Source Analysis Functions of the Window - Revision history

Jaehyun: /* Overview */

2022-01-05T11:34:04Z

‎Overview

Jaehyun: /* Source Box */

2021-12-17T13:24:52Z

‎Source Box

Dominik at 13:02, 25 November 2021

2021-11-25T13:02:00Z

Dominik at 12:52, 25 November 2021

2021-11-25T12:52:08Z

Harald at 10:21, 5 May 2021

2021-05-05T10:21:58Z

Harald: /* 3D Window */

2021-05-05T10:21:33Z

‎3D Window

Robert: /* 3D Window */

2021-05-04T10:52:43Z

‎3D Window

Robert: /* 3D Window */

2021-05-04T10:50:15Z

‎3D Window

Robert: /* Parameter Box */

2021-05-04T10:32:10Z

‎Parameter Box

Robert: /* Channel Box */

2021-05-04T10:24:47Z

‎Channel Box

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 Note that the 3D window will not normally appear automatically (unless specified in the <span style="color:#3366ff;">'''Options / Preferences'''</span> menu), and the head box will take up more space if the 3D window is not displayed.
-[[Image:Functions SAwindow (1).gif ]]
+[[Image:Functions_SAwindow_(1).png|500px]]
-<!-- ''(Click on the region of interest to jump to the associated section. Use the Back button of the Windows® help to jump back to this page.)'' -->
-−
 The '''title bar''' contains information about the data file, the filename, the condition name, the filter settings, and the selected time interval.
@@ Line 32: / Line 30: @@
 The same is possible for the horizontal double line bounding the variance box.
 == Channel Box ==

