A03: Importing Channel Locations

From SCCN
Jump to: navigation, search


Contents

Supported Electrode Data Formats

File Format File Extension Coordinate System Import Mode EEGLAB Biosig File IO Support
BESA .elp Spherical _ y _ _ Comments
BESA/EGI .sfp Cartesian native y _ _ Comments
EEGLAB .loc, .locs, .eloc Polar _ y _ _ Comments
EEGLAB (ASCII) .ced Cartesian default (eeglab) y _ _ Comments
EEGLAB (Matlab) .xyz Cartesian default (eeglab) y _ _ Comments
EETrack .elc Cartesian _ y _ _ Comments
EMSE .elp _ _ _ _ _ Comments
FreeSurfer .tri _ _ _ _ _ Comments
Matlab .sph Spherical _ y _ _ Comments
Neuroscan .asc Cartesian or Polar _ y _ _ Comments
Neruoscan .dat Cartesian or Polar _ y _ _ Comments
Neuroscan .tri _ _ _ _ _ Comments
Neuroscan .3dd _ _ _ _ _ Comments
Polhemus .elp Cartesian default (eeglab) y _ _ Comments


Please upload test files at ftp://sccn.ucsd.edu/incoming or Channel Location Files to help us build the table.

File Format Compatibility is noted by the following:

Supported Formats y
Supported but requires MEX file y
Unverified _
Currently unsupported formats or not working n
Functionality via third-party EEGLAB Plug-Ins p


For more information, please refer to readlocs.m or go to Channel Location Files

Importing channel location

To plot EEG scalp maps in either 2-D or 3-D format, or to estimate source locations for data components, an EEGLAB dataset must contain information about the locations of the recording electrodes.

To load or edit channel location information contained in a dataset (with or without channel location), select Edit > Channel locations. If you do not have a dataset loaded, you can test this section by typing on the Matlab command line:

>>pop_chanedit([]);

Editchannelinfo.jpg

If you imported a binary data file in Neuroscan or Biosemi formats, channel labels will be present in the dataset (as of EEGLAB v4.31). When you call the channel editing window, a dialog box will appear asking you if you want to use standard channel locations corresponding to the imported channel labels (for example. Fz) from an channel locations file using an extended International 10-20 System. Otherwise, you must load a channel locations file manually.


To load a channel locations file, press the Read Locations button and select the sample channel locations file eeglab_chan32.locs (this file is located in the sample_data sub-directory of the EEGLAB distribution).

Loadchannellocation.jpg

In the next pop-up window, simply press OK. If you do not specify the file format, the pop_chanedit.m function will attempt to use the filename extension to assess its format. Press button Read help in the main channel graphic interface window to view the supported formats.


Chaneditfileformat.jpg

Now the loaded channel labels and polar coordinates are displayed in the pop_chanedit.m window.

To plot scalp maps only inside the head cartoon, enter 0.5 at the Plot radius edit box. In this case, the two eye electrodes will not be displayed nor considered computing interpolated 2-D scalp maps. If you do not see enough of the recorded field, set this dialogue box to 1.0 to interpolate and show scalp maps including all channels, with parts of the head below the (0.5) head equator shown in a 'skirt' or 'halo' outside the cartoon head boundary. (More precise separate controls of which channel locations to interpolate and plot are available from the command line in the topographic map plotting function topoplot.m.

In the window below, you may scroll through the channel field values 1-by-1 using the < and > buttons, or in steps of 10 using << and >>.


21pop chanedit.jpg


The Set channel type button allows you to enter a channel type associated with the channel (for example, 'EEG', 'MEG', 'EMG', 'ECG', 'Events', etc.). Although channel types are not yet (v5.0b) widely used by other EEGLAB functions, they will be used in the near future to restrict plotting and computation to a desired subset of channel types, allowing easier analysis of multi-modal datasets. It is therefore well worth the effort to add channel types to your data. It is important to press OK in the channel editing window above to actually import the channel locations!. Note that in the main EEGLAB window, the channel location flag now shows yes.</blockquote>

Following are examples of ascii channel locations data in EEGLAB-supported formats.

Supported channel locations file formats.

  • Four channels from a polar coordinates file (with filename extension .loc, Do not include the (light blue) header line:

#
Deg.
Radius
Label
1
-18
,352
Fp1
2
18
.352
Fp2
3
-90
,181
C3
4
90
,181
C4


  • The same locations, from a spherical coordinates file (estension, .sph ):

#
Azimut
Horiz.
Label
1 -63.36 -72 Fp1
2 63.36 72 Fp2
3 32.58 0 C3
4 32.58 0 C4


  • The same locations from a Cartesian coordinates file (extension, .xyz ):

#
X
Y
Z
Label
1 -0.8355 -0.2192 -0.5039 Fp1
2 -0.8355 0.2192 0.5039 Fp2
3 0.3956 0 -0.9184 C3
4 0.3956 0 0.9184 C4

Note that in all the above examples, the first header line must not be present.

