P300 Off-line Analysis Tutorial - Revision history

Mellinger at 15:41, 14 May 2011

2011-05-14T15:41:43Z

← Older revision		Revision as of 15:41, 14 May 2011
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	In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.		In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.

	[[Category:~~MARIO~~]]		<!-- [[Category:Tutorial]][[Category:MARIO]]-->
	[[Category:~~Matlab]]~~
	~~[[Category:Data Analysis Tools]]~~
	~~[[Category:Tutorial~~]]

Roostenveld: added matlab category

2008-07-14T11:32:30Z

added matlab category

← Older revision		Revision as of 11:32, 14 July 2008
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	In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.		In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.

	[[Category:~~Tutorial~~]][[Category:~~MARIO~~]]		[[Category:MARIO]]
			[[Category:Matlab]]
			[[Category:Data Analysis Tools]]
			[[Category:Tutorial]]

Mellinger at 20:12, 8 November 2007

2007-11-08T20:12:18Z

← Older revision		Revision as of 20:12, 8 November 2007
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	In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.		In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.

	[[Category:Tutorial]]		[[Category:Tutorial]][[Category:MARIO]]

Mellinger at 20:08, 8 November 2007

2007-11-08T20:08:06Z

← Older revision		Revision as of 20:08, 8 November 2007
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	In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.		In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.

			[[Category:Tutorial]]

Atennissen at 20:11, 22 May 2007

2007-05-22T20:11:21Z

← Older revision		Revision as of 20:11, 22 May 2007
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	==Feature Extraction Analysis==		==Feature Extraction Analysis==
	The Analysis field in the Feature Extraction panel will appear automatically depending on the files loaded~~, while the~~ Feature Extractor field shows the only currently ~~possible choice~~.		The Analysis field in the Feature Extraction panel will appear automatically depending on the files loaded. The Feature Extractor field shows the only currently available option (MEM).

	You can view/edit analysis details by clicking "Set Analysis Details"		You can view/edit analysis details by clicking "Set Analysis Details"

	[[Image:P300_2.jpg]]		[[Image:P300_2.jpg]]

	This form reports all the remaining settings for the P300 analysis. Most of the values are set as default values. With settings such as the ones reported in figure, the analysis software will:		This form reports all the remaining settings for the P300 analysis. Most of the values are set as default values. With settings such as the ones reported in this figure, the analysis software will:

	*sample the spectrum at points starting from 0.1 Hz to 15 Hz		*sample the spectrum at points starting from 0.1 Hz to 15 Hz
	*take a 650 ms long epoch of data.		*take a 650 ms long epoch of data.

	You can modify these settings according to your aims. When you are finished, remember to confirm your choices by clicking on DONE. It will ~~make~~ the program accept changes.		You can modify these settings according to your aims. When you are finished, remember to confirm your choices by clicking on DONE. It will allow the program accept changes.

	At this point you can start the analysis by pressing the Evaluate and Plot button.		At this point you can start the analysis by pressing the Evaluate and Plot button.

Atennissen at 15:38, 22 May 2007

2007-05-22T15:38:09Z

Atennissen at 20:32, 10 May 2007

2007-05-10T20:32:36Z

← Older revision		Revision as of 20:32, 10 May 2007
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	===String Prediction===		===String Prediction===
	Mario also allows to check ~~what is~~ the word that the BCI2000 system would have predicted if the current feature was used online.		Mario also allows you to check the word that the BCI2000 system would have predicted if the current feature was used online.

	[[Image:P300_8.jpg]]		[[Image:P300_8.jpg]]

	In ~~the case in~~ example, since the sequence should have been SPELLWITHBCI, only 4 characters out of 12 (33%) have been correctly predicted. This score is well above chance, though quite inefficient.		In this example, since the sequence should have been SPELLWITHBCI, only 4 characters out of 12 (33%) have been correctly predicted. This score is well above chance, though quite inefficient.


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	In summary, we must select the latency and the channel where the maxima ~~occurs~~ of a ERP component whose spatio-temporal shape is compatible with the P300 phenomenon. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.		In summary, we must select the latency and the channel where the maxima of an ERP component whose spatio-temporal shape is compatible with the P300 phenomenon occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.

Atennissen at 20:25, 10 May 2007

2007-05-10T20:25:17Z

Show changes

Fcincotti: P3Tutorial moved to P300 Off-line Analysis Tutorial: more descriptive title

2006-12-15T20:37:23Z

P3Tutorial moved to P300 Off-line Analysis Tutorial: more descriptive title

← Older revision		Revision as of 20:37, 15 December 2006
(No difference)

Fcincotti at 20:25, 15 December 2006

2006-12-15T20:25:26Z

New page

==Starting an analysis session==
Every recording session has its own history. It is very difficult to say in advance what might happen during the recording. So we will assume that everything was perfect (the subject collaborated, no channel went lost, etc); later on we will consider the main causes of contamination, how to recognize it and what to do.