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 == Source Box ==
-The source box shows the source waveforms of the current solution. The source waveforms are computed over the whole epoch of the current data set using the currently chosen head model. (The head model is set and displayed in the parameter box.) If no solution is available the source box is empty.
+The source box shows the source waveforms of the current solution. The source waveforms are computed over the whole epoch of the current data set using the currently chosen head model. (The head model is set and displayed in the [[#Parameter Box|parameter]] box.) If no solution is available the source box is empty.
 A single dipole or a spatial component has one source waveform, a regional source has three waveforms for EEG and two for MEG (one waveform for each component). A spatial component is labeled SC just below its waveform.
-[[Image:Functions SAwindow (4).gif]]
+[[Image:Functions SAwindow Source Box.png|500px]]
-−
-(Click on the region of interest to view a description)
-−
 At the top of the source box you will find the following buttons:
 * The <span style="color:#3366ff;">'''All on'''</span> button activates or deactivates all sources (switches all sources on or off). Spatial components whose principal vector does not match with the current data set cannot be activated.
 * The <span style="color:#3366ff;">'''All fit'''</span> button enables all active sources (not spatial components) for fitting.
 * The<span style="color:#3366ff;">''' Start fit '''</span>button fits the enabled sources within the specified fit interval(s). If no fit interval is set the sources the whole epoch is used for fitting, if a cursor is set they are fitted only at the cursor sample. Another way to start fitting is given by the ''Fit Enabled Sources''... entry in the standard popup menu.
-* The <span style="color:#3366ff;">'''BrainVoyager '''</span>button will start the BrainVoyager program. If the BrainVoyager path has not been set correctly the BrainVoyager tab of the ''Preferences ''dialog box is displayed to allow you to set the valid path. If the BrainVoyager program is already running the current solution is sent to BrainVoyager for display in the structural MRT image (c.f. ''Integration with MRI/fMRI'').
+* The <span style="color:#3366ff;">'''Image selection button'''</span> button allows for a quick computation of a [[Source_Analysis_3D_Imaging#Overview|3D image]]. The type of the image to be computed is shown in the button label. By default, this is the previously computed 3D image. For details on the available image types in BESA Research, please refer to chapter [[Source_Analysis_3D_Imaging#Overview|3D imaging]].
 Each source waveform has two push buttons assigned to it:
 * The <span style="color:#3366ff;">'''On/Off'''</span> buttons to the left of the source waveforms activate or deactivate the associated sources. Spatial components whose principal vector does not match with the current data set cannot be activated. If a source is inactive, it does not contribute to the model.
-* The <span style="color:#3366ff;">'''Fit/No fit '''</span>buttons below the <span style="color:#3366ff;">'''On/Off'''</span> buttons enable or disable the associated source for fitting. If a source is selected, it is enabled for fitting automatically. On the other hand, a source is automatically selected if you push the corresponding <span style="color:#3366ff;">'''Fit/No fit'''</span> button. Note that spatial components have no <span style="color:#3366ff;">'''Fit/No fit'''</span> button since they cannot be enabled for fitting. You can enable several sources for fitting by keeping the <span style="color:#3366ff;">'''Control-key'''</span> on your keyboard pressed and pushing the <span style="color:#3366ff;">'''Fit/No fit'''</span> buttons of the sources you would like to fit simultaneously. If the model waveforms of fit enabled sources are displayed in the channel box (the <span style="color:#3366ff;">'''Model'''</span> button in the channel box shows ''M-F''), or if the model data of fit enabled sources are mapped in the 3D window, only sources whose <span style="color:#3366ff;">'''Fit/No fit'''</span> button is down are taken into account for the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map.
-* The <span style="color:#3366ff;">'''Map/No map'''</span> buttons are visible only if the model waveforms of fit enabled sources are displayed in the channel box (the<span style="color:#3366ff;">''' Model'''</span> button in the channel box shows ''M-F'') or if the model data of fit enabled sources are mapped in the 3D window. They are available for spatial components only, since other sources use the <span style="color:#3366ff;">'''Fit/No fit'''</span> buttons to enable/disable the source for mapping or to display the model waveforms. Only spatial components whose <span style="color:#3366ff;">'''Map/No map'''</span> button is down are taken into account in the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map. You can enable several sources for mapping by keeping the <span style="color:#3366ff;">'''Control-key'''</span> on your keyboard pressed and pushing the <span style="color:#3366ff;">'''Map/No map '''</span>buttons (for spatial components) or <span style="color:#3366ff;">'''Fit/No fit'''</span> buttons (for other source types) of the sources you would like to contribute to the model waveforms or model map.
+* The <span style="color:#3366ff;">'''Fit/No fit '''</span>buttons below the <span style="color:#3366ff;">'''On/Off'''</span> buttons enable or disable the associated source for fitting. If a source is selected, it is enabled for fitting automatically. On the other hand, a source is automatically selected if you push the corresponding <span style="color:#3366ff;">'''Fit/No fit'''</span> button. Note that spatial components have no <span style="color:#3366ff;">'''Fit/No fit'''</span> button since they cannot be enabled for fitting. You can enable several sources for fitting by keeping the ''Control-key'' on your keyboard pressed and pushing the <span style="color:#3366ff;">'''Fit/No fit'''</span> buttons of the sources you would like to fit simultaneously. If the model waveforms of fit enabled sources are displayed in the channel box (the <span style="color:#3366ff;">'''Model'''</span> button in the channel box shows ''M-F''), or if the model data of fit enabled sources are mapped in the 3D window, only sources whose <span style="color:#3366ff;">'''Fit/No fit'''</span> button is down are taken into account for the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map.
-Use the <span style="color:#3366ff;">'''Waveform Scale'''</span> buttons (labeled with two arrows) at the bottom right of the source box to adjust the waveform amplitude scale. If you hold the <span style="color:#3366ff;">'''Control-key'''</span> in combination, the scale is reset to default.
+Use the <span style="color:#3366ff;">'''Waveform Scale'''</span> buttons (labeled with two arrows) at the bottom right of the source box to adjust the waveform amplitude scale. If you hold the ''Control-key'' in combination, the scale is reset to default.

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 [[Image:Functions SAwindow (4).gif]]
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 You may double click on the '''source label''' to specify a new label.
 If you click the right mouse button somewhere in the source box, the <span style="color:#3366ff;">'''Source Box'''</span> popup menu appears with commands specific to this box.