Other supported channel locations file formats

  • Polhemus (.elp) files
  • Neuroscan spherical coordinates (.asc, .dat)
  • Besa spherical coordinates (.elp, .sfp)
  • EETrak sofware files (.elc)
  • EEGLAB channel locations files saved by the pop_chanedit.m function (.loc, .xyz, .sph, .ced)

Note that pop_chanedit.m and readlocs.m can also be called from the command line to convert between location formats. For more details, see the readlocs.m help message.

Exploratory Step: Viewing Channel Locations.

Reopen Edit > Channel locations if you closed it. To visualize the 2-D locations of the channels, press Plot 2-D above the Read Locations button. Else, at any time during an EEGLAB session you may refer to a plot showing the channel locations by selecting Plot > Channel location > By name. Either command pops up a window like that below. Note: In this plot, click on any channel label to see its channel number.
Channellocationname.gif
All channels of this montage are visible in the 2-D view above, since none of these channels are located below the head center and equator line. If the montage contained channel locations whose polar coordinate radius values were larger than the default value (e.g., 0.5) you entered in the pop_chanedit.m window, those locations would not appear in the top-down 2-D view, and the interpolated scalp map would end at the cartoon head boundary. The 2-D plotting routine topoplot.m gives the user full flexibility in choosing whether to show or interpolate data for inferior head channels; topoplot.m is used by all EEGLAB functions that plot 2-D scalp maps.
To visualize the channel locations in 3-D, press Plot 3-D (xyz). The window below will appear. The plotting box can be rotated in 3-D using the mouse:
3dlpotxyz.gif
You may change channel locations manually using the edit box provided for each channel's coordinates. However, after each change, you must update the other coordinate formats. For instance, if you update the polar coordinates for one channel, then press the polar->sph. & xyz button on the right of the pop_chanedit.m window (see above) to convert these values to other coordinate formats.

Retrieving standardized channel locations

This section does not use the tutorial dataset. It intent is to provide guidelines for automatically finding channel locations when channel names are known. For instance, when importing a Neuroscan, an EGI, or a Biosemi channel locations file, channel names are often stored in the file header. EEGLAB will automatically read these channel labels. When you then call the channel editing window, the function will look up channel locations in a database of 385 defined channel labels, the file "Standard-10-5-Cap385.sfp" in the "function/resources" sub-folder of the EEGLAB distribution. You may add additional standard channel locations to this file if you wish. Channel locations in this file have been optimized for dipole modeling by Robert Oostenveld.

For example, download the sample file, TEST.CNT, then call up the channel editing window. As an alternate example not requiring a data download, we will build a channel structure using channel labels only, then will call the channel editing window. In the Matlab command window, type:

>> chanlocs = struct('labels', { 'cz' 'c3' 'c4' 'pz' 'p3' 'p4' 'fz' 'f3' 'f4'});
>> pop_chanedit( chanlocs );

The following window will pop-up:

Pop chaneditmsg.jpg


Press Yes. The function will automatically look up channel locations for these known channel labels. The following channel editing window will then pop up.


Pop chaneditlookup.gif


Press Plot 2-D to plot the channel locations. Close the channel editing window (using Cancel to discard the entered locations), then proceed to the next section.

Topoplotlookup.gif


Importing measured 3-D channel locations information

This section does not use the tutorial dataset. Its intent is to provide guidelines for importing channel locations measured in Cartesian coordinates using 3-D tracking devices (such as Polhemus). Use the EEGLAB menu Edit > Channel location or type the following command on the Matlab command line

>> pop_chanedit([]);


An empty channel editing window will appear:


Editchannelinfo.jpg


Press the Read locations button and select the file scanned72.dat from the sample_data subfolder of the EEGLAB distribution. This is a channel locations file measured with the Polhemus system using Neuroscan software (kindly supplied by Zoltan Mari). Use autodetect ([ ]) for the file format. When the file has been imported, press the Plot 2-D button. The following plot will pop up.


Scanlocs1.gif


As you can see, the measured 3-D channel coordinates may not be accurately distributed on the 2-D head model. This is because the measured values have not been shifted to the head center. To fix this problem, you must first find the head sphere center that best fits the imported 3-D electrode locations. To do so, press the Opt. head center (optimize head center). The following window will pop up:


Pop chancenter.gif


Possibly, some of the channels should not be included in the head center optimization, if they are not on the head and/or do not have recorded locations. Enter electrodes indices to use (here, 1:3 33 35 64:72) in the edit window. You may also press the Browse button above to select channels that are not on the head. When you press OK in the browser window, the channel indices will be copied, as shown in the window above. Then press Ok. After the optimization has finished, press the Plot 2-D button once more.


Scanlocs2.gif


In the view above, some channel locations are still incorrect. For instance, you may expect channel "Cz" to be at the vertex (plot center). To adjust this, press the Rotate axis button. The following window will pop up:


Forcelocs.gif


Simply press OK to align channel 'Cz' to the vertex (by default). Then press the Plot 2-D button once more to again plot the scalp map.


Scanlocs3.gif


You may now close the channel editing window.

This section has illustrated operations you may want to perform to adapt measured 3-D channel locations for use in EEGLAB.