If the recording session run smoothly, in the folder c:\bci2000\data\Mu\TestSubj you should have now eight files named TestSubjS001R01.dat to TestSubjS001R08.dat, corresponding to the eight runs, respectively.

Before you start the analysis you should locate on your hard disk the correct montage file. This is a file that describes the list of channels that were acquired. In this tutorial we will use OneAndOnly_16ch.eloc.txt, which is located in the folder C:\BCI2000\Tutorial\Montages\. If you need to edit the *.mmf file, check its data format. < the of performances optimize that parameters try will we then online; performed BCI2000 analyses same off-line replicate to first>

==Opening files with Mario==
After having run mario.exe, press "Select Data Files".

[[Image:P300_1.jpg]]

A dialog window will ask you to select the dat files. You can either select a single data file, or select multiple files. This time, we will select all files in the dataset.

A green box will surround the Raw Data box in the main window.

As an optional (but recommended) operation, push the LOAD MONTAGE button and choose the mmf file. This will allow you to see the labels of each channel the following steps, and to allow to apply spatial filters that depend on the electrode position.

At least you can load an additional parameters file according according to different choices from those carried out during the experimentation.

At this point, you can check that P300 is selected in the Analysis menu (indicating that a P300 dataset has been recognized) and push the LOAD DATA button to confirm your choices. This will enable the EDIT CHANNEL LIST button you can use to select the channels you want to include in your analysis.

==Selecting Channels==

Pushing the the EDIT CHANNEL LIST button, two forms will show you the channels list (valids' and not-valids' one) and an image reassuming valid channels and their location.

Clicking on Add and Remove buttons you can move whichever channel from one list to the other enabling or disabling it.

==Selecting the Spatial Filter ==

Coming back to main window, you can therefore choose which filter to apply for your elaborations, selecting it between the possible supplied solutions.

You can choose between:

*RAW;
*CAR;
*Large Laplacian;
*Small Laplacian.

Common Average Reference (CAR) will be fine for most the situations.

We hope to release soon an user defined solution for any custom analysis.

==Feature Extraction Analysis==
The Analysis field in the Feature Extraction panel will appear automatically according to loaded files while the Feature Extractor field shows currently the only possible choice.

You can view/edit analysis details by pushing "Set Analysis Details"

[[Image:P300_2.jpg]]

This form reports all the remaining settings for the P300 analysis. Most of the values are set as default values. With settings as the ones reported in figure, the analysis software will:

*sample the spectrum at points starting from 0.1 Hz to 15 Hz;
*take a 650 ms long epoch of data.

You can modify these settings according to your aims. When you are done, remember to confirm your choices by pushing DONE. It will make the program accept changes.

At this point you can start the analysis by pressing the Evaluate and Plot button.

[[Image:P300_3.jpg]]

==View results==
The first figure that appears is the R-square matrix (channels x elapsed time after stimulus)

===R-square matrix===
The r-square matrix highlights the most relevant ERP features for the separation of potentials due to frequent or rare stimuli.

[[Image:P300_4.jpg]]

Each row of the matrix is related to a single channel, while a column represents a fixed latency. The color codes the statistical significance of the difference between the two kind of evoked potentials.

Thus a red color would mean that the ERP consequent to a rare stimulus is significantly more positive than the ERP consequent to a frequent stimulus.

This figure is independent of the channel and latency setting that were set in the parameter dialog (since it summarizes all results).

Clicking on the matrix will modify the channel/latency settings for the other figures; in fact the cell of the matrix that was clicked is characterized by one channel and one latency, whose waveform and topography (respectively) will be shown in the other two figures.

You can choose whether to overwrite or to put the most recently evoked figures beside the previous one. Two sets of waveform/topography figures are available, and are linked to the click of the left or right mouse button.

Clicking on any point of map will open four more windows:

*Amplitude waveforms at selected channel(s)
*Topographic plots at selected latency(es)
*ERP response to each stimulus
*An off-line prediction of the string read

===Amplitude Waveform===
The whole timecourse of ERPs generated are displayed in the top panel, regardless of the specific stimulus (line of letters) that generated it. Rare ERPs are plotted in solid lines, while frequent ERPs are dotted. If two channels were selected in the P300 parameter dialog, they are plot in red and in blue, respectively.

[[Image:P300_5.jpg]]

The bottom panel shows the r-square time course. It is roughly proportional to the difference between rare and frequent ERPs, but since r-square is sensitive to the dispersion (variance) of single trials, small differences in amplitude can bring to a high r-square if they are very reproducible.

Topographic plots
This figure represents the scalp distribution of the r-square.

