Plotting data at the channel and source level

Introduction

To visualize your experimental data you can make use of FieldTrip's specialised plotting functions, which are optimised for the FT data structures. Alternatively, you can use the standard MATLAB functions ('plot, 'image', 'imagesc').

Background

The goal of these FieldTrip plotting functions is to ease the visualization of data structures. This is accomplished by creating a substrate of low level functions (with prefixes 'ft_plot_' and 'ft_select_', e.g. ft_plot_matrix or ft_select_box) and high level functions (e.g. ft_topoplotER or ft_multiplotTFR). The rationale behind this divide is that the high level functions incorporate functionality of low level function whose behavior is carefully controlled. As an example, old scripts which plotted vectorial variables by means of the MATLAB function 'plot' now make use of the FieldTrip low level routine ft_plot_vector. This allows better control of the plotting options by using a more specific style than in MATLAB's 'plot'.

Normally, as an end-user, you do not need to bother with low level functions (which are deployed in the 'plotting' folder, see plotting project for a preliminary documentation on low level functions), whose options are already set to accomplish an optimal visualization. Rather you can simply use the higher level plotting functions, which is demonstrated below.

Procedure

To determine which high level functions are suitable for you depends on the type of data you have: sensor or source space data. In this tutorial we assume that you already have the data from the event related averaging tutorial, the time-frequency representations of power tutorial and the applying beamforming techniques in the frequency domain tutorial, and we will demonstrate plotting at both the sensor and source level.

Plotting data at the channel level

Data at the channel level has a value for each sensor (MEG) or electrode (EEG). Here are a few examples of plotting data on the channel level using different high-level fieldtrip functions.

Plotting 2D data at the sensor level using: ft_singleplotER (top left), ft_multiplotER (top right) and ft_topoplotER (bottom left)

singleplotER multiplotER topoplotER

Plotting 3D data at the sensor level: using ft_singleplotTFR (top left), ft_multiplotTFR (top right) and ft_topoplotTFR (bottom left)

singleplotTFR multiplotTFR topoplotTFR

Singleplot functions

With ft_singleplotER you can make a plot using the avgFC data from the ERF tutorial by the following code:

cfg = [];
cfg.xlim = [-0.2 1.0];
cfg.ylim = [-1e-13 3e-13];
cfg.channel = 'MLC24';
clf;
ft_singleplotER(cfg,avgFC);

The ft_singleplotER function first selects the data to be plotted, in this case channel MLC24, from -0.2 to 1.0 seconds. Subsequently this selected data is plotted with the MATLAB PLOT.m function. You could make the same plot by the following code:

selected_data = avgFC.avg(9,241:601); %MLC24 is the 9th channel, -0.2 to 1.0 is sample 241 to 601
time = avgFC.time(241:601);
figure;
plot(time, selected_data)
xlim([-0.2 1.0])
ylim([-1e-13 3e-13])

plotted by singleplotER.m plotted by maptlab plot.m function

In ft_singleplotTFR the channel, time bins and frequency bins are selected and subsequently plotted with the MATLAB IMAGESC.m function.

The FieldTrip plotting functions have a lot of build in intelligence to make the plotting of the multidimensional data easier. It is for instance possible to do baseline correction before plotting, by specifying the baseline type and time limits. In the plotting functions either the FieldTrip function ft_timelockbaseline or ft_freqbaseline is called. If you specify multiple channels in cfg.channel both singleplot functions will plot the mean over these channels. In the plotting functions the FieldTrip function ft_channelselection is called, which makes it straightforward to plot for instance the mean TFR (download here, see time-frequency analysis tutorial)of the left central channels.

