Source Coherence How to... - Revision history

Harald at 10:46, 5 May 2021

2021-05-05T10:46:46Z

Harald: /* How to Compute a Probability Map */

2021-05-05T10:46:28Z

‎How to Compute a Probability Map

Harald: /* How to Compute a Probability Map */

2021-05-05T10:45:37Z

‎How to Compute a Probability Map

Harald: /* How to Start the Beamformer from the Time-Frequency Window */

2021-05-05T10:27:26Z

‎How to Start the Beamformer from the Time-Frequency Window

Jaehyun: /* How to Compute Time Lags between oscillations using Phase Diagrams */

2018-05-28T08:38:10Z

‎How to Compute Time Lags between oscillations using Phase Diagrams

Jaehyun: /* How to Start the Beamformer from the Time-Frequency Window */

2017-07-07T09:23:35Z

‎How to Start the Beamformer from the Time-Frequency Window

Jaehyun: /* How to Start DICS computation from the Time-Frequency Window */

2017-07-07T09:17:44Z

‎How to Start DICS computation from the Time-Frequency Window

Jaehyun at 08:24, 26 May 2017

2017-05-26T08:24:08Z

Alexa at 13:10, 7 April 2017

2017-04-07T13:10:26Z

Abinash at 12:57, 7 April 2017

2017-04-07T12:57:34Z

@@ Line 2: / Line 2: @@
 |title = Module information
 |module = BESA Research Complete
-|version = 6.1 or higher
+|version = BESA Research 6.1 or higher
 }}

@@ Line 85: / Line 85: @@
 # loading the paradigm (menu "''ERP/Open Paradigm''", select paradigm file "<span style="color:#ff9c00;">'''Auditory/AC_Osc.pdg'''</span>")
 # performing an artifact scan (paradigm tab "'''Artifact'''", press the "<span style="color:#3366ff;">'''Scan'''</span>..." button and adjust the amplitude threshold to about 135µV)
-# starting analysis (paradigm tab "Coherence", press the "<span style="color:#3366ff;">'''Start Time-Frequency Analysis'''</span>" button)
+# starting analysis (paradigm tab "'''Coherence'''", press the "<span style="color:#3366ff;">'''Start Time-Frequency Analysis'''</span>" button)

@@ Line 79: / Line 79: @@
 '''Statistical testing with one condition'''
-This example uses the simulated data set in the file "<span style="color:#ff9c00;">'''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''</span>" (see also BESA Research Tutorial on source coherence on www.besa.de).
+This example uses the simulated data set in the file "<span style="color:#ff9c00;">'''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''</span>" (see also BESA Research Tutorial on Time-frequency analysis, connectivity analysis, and beamforming on https://www.besa.de).
 After the data file is loaded, start coherence analysis by
@@ Line 85: / Line 85: @@
 # loading the paradigm (menu "''ERP/Open Paradigm''", select paradigm file "<span style="color:#ff9c00;">'''Auditory/AC_Osc.pdg'''</span>")
 # performing an artifact scan (paradigm tab "'''Artifact'''", press the "<span style="color:#3366ff;">'''Scan'''</span>..." button and adjust the amplitude threshold to about 135µV)
-# starting analysis (paradigm tab "Coherence", press the "<span style="color:#3366ff;">'''Go'''</span>" button)
+# starting analysis (paradigm tab "Coherence", press the "<span style="color:#3366ff;">'''Start Time-Frequency Analysis'''</span>" button)
@@ Line 120: / Line 120: @@
 '''Statistical testing comparing conditions'''
-This example uses the error-related negativity data set in the file&nbsp;<span style="color:#ff9c00;">''''Examples/TFC-Error-Related'''</span> <span style="color:#ff9c00;">'''Negativity/Correct+Error.foc''''</span> (see also BESA Research Tutorial on source coherence on [http://www.besa.de www.besa.de]).
+This example uses the error-related negativity data set in the file&nbsp;<span style="color:#ff9c00;">''''Examples/TFC-Error-Related'''</span> <span style="color:#ff9c00;">'''Negativity/Correct+Error.foc''''</span> (see also BESA Research Tutorial on source coherence on [https://www.besa.de www.besa.de]).
 After the data file is loaded, start coherence analysis by