@@ Line 121: / Line 121: @@
 * The <span style="color:#3366ff;">'''All fit'''</span> button enables all active sources (not spatial components) for fitting.
 * The<span style="color:#3366ff;">''' Start fit '''</span>button fits the enabled sources within the specified fit interval(s). If no fit interval is set the sources the whole epoch is used for fitting, if a cursor is set they are fitted only at the cursor sample. Another way to start fitting is given by the ''Fit Enabled Sources''... entry in the standard popup menu.
-* The <span style="color:#3366ff;">'''Image selection'''</span> button allows for a quick computation of a 3D image. The type of the image to be computed is shown in the button label. By default, this is the previously computed 3D image. For details on the available image types in BESA Research, please refer to chapter 3D imaging.
+* The <span style="color:#3366ff;">'''Image selection button'''</span> button allows for a quick computation of a 3D image. The type of the image to be computed is shown in the button label. By default, this is the previously computed 3D image. For details on the available image types in BESA Research, please refer to chapter 3D imaging. When you click on this button while keeping CTRL button pressed the new computation will be performed applying weighting based on current image. When you click on this button while keeping SHIFT button pressed the computation will be performed from scratch (leadfields will be re initialized)
 * The <span style="color:#3366ff;">'''BrainVoyager '''</span>button will start the BrainVoyager program. If the BrainVoyager path has not been set correctly the BrainVoyager tab of the ''Preferences ''dialog box is displayed to allow you to set the valid path. If the BrainVoyager program is already running the current solution is sent to BrainVoyager for display in the structural MRT image (c.f. ''Integration with MRI/fMRI'').

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

@@ Line 310: / Line 310: @@
 '''Using the Keyboard'''
-A number of key combinations are useful for navigation/display in the 3D window if the 3D window is active (the title bar is blue). The most important commands with their default keys are listed here. Note that you can change the default keys in the ''Define hot keys'' dialog box, which also allows to specify additional key commands.
+A number of key combinations are useful for navigation/display in the 3D window if the 3D window is active. The most important commands with their default keys are listed here. Note that you can change the default keys in the ''Define hot keys'' dialog box, which also allows to specify additional key commands.
 Command default key(s) and effects:

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 <div><ul>
-<li style="display: inline-block;"> [[File:Functions SAwindow (12).gif|thumb|425px|Fig. 1]] </li>
+<li style="display: inline-block;"> [[File:3D_Window_-_Cortical_Map.png|thumb|425px|Fig. 1]] </li>
-<li style="display: inline-block;"> [[File:3Dwindow.png|thumb|425px|Fig. 2]] </li>
+<li style="display: inline-block;"> [[File:3D_Window_-_Rolandic.png|thumb|425px|Fig. 2]] </li>
 </ul></div>
 <!-- ''(Click on the region of interest to view a description.)'' -->

@@ Line 302: / Line 302: @@
 <!-- ''(Click on the region of interest to view a description.)'' -->
-The sources of the current solution are displayed in the anatomical view (fig. 2), or in the cortical imaging view if this is activated via the popup menu using the right mouse button. The selected source is displayed with a golden halo around the source body.
+The sources of the current solution are displayed in the anatomical view (fig. 2), or in the cortical imaging view if this is activated via the popup menu using the right mouse button. The selected source is displayed with a golden halo around the source body. If EEG/MEG data is coregistered with MRI the confidence elipsoids and error rims are displayed around fitted sources
 The '''3D window toolbar''' is explained in details in the ''3D Window Toolbar'' section in the BESA help ''Reference'' chapter.

@@ Line 186: / Line 186: @@
 * '''Talairach coordinates''':
 *# Talairach coordinates calculated using the individual MRI information of the current condition. The button is labeled <span style="color:#3366ff;">'''Talairach'''</span>.
-*# Approximate ''Talairach coordinates'' estimated by a default transformation to the BESA Research standard brain that is used for the 3D anatomical view if an individual MRI is not available for the current condition. The button is labeled <span style="color:#3366ff;">'''Tal.'''</span> (''appr''.). For additional information, please see the chapter ''Integration with MRI and fMRI''),
+*# Approximate ''Talairach coordinates'' estimated by a default transformation to the BESA Research standard brain that is used for the 3D anatomical view if an individual MRI is not available for the current condition. The button is labeled <span style="color:#3366ff;">'''Tal.'''</span> (''appr''.). For additional information, please see the chapter [[Integration with MRI and fMRI]]),
 * '''(Cartesian) unit sphere coordinates''' (BESA coordinates): Defined by the best fit sphere. The button is labeled <span style="color:#3366ff;">'''Cart./US'''</span>.
@@ Line 192: / Line 196: @@
 * '''Polar unit sphere coordinates''' (polar BESA coordinates): Same coordinate system as above, but the coordinates are given in'' polar coordinates''. The button is labeled <span style="color:#3366ff;">'''Polar/US'''</span>.
-Note: A detailed description of the coordinate systems is given in the chapter ''Working with Electrodes'' ''and Surface Locations''.
+Note: A detailed description of the coordinate systems is given in the chapter [[Electrodes and Surface Locations]].
 To the left of the <span style="color:#3366ff;">'''Coordinate System'''</span> button the location and orientation coordinates of the selected source are given in the text fields labeled as follows:
@@ Line 220: / Line 224: @@
 Click on the '''source label''' to specify a new label.
 == Head Box ==