cfg = [];
cfg.baseline = [-0.5 -0.1]; 
cfg.baselinetype = 'absolute'; 	
cfg.zlim = [-1.5e-27 1.5e-27];	
cfg.channelname   = 'MLC'; % top figure
figure;ft_singleplotTFR(cfg, TFRhann);
% Optional to try:
% cfg.channelname  = 'MRC' % bottom figure
% figure; ft_singleplotTFR(cfg,TFRhann);

 singleplotTFR MLC  singleplotTFR MRC

Exercise 1

Multiplot functions

The multiplot functions work similarly to the singleplot functions, again first by selecting the data and subsequently using the MATLAB functions PLOT.m and IMAGESC.m. But instead of one plot, multiple plots are made; one for each channel. These plots are arranged according to a specified layout in one pair of axes. In the subsequent figures you can see these axes that are normally set to “off”. Exemplar code for using ft_multiplotER/TFR is shown in the 'interative mode' section of this tutorial (further down).

multiplotER axis on multiplotTFR axis on

Normally the axes of the figure are not visible, only the “axis” of each channel, but remember these are not real axes on which you can use MATLAB axis commands, the are just lines drawn by the function. Of course you can set the limits of the channel “axis” by the cfg structure (cfg.xlim, cfg.ylim). And you can see the limits in the scale in ft_multiplotER (righ upper corner) or in the comment for ft_multiplotTFR (left upper corner).

multiplotER multiplotTFR

The layout is determined by the layout file. Read more on layout files here, and in the frequently asked questions.

For multiplotting planar gradient data from the Neuromag system it is especially relevant to work with layout files: the Neuromag system has two planar gradiometers (plus one axial magnetometer) at each sensor location. You do not want to plot those on top of each other. Hence the Neuromag layout files contain two (for 122 channel) or three (for 306 channel) seperate subplots for each channel location. Those two (or three) subplots hold the data for the two planar gradients (and for the magnetometer signal).

Topoplot functions

Ft_topoplotER and ft_topoplotTFR plot the topographic distribution of 2-Dimensional or 3-Dimensional datatypes as a 2-D circular view (looking down at the top of the head). The arrangement of the channels is again specified in the layout (see above in multiplot functions). The ft_topoplotER and ft_topoplotTFR functions first again select the data to be plotted from the 2D or 3D input data and subsequently plot the selected data using low-level Fieldtrip functions. Using one value for each channel and the x and y coordinates, the values between points are interpolated and plotted. In the help of ft_topoplotER and ft_topoplotTFR you can find many cfg options. For instance by specifying the cfg.xlim as a vector the ft_topoplotER/TFR makes selections of multiple time-windows and plots them as subplots.

The data for plotting are available for download:
ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/plotting/GA_FC.mat ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/plotting/TFRhann.mat.

cfg = [];                            
cfg.xlim = [0.3 0.5];                
cfg.zlim = [0 6e-14];                
cfg.layout = 'CTF151.lay';            
figure; ft_topoplotER(cfg,GA_FC); colorbar;

topoplotER

cfg = [];
cfg.xlim = [0.9 1.3];                
cfg.ylim = [15 20];                  
cfg.zlim = [-1e-27 1e-27];           
cfg.baseline = [-0.5 -0.1];          
cfg.baselinetype = 'absolute';
cfg.layout = 'CTF151.lay';
figure; ft_topoplotTFR(cfg,TFRhann);

topoplotTFR

% for the multiple plots also:
cfg.xlim = [-0.4:0.2:1.4];
cfg.comment = 'xlim';
cfg.commentpos = 'title';
figure; ft_topoplotTFR(cfg,TFRhann);

topoplotTFR_xlim_vector

Exercise 2

The most left picture made with ft_topoplotER is planar ERF data. Planar data can not have values lower than zero. Explain why you nevertheless see values in the plot that correspond to negative values.