@@ Line 7: / Line 7: @@
 == How to Start the Beamformer from the Time-Frequency Window ==
-This chapter shows how to start the BESA Multiple Source Beamformer from the time-frequency window. The displayed screenshots are taken using the file '''BESA5/Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc''' (see BESA Tutorial 6: "''Tutorial on source coherence''" on our website http://www.besa.de).
+This chapter shows how to start the BESA Multiple Source Beamformer from the time-frequency window. The displayed screenshots are taken using the file '''BESA5/Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc''' (see BESA Tutorial 12: "''Tutorial on Time-frequency analysis, Connectivity analysis, and beamforming''" which you can download from our website https://www.besa.de).
 The time-frequency beamformer is especially useful to image induced oscillatory activity in- or decrease. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot.

@@ Line 57: / Line 57: @@
-. Select the menu entry ''''''View Phase Diagram''''''. In all channels where coherence was shown previously, the plot changes to display the phase diagram. Inside the marked time-frequency region, the mean phase difference ϕ<sub>i</sub> within the time window is calculated for each frequency ν<sub>i</sub>, and the values are plotted. The phase is calculated from the cross-spectral matrices of the single trials. The error bars shown in the display are the standard deviations of the phase over the time.
+. Select the menu entry '''View Phase Diagram'''. In all channels where coherence was shown previously, the plot changes to display the phase diagram. Inside the marked time-frequency region, the mean phase difference ϕ<sub>i</sub> within the time window is calculated for each frequency ν<sub>i</sub>, and the values are plotted. The phase is calculated from the cross-spectral matrices of the single trials. The error bars shown in the display are the standard deviations of the phase over the time.
 The time lag is calculated from a regression fit to the values. The fitting procedure takes phase shifts of π into account, which can occur due to volume currents, or due to dipole orientations. First, a straight line is fitted to the data. Then, one of two different approaches are used to compute the time lag, depending on the characteristics of the values.
-* If extrapolation of the line to ν= 0 Hz yields a phase difference of approximately 0 or approximately π, or if a zero crossing at the origin is within the error margins of the fit, the delay can be calculated directly from the data values. For each data value, the relationship ∆t<sub>i </sub><nowiki>= ϕ</nowiki><sub>i</sub>/ (2π ν<sub>i</sub>) holds. The time lag is calculated as the weighted mean, where the weights are given by the individual errors of fi (the errors are given by the standard deviation over the time samples).
+* If extrapolation of the line to ν = 0 Hz yields a phase difference of approximately 0 or approximately π, or if a zero crossing at the origin is within the error margins of the fit, the delay can be calculated directly from the data values. For each data value, the relationship ∆t<sub>i</sub> = ϕ<sub>i</sub> / (2π ν<sub>i</sub>) holds. The time lag is calculated as the weighted mean, where the weights are given by the individual errors of fi (the errors are given by the standard deviation over the time samples).
-* If the regression line does not cross the origin, the gradient of the fit is used to calculate the time lag as ∆t=grad(f(ν)) / 2π
+* If the regression line does not cross the origin, the gradient of the fit is used to calculate the time lag as ∆t = grad(f(ν)) / 2π
-'''Note:''' In both cases, any frequency only enters the calculation if the coherence value reaches or exceeds 70% of the current color map maximum for at least one time sample inside the selected time-frequency window. At least 3 valid values are required for the estimation. Channels with less than 3 valid values are not evaluated.
+'''Note''': In both cases, any frequency only enters the calculation if the coherence value reaches or exceeds 70% of the current color map maximum for at least one time sample inside the selected time-frequency window. At least 3 valid values are required for the estimation. Channels with less than 3 valid values are not evaluated.
 Phase values and fitted lines are only displayed for the channels where the above condition is satisfied. In the example below, the condition was only fulfilled for one channel (ACsL) due to the good separation of activities by the source montage. The calculated delay is displayed beside the channel label (in this case: 5 milliseconds).
@@ Line 72: / Line 72: @@
-To get back to coherence, '''right-click '''into the reference channel and select ''''Coherence'''' from the popup menu that appears.
+To get back to coherence, '''right-click '''into the reference channel and select '''Coherence''' from the popup menu that appears.
 == How to Compute a Probability Map ==