@@ Line 46: / Line 46: @@
-Below the first row of buttons, there is a '''description of the current condition''' containing the condition name, the filter settings and the condition epoch. Below the condition epoch, the baseline of the current condition is displayed as horizontal black line.
+Below the first row of buttons, there is a '''description of the current condition''' containing the condition name, the filter settings and the condition epoch. Below the condition epoch, the baseline of the current condition is displayed as horizontal black/red line.
 At the bottom, you see the''' figure legend '''describing the used colors and the number of displayed channels (or PCA components).
@@ Line 58: / Line 58: @@
 * The <span style="color:#3366ff;">'''Sort'''</span> button (fourth button from the left) changes the ordering of the channels. Pushing this button switches between original order (button is labeled <span style="color:#3366ff;">'''Order'''</span> or <span style="color:#3366ff;">'''Ord'''</span>.), sorting by the amplitude of the measured data (||Data|| or ||D||), and sorting by the amplitude of the residual (||Res.|| or ||R||). In practice, by using one of the sorting modes ||Data|| or ||Residual||, you will only have to display the first few channels during the fitting procedure, since the channels with the largest signals are shown at the top.
 * Use the <span style="color:#3366ff;">'''P.C.A.'''</span> button to start a Principal Components Analysis (PCA) over the marked fit interval(s) (if no fit interval is set the PCA is computed over the whole epoch). The percentage variance accounted for by each component is shown at the left of each waveform. When the PCA is displayed, data, model, and residual waveforms are not visible. Note that if the <span style="color:#3366ff;">'''Residual '''</span>button is down and the <span style="color:#3366ff;">'''Data'''</span> button is up, the PCA is computed for the residual data and not the measured data.
-* The button at the far right is the <span style="color:#3366ff;">'''EEG/MEG'''</span> button. Pushing this button toggles between the data sets (EEG and MEG) of the current condition, if combined EEG and MEG have been recorded. The label of the button shows which data set is currently displayed.
+* The button at the far right is the <span style="color:#3366ff;">'''EEG/MEG/MEEG'''</span> button. Pushing this button toggles between the data sets (EEG, MEG and MEEG) of the current condition, if combined EEG and MEG have been recorded. The label of the button shows which data set is currently displayed.
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 The channel box is bounded at the right by three scroll bars. Use the topmost one to change the number of displayed channels. The scroll bar below ('''select displayed channels''') can be used to scroll through the channels. The bottom one, consisting only of two arrows, changes the amplitude scaling of the displayed signals ('''scale waveforms''').
-The <span style="color:#3366ff;">'''MAG '''</span>and <span style="color:#3366ff;">'''GRD'''</span> buttons at the bottom of the channel box appear only if an MEG data set containing both magnetometer and gradiometer sensors is displayed. The buttons are used to toggle the display of the magnetometer and gradiometer channels.
+The <span style="color:#3366ff;">'''MAG'''</span> and <span style="color:#3366ff;">'''GRD'''</span> buttons at the bottom of the channel box appear only if an MEG data set containing both magnetometer and gradiometer sensors is displayed, or if MEEG mode is active. The buttons are used to toggle the display of the magnetometer and gradiometer channels. In case of the <span style="color:#3366ff;">'''MEEG'''</span> mode, <span style="color:#3366ff;">'''EEG'''</span> and either of <span style="color:#3366ff;">'''MAG'''</span> and <span style="color:#3366ff;">'''GRD'''</span> buttons (or both) are displayed. Combination of any MEG mode with the EEG data can then be toggled in that way.
 In the figure above you see one '''fit interval''', shown in a darker color. The fit interval is used for fitting, computing the PCA, and more.