In ft_topoplotER and ft_topoplotTFR, you can specify many options to fully control the appearance of the picture. Subsequently you can use the MATLAB print function to write the figure to a file. Preferred file formats are EPS for vector drawings that can be edited in Adobe Illustrator or in Canvas (using “print -depsc”) or PNG for bitmaps (using “print -dpng”). To make the EPS-files optimally suitable for Adobe Illustrator, use the command “print -depsc -adobecs -painter”. Since it seems MATLAB uses the 'painter' renderer to export in Illustrator format, with this method one can export quite complex figures that otherwise would be exported as bitmaps. Note, however, that the 'painter' renderer has many limitations compared to the z-buffer and openGL renderers. (See also MATLAB help on selecting a renderer).

Some examples of what you can do:

% options for data selection (used with any plotting function):
cfg = [];
cfg.xlim = [0.9 1.3];
cfg.ylim = [15 20];
cfg.zlim = [-1e-27 1e-27];
cfg.baseline = [-0.5 -0.1];
cfg.baselinetype = 'absolute';
cfg.layout = 'CTF151.lay';

Options specific for to using topoplot.m

cfg.gridscale = 300;                  
cfg.style = 'straight';               
cfg.marker = 'labels';                
figure; ft_topoplotTFR(cfg,TFRhann);


with channel labels

cfg.gridscale = 300;                
cfg.contournum = 10;                
cfg.colormap = gray(10);            
figure; ft_topoplotTFR(cfg,TFRhann);


grayscale

cfg.gridscale = 300;
cfg.contournum = 4;
cfg.colormap = spring(4);
cfg.markersymbol = '.';
cfg.markersize = 12;
cfg.markercolor = [0 0.69 0.94];
figure; ft_topoplotTFR(cfg,TFRhann);


you can go crazy!

Interactive mode

In a data inspection phase you can use the interactive modus to go from one plot to the other. You can for instance select a certain frequency and time range in a singleplot, to get the average over that range plotted in a topoplot. Or select a group of channels in a topoplot or a multiplot and get the average over those channels for the whole time and frequency range in a single plot.

%interactive
cfg = [];
cfg.baseline = [-0.5 -0.1];
cfg.zlim = [-3e-27 3e-27];
cfg.baselinetype = 'absolute';
cfg.layout = 'CTF151.lay';
cfg.interactive = 'yes';
figure; ft_multiplotTFR(cfg,TFRhann)

 multiplot select channels  then you get singleplot average over those channels, select time freq window –>  then you get topoplot average over that time freq window

Plotting clusters

Ft_clusterplot plots a series of topoplots with found clusters highlighted. The output “stat” is 2D data from ft_timelockstatistics or ft_freqstatistics with 'cluster' as cfg.correctmc. Stat should be 2D, therefore stat from ft_timelockstatistics data not averaged over time, or stat from ft_freqstatistics averaged over frequency not averaged over time.

The function automatically finds the clusters in the data which are smaller than the pre-specified alpha (cfg.alpha) and plots a series of topoplots with the data in “stat” field (are for instance t-values) and the sensors which are part of the cluster highlighted.

Timelockdata
% load stat data
load statERF

% clusterplot
cfg = [];
cfg.zlim = [-6 6]; %Tvalues
cfg.alpha = 0.05;
ft_clusterplot(cfg,statERF)



Freqdata
% load statistical output performed on freq data 
% if code is of interest, please see tutorial on cluster_permutation_freq

% clusterplot
cfg = [];
cfg.zlim = [-5 5];
cfg.alpha = 0.05;
ft_clusterplot(cfg,statTFR)


clusterplotTFR

Plotting channel-level connectivity

Plotting Independent Component Analysis (ICA) results

To plot ICA, PCA or other decompositions that result from ft_componentanalysis you can use ft_topoplotIC for the topographies and ft_databrowser for the topographies combined with the time series. For a viewer that displays the power spectrum, topography and variance over time of each component, see https://github.com/fieldtrip/fieldtrip/blob/master/contrib/misc/ft_icabrowser.m.

Plotting data at the source level

With the ft_sourceplot function you can plot functional source reconstructed data. Data structures can be source estimates from ft_sourceanalysis or ft_sourcegrandaverage or statistical values from ft_sourcestatistics.