@@ Line 7: / Line 7: @@
 == How to Start the Beamformer from the Time-Frequency Window ==
-This chapter shows how to start the BESA Multiple Source Beamformer from the time-frequency window. The displayed screenshots are taken using the file '''BESA5/Examples/Learn-by-Simulations/AC''-''Coherence/AC-Osc20.foc''' (see BESA Tutorial 6: "''Tutorial on source coherence''" on our website http://www.besa.de).
+This chapter shows how to start the BESA Multiple Source Beamformer from the time-frequency window. The displayed screenshots are taken using the file '''BESA5/Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc''' (see BESA Tutorial 6: "''Tutorial on source coherence''" on our website http://www.besa.de).
 The time-frequency beamformer is especially useful to image induced oscillatory activity in- or decrease. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot.
-In the time-frequency diagram of any channel, left-drag to mark a time-frequency region of interest, e.g. a region of power increase. When the left mouse button is released, select '''Image' ''from the popup menu.
+In the time-frequency diagram of any channel, left-drag to mark a time-frequency region of interest, e.g. a region of power increase. When the left mouse button is released, select '''Image''' from the popup menu.
-−
 [[Image:Image001.gif]]
 [[Image:Image002.gif]]
-Note: The text within the window emphasizes that it is recommended to use the same duration for the Baseline Interval and the Target Interval to obtain a reliable beamformer image. The reason is the dependence on the noise estimate on the number of trials that enter the covariance matrix computation. The same recommendation holds if two conditions are compared: It is recommended to define conditions such that they contain approximately the same number of trials. If the baseline interval defined in the Time-Frequency window (the red bar on the x-axis) is larger than the target time interval specified by the dragged rectangle, the baseline interval in the'' 'Image' ''dialog window is automatically shortened to match the duration of the Target Interval. If for some reason these requirements cannot be met, it is recommended to compute a beamformer image with regularization. This is achieved by adjusting the SVD cutoff in the Source Analysis window using the menu entry '''Image/Settings'.''
+Press the <span style="color:#3366ff;">'''Go'''</span> button to start the beamformer computation.
 BESA Research now computes mean time-frequency covariance matrices for the target and the reference interval. The source analysis window opens with an enlarged 3D imaging display that compares the power in the target and the reference interval as computed with a bilateral beamformer. The result is superimposed onto the individual or standard MRI.
-For more information on the multiple-source beamformer (MSBF), please refer to chapter ''"Source'' ''Analysis".''
+For more information on the multiple-source beamformer (MSBF), please refer to chapter '''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29|Source Analysis 3D imaging / Multiple Source Beamformer]]'''.
-−
 [[Image:Image003.gif]]
 == How to Start DICS computation from the Time-Frequency Window ==

@@ Line 39: / Line 39: @@
 == How to Start DICS computation from the Time-Frequency Window ==
-How to create DICS images you will find in the chapter “''Source Analysis / 3D Imaging / Dynamic Imaging of Coherent Sources (DICS)”.''
+How to create DICS images you will find in the chapter '''[[Source_Analysis_3D_Imaging#Dynamic_Imaging_of_Coherent_Sources_.28DICS.29|Source Analysis / 3D Imaging / Dynamic Imaging of Coherent Sources (DICS)]]'''.
-−
 == How to Compute Time Lags between oscillations using Phase Diagrams ==

@@ Line 1: / Line 1: @@
+{{BESAInfobox
+|title = Module information
 = Source Coherence: How to... =

← Older revision		Revision as of 12:57, 7 April 2017
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	The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.		The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.
		+
		+	[[Category:Research Manual]]
		+
		+	{{BESAManualNav}}