[[Image:P300_6.jpg]]

The color coding is the same as the r-square matrix figure, and values on each channel are interpolated to create a continuous bidimensional map. The higher the number of electrodes, the more accurate is the map. The number of channels shown on the scalp may not coincide with the whole number of electrodes in case of a Surface Laplacian spatial filtering, since in that case the value of the laplacian is not computed on the border channels.

===ERP rensponse===

[[Image:P300_7.jpg]]

The figure shows the medium temporal course for the 12 stimuli. Red graphs are rare events while blue ones are frequent events.

===String Prediction===
Mario also allows to check what is the word that the BCI2000 system would have predicted if the current feature was used online.

[[Image:P300_8.jpg]]

In the case in example, since the sequence should have been SPELLWITHBCI, only 4 characters out of 12 (33%) have been correctly predicted. This score is well above chance, though quite inefficient.

{| border="3" cellspacing="5" cellpadding="20" align="center"
|S
|P
|E
|L
|L
|W
|I
|T
|H
|B
|C
|I
|-
|style="background:#ff3322" |4
|style="background:#ff3322" |M
|E
|L
|L
|style="background:#ff3322" |4
|style="background:#ff3322" |_
|T
|style="background:#ff3322" |A
|style="background:#ff3322" |K
|style="background:#ff3322" |G
|style="background:#ff3322" |4
|}

In summary, we must select the latency and the channel where the maxima occurs of a ERP component whose spatio-temporal shape is compatible with the P300 phenomenon. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.

← Older revision		Revision as of 15:38, 22 May 2007
Line 4:		Line 4:
	If the recording session runs smoothly, you should now have eight files named TestSubjS001R01.dat to TestSubjS001R08.dat, in the folder c:\bci2000\data\Mu\TestSubj, corresponding to the eight runs, respectively.		If the recording session runs smoothly, you should now have eight files named TestSubjS001R01.dat to TestSubjS001R08.dat, in the folder c:\bci2000\data\Mu\TestSubj, corresponding to the eight runs, respectively.

	Before you start the analysis you should locate on your hard disk the correct montage file ~~on your hard disk~~. This is a file that describes the list of channels that were acquired. In this tutorial we will use OneAndOnly_16ch.eloc.txt, which is located in the folder C:\BCI2000\Tutorial\Montages\. If you need to edit the *.mmf file, check its data format.		Before you start the analysis you should locate, on your hard disk, the correct montage file. This is a file that describes the list of channels that were acquired. In this tutorial we will use OneAndOnly_16ch.eloc.txt, which is located in the folder C:\BCI2000\Tutorial\Montages\. If you need to edit the *.mmf file, check its data format.

	==Opening Files with Mario==		==Opening Files with Mario==
Line 29:		Line 29:
	==Selecting the Spatial Filter ==		==Selecting the Spatial Filter ==

	Return to the main window ~~and you can~~ choose which filter to apply for your ~~analyses~~, selecting from the following filter choices:		Return to the main window to choose which filter to apply for your analysis, selecting from the following filter choices:

	*RAW		*RAW
Line 38:		Line 38:
	Common Average Reference (CAR) will be fine for most of the situations.		Common Average Reference (CAR) will be fine for most of the situations.

	We hope soon, to release ~~soon~~ a user defined solution for any custom analysis.		We hope soon, to release a user defined solution for any custom analysis.

	==Feature Extraction Analysis==		==Feature Extraction Analysis==
	The Analysis field in the Feature Extraction panel will appear automatically ~~according to~~ the files loaded while the Feature Extractor field shows the only currently possible choice.		The Analysis field in the Feature Extraction panel will appear automatically depending on the files loaded, while the Feature Extractor field shows the only currently possible choice.

	You can view/edit analysis details by clicking "Set Analysis Details"		You can view/edit analysis details by clicking "Set Analysis Details"
Line 49:		Line 49:
	This form reports all the remaining settings for the P300 analysis. Most of the values are set as default values. With settings such as the ones reported in figure, the analysis software will:		This form reports all the remaining settings for the P300 analysis. Most of the values are set as default values. With settings such as the ones reported in figure, the analysis software will:

	*sample the spectrum at points starting from 0.1 Hz to 15 Hz;		*sample the spectrum at points starting from 0.1 Hz to 15 Hz
	*take a 650 ms long epoch of data.		*take a 650 ms long epoch of data.

Line 139:		Line 139:


	In summary, we must select the latency and the channel where the maxima of an ERP component whose spatio-temporal shape is compatible with the P300 phenomenon occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.		In summary, we must select the latency and the channel where the maxima of an ERP component, whose spatio-temporal shape is compatible with the P300 phenomenon, occurs. Testing the speller can suggest which component has the highest probability to predict the user's selected letter.