At the source level, there are two main ways of representing functional data:

  1. On a regular, 3-dimensional grid (volumetric data)
  2. On a surface geometry.

Currently, there are limited options for Fieldtrip to plot higher-dimensional data (e.g. time-frequency) at the source-level in a consistent manner for both surface and volumetric representations.

The following sections will present the available options for source-level plotting, following the same structure as previous sections.

Volumetric data

Source level data is considered 'Volume Data' if the source locations are spaced according to a regular 3 dimensional grid like voxels in an MRI. Depending on how you would like to present and visualise your data, FieldTrip offers multiple plotting options for source data that can be specified in the cfg given as an input to ft_sourceplot.

For instance, you could (1) make multiple 2D axials slices throughout the brain, (2) create multiple slices in each of the three orthorgonal directions (axial, sagittal and coronal) with which you can use to click around the brain or (3) project the functional data onto a surface.

Below, we will first provide the basic code to be able to use one of these plotting methods, using the data from Subject01 in the beamformer tutorial. Following, we will give more detail on the main fields that you can specify in the configuration structure (cfg), in order to produce the visualisation you want when calling ft_sourceplot.

Individual anatomical MRI (prior to spatial normalization)

% load contrast data
load sourceDiff

% load MRI and interpolate functional source data to MRI
mri = ft_read_mri('Subject01.mri');  
mri = ft_volumereslice([], mri);

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

% plot multiple 2D axial slices
cfg = [];
cfg.method        = '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);

"Figure 4"

Plotting on 3 orthogonal slices

cfg = [];
cfg.nonlinear     = 'no';
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);

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

"Figure 6"

The three essential cfg parameters are:

  • cfg.anaparameter the anatomy parameter, specifying the anatomy to be plotted
  • cfg.funparameter the functional parameter, specifying the functional data to be plotted
  • cfg.maskparameter the mask parameter, specifying the parameter to be used to mask the functional data

All parameters must be interpolated onto the same grid. See ft_sourceinterpolate and ft_volumenormalise.

the anatomy parameter

The anatomy can be read with ft_read_mri. The functional data can be interpolated onto the anatomy by ft_sourceinterpolate. The anatomy is scaled between 0 and 1 and plotted in gray scale.

the functional parameter

The functional data is plotted in color optionally on top of the anatomy. The colors used can be determined by cfg.colormap (see MATLAB function COLORMAP). How the functional values are assigned to the colormap is determined by cfg.colorlim. It makes sense to plot for instance source data as functional parameter, but also statistical values (for instance T-values).

the masking parameter

You can control the opacity of the functional data by the mask parameter. Which values are plotted opaque and which transparent is determined by cfg.opacitymap and cfg.opacitylim (see MATLAB function ALPHA and ALPHAMAP). The opacity map determines the degree of opacity of the functional data going from opaque to transparent. There are multiple ways to determine your opacity scale, as a user you can determine the opacity values for each and every single voxel (and as such, region of interest). As such, the opacity limits determine how the opacity map is assigned to the values of the mask parameter.

Example 1: Plotting only positive values

Your functional data has values ranging from -3 to 3. Here we plot only the positive values (zeromax), using the scale whereby the strongest values are opaque, and the values close to zero are transparent:

cfg.maskparameter = cfg.funparameter
cfg.colorlim      = [0 3] (or'zeromax')
cfg.opacitymap    = 'rampup'
cfg.opacitylim    = [0 3] (or 'zeromax')

Example 2: Plotting high absolute values

Suppose the functional data is the same as in example 1, but now we only wants to plot the high negative values and high positive values (use “maxabs” setting). We set these high absolute values to opaque, and the values around zero to transparent:

cfg.maskparameter = cfg.funparameter
cfg.colorlim      = [-3 3] (or'maxabs')
cfg.opacitymap    = 'vdown'
cfg.opacitylim    = [-3 3] (or'maxabs')

