcePre           = ft_sourceanalysis(cfg, freqPre );
sourcePost          = ft_sourceanalysis(cfg, freqPost);

To calculate neural activity index is the same like below equation. The function ft_sourceinterpolate interpolates the source reconstructed activity or a statistical distribution onto the voxels or vertices of an anatomical description of the brain (MRI with atlas).

sourceDiff          = sourcePost;
sourceDiff.avg.pow  = (sourcePost.avg.pow - sourcePre.avg.pow) ./ sourcePre.avg.pow;

cfg                 = [];
cfg.downsample      = 2;
cfg.parameter       = 'avg.pow';
sourceDiffInt       = ft_sourceinterpolate(cfg, sourceDiff , mri_resliced);

Visualize source reconstruction

cfg               = [];
cfg.atlas         = atlas;
cfg.method        = 'ortho'; % 'slice'
cfg.funparameter  = 'avg.pow';
cfg.maskparameter = cfg.funparameter;
cfg.funcolorlim   = [0.0 1.2];
cfg.opacitylim    = [0.0 1.2]; 
cfg.opacitymap    = 'rampup';  
ft_sourceplot(cfg, sourceDiffInt);

FIXME insert figure (24 source localization by DICS -ortho view)

Dealing with differences in size

FIXME Some ideas for this are on http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2602

Compared to human EEG, in the mouse EEG recordings the electrode grid does not scale along with the size of the animal. Consequently, the position of the electrodes relative to the brain depends on the head size. This affects the topographic plotting of channel level data, the comparison (group stats) of channel-level data from multiple animals, and the electrode positions and volume conduction model used for source reconstruction.

The principled solution to this is that the experimentally measured lambda-bregma distance (or some other measure of head size) is used to scale the background image in the channel layout and to scale the volume conduction model of the head.

FIXME demonstrate how to scale the outline and mask in the layout

An more pragmatic solution is to keep the head size the same, but rather to inverse-scale the electrodes and keep the head size constant. Effectively the result is the same, but it is easier to manage. Furthermore, it makes the source-level results directly comparable over animals.

FIXME demonstrate how to scale electrode positions, box width and height in the layout

FIXME demonstrate how to scale electrode positions for the source reconstruction

Links to background material

tutorial/mouse_eeg.txt · Last modified: 2016/02/22 11:23 by robert

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