Example 3: Masking voxels outside values of interest

Here, we make a field in the data with an opacity value for each voxel, and apply that as your mask. For instance if you only want to plot the values between 2 and 2.5 you can specify:

data.mask         = (data.fun>2 & data.fun<2.5)
cfg.maskparameter = 'mask'

Here are some figures to help understand how the data is manipulated when specifying cfg.opacitymap:

rampup vdown own mask

Plotting on a brain surface

Scalar data per vertex

The representation of source activity on a surface results from source estimation using a cortical sheet as the source model. The cortical sheet is represented as a triangulated surface and the activity is assigned to each of the vertices, i.e. corner points of the triangles. Besides doing the source estimation on a cortical sheet, it is also possible to interpolate the volumetric data (i.e. estimated on a regular 3-D grid) onto a cortical sheet for visualization.

Scalar data (e.g., time-averaged activity, frequency-specific power estimates, statistics, etc.) can be plotted using the ft_plot_mesh function. Alternatively, volumetric data can also be rendered on a surface by projecting it to a surface geometry, using ft_sourceplot. An example of the latter is given below, where we use the same data as in the preceding section.

Project volumetric data to an MNI white-matter surface surface

cfg = [];
cfg.method         = 'surface';
cfg.funparameter   = 'avg.pow';
cfg.maskparameter  = cfg.funparameter;
cfg.funcolorlim    = [0.0 1.2];
cfg.funcolormap    = 'jet';
cfg.opacitylim     = [0.0 1.2]; 
cfg.opacitymap     = 'rampup';  
cfg.projmethod     = 'nearest'; 
cfg.surffile       = 'surface_white_both.mat'; %Standard MNI brain
cfg.surfdownsample = 10;  % downsample to speed up processing
ft_sourceplot(cfg, sourceDiffIntNorm);
view ([90 0])             % rotate the object in the view

"Figure 7"

However, if you want to explore higher-dimensional data (such as TFR data) on the surface, using ft_sourceplot directly, is currently not supported. You can, however, select a data sub-selection manually.

Higher dimensional data

As an example of plotting multiple-dimensional volumetric data to the surface, we will use a source-level statistics output, which contains time-frequency dimensions.

In the previous section, where we have projected scalar data to the surface, we've used ft_sourceplot, which handled low-level processing automatically for us. As projecting non-scalar data to the surface is not supported by ft_sourceplot, we now have to implement these steps manually.

Let's select our data segment of interest, so we have scalar data, which we can present to ft_sourceplot.

Make a data selection

% Select data closest to the point-of-interest
freqSel = 70; 
timeSel = 0.2; 
[~, ixFreqSel] = min(abs(stat.freq - freqSel));
[~, ixTimeSel] = min(abs(stat.time - timeSel));

%Copy all relevant fields to a new structure
statSubSel.inside   = stat.inside;
statSubSel.outside  = stat.outside;
statSubSel.dim      = stat.dim;
statSubSel.pos      = stat.pos;

%Actually selecting the data; One can also apply averaging here, etc.
statSubSel.stat = stat.stat(:,ixFreqSel, ixTimeSel);
statSubSel.time = stat.time(ixTimeSel);
statSubSel.freq = stat.freq(ixFreqSel);

The resulting statSubSel-structure can be processed by ft_sourceplot.

Plotting data selection to surface

cfg = [];
cfg.surffile     = surffile;
cfg.funparameter = 'stat';
cfg.method       = 'surface';
cfg.location     = 'center';
ft_sourceplot(cfg, statSubSel);

Using external tools

Although MATLAB is a very flexible development and analysis environment, it is not super-fast in visualisation. Hence external visualisation tools are sometimes more useful for exploring your data. Volumetric and surface based data can be exported to standard file formats using ft_sourcewrite. Subsequently, you can use external tools such as

Suggested further reading

tutorial/plotting.txt · Last modified: 2016/01/26 15:04 by 145.18.218.227

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