Differences between revisions 1 and 29 (spanning 28 versions)

Computing and displaying dipoles

Authors: Elizabeth Bock, John C Mosher

Contents

Computing sources using the GLS
Dipole Scanning
Displaying Dipoles
Dipole models from Neuromag's Xfit and CTF's DipoleFit

Computing sources using the GLS

This process allows for a systematic scanning of sources using performance measures to display single dipoles. For this tutorial we will use the Generalized Least Squares (GLS) source modeling available in Brainstorm.

Select the protocol TutorialCTF. Right-click on Subject01 / Left / ERF > Compute sources.
In this window, you should select Expert Mode. You will see the following menu. Select [Test] Mosher GLS. Click OK. Use the default settings in the next menu and click OK.

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Two results were added under the ERF: GLS and GLS-P.
- GLS:
- GLS-P:

Dipole Scanning

For this tutorial we will do the scanning on the GLS results. However, the dipole scanning is also available for sources computed with minimum norm Z-scored (i.e. MN MEG(Constr) | zscored), dSPM and sLORETA.

Drag and drop the GLS-P link into the Process 1 box. Click Run > Sources > Dipole scanning.

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Use the defaults options:
- Time Window: This is the window over which the scanning will occur. The default option is to use the entire epoch.
- Time between dipoles: This allows you to change the resolution of the scanning. To use all time points, enter a 0 (default).
The resulting dipole file is added under the Left condition.

Displaying Dipoles

Right-click ERF|GLSP-dipole-scan > Display on cortex. The Dipoles panel is now open and dipoles are displayed on the cortex. You can now explore the results using the options in the Dipoles panel:
- Data options: filter the available dipoles according the specific measurement. For the GLSP, these are defined as:
  - Z-score:
  - Goodness:
  - Chi-square:
  - Reduced Chi-square:
  - Confvolume:
- Display options: these options allow for adjusting how the selected dipoles (according to the Data options) are displayed
  - Show max goodness: will show the dipole with the maximum goodness (within the constraints of the Data options) at the time point selected. If Show all time is selected, then this represents the maximum goodness over all time points.
  - Show all time: plots all selected dipoles at all time points. Unselecting this options will show only the current time point.
  - 3D - Color dipoles according to Time, Goodness of Fit, Z-score, Group: adjusts the colormap to reflect the measure.
In the Dipoles panel, select Show max goodness of fit, Show all time, and color the dipoles according to Goodness of Fit. You should see the following display. Explore the panel options to familiarize yourself with the capabilities.

Additional Example

Dipole scanning can also be restricted to a scout. In this example, the scanning is restricted to a scout named '2' and colored according to Goodness of Fit

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Dipole models from Neuromag's Xfit and CTF's DipoleFit

Brainstorm can import dipoles that have been generated using external software:

Neuromag Source Modelling module, xfit: The .bdip format is described in bdip_format.pdf. For more information about xfit and the bdip format see Neuromag Software Manuals.

CTF DipoleFit: The DipoleFit software and the .dip format is described in the CTF Software Manuals.

To import

Select the study where you want to import the dipole file
Right click and select ‘Import dipoles’ (Figure 1)
For Neuromag, you will be prompted to specify the number of subsets used for dipole fitting. In most cases, this will be one. If subsets are used, as defined in the text file $HOME/.meg_analysis/xfit_selections, then the number of subsets used needs to be input when prompted. (Figure 2)

Figure 1. Importing dipoles

Figure 2. Neuromag option for channel subsets

When displaying dipole files with multiple groups and/or subsets, the Loaded dipoles panel appears with a list of dipoles, grouped according to event (Group #1, Group#2, etc) and by channel subset, if used (Subset #1, Subset#2, etc.)
- Select the Group(s) to plot
- Clicking on a subset will select all Groups with that subset. For example, selecting Subset #1 will select Group #1 (1), Group #2 (1), Group #3 (1), etc.

Examples

Example 1 shows 5 subsets (channel groups of Left, Right, Anterior, Posterior, All Channels). When subset #2 is selected, dipoles fitted to the right channels are displayed. In this case, Show all time is selected for the 4 Groups (events) and colored according to Goodness of Fit

Example 2 shows all groups and subsets at one time point (0.3 ms), with goodness of fit greater than 80%, colored according to Group.

-  ⇤ ← Revision 1 as of 2013-11-12 22:50:46 → 
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+   ← Revision 29 as of 2016-03-15 16:14:58 → ⇥
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  Editor: FrancoisTadel
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= Single Dipole Scanning =
+= Computing and displaying dipoles =
''Authors: Elizabeth Bock, John C Mosher''
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+Line 4:
+<<TableOfContents(2,2)>>

== Computing sources using the GLS ==
-Line 5:
+Line 9:
-Go to the protocol ''TutorialCTF''.
+. Select the protocol ''TutorialCTF''.  Right-click on ''Subject01 / Left / ERF'' > ''Compute sources''.
 1. In this window, you should select ''Expert Mode''.  You will see the following menu.  Select ''[Test] Mosher GLS''.  Click OK.  Use the default settings in the next menu and click OK.<<BR>><<BR>> {{attachment:compute_GLS.png||height="450",width="279"}}  --- {{attachment:compute_GLS_options.png||height="593",width="289"}}
 1. Two results were added under the ERF: GLS and GLS-P.<<BR>><<BR>> {{attachment:tree_display_GLSP.png||height="188",width="279"}}
  * '''GLS''':
  * '''GLS-P''':
-Line 7:
+Line 15:
-== Computing sources using the GLS ==
+== Dipole Scanning ==
For this tutorial we will do the scanning on the GLS results.  However, the dipole scanning is also available for sources computed with minimum norm Z-scored (i.e. MN MEG(Constr) | zscored), dSPM and sLORETA.
-Line 9:
+Line 18:
-.  Right-click on ''Subject01 / Left /ERF'' > ''Compute sources''. <<BR>><<BR>>
+. Drag and drop the GLS-P link into the Process 1 box.  Click ''Run > Sources > Dipole scanning''.<<BR>><<BR>> {{attachment:process_box_GLSP.png||height="465",width="300"}} ---   {{attachment:select_process_dipolescanning.png||height="262",width="250"}}
 1. Use the defaults options:
  * '''Time Window''': This is the window over which the scanning will occur. The default option is to use the entire epoch.
  * '''Time between dipoles''': This allows you to change the resolution of the scanning.  To use all time points, enter a 0 (default).<<BR>><<BR>> {{attachment:dipole_scanning_options.png||height="250",width="325"}}
 1. The resulting dipole file is added under the Left condition.<<BR>><<BR>> {{attachment:tree_display_dipolefile.png||height="200",width="260"}}
-Line 11:
+Line 24:
-{{attachment:.png}}
+== Displaying Dipoles ==
 1. Right-click ''ERF|GLSP-dipole-scan > Display on cortex''.  The ''Dipoles'' panel is now open and dipoles are displayed on the cortex.  You can now explore the results using the options in the ''Dipoles'' panel:<<BR>><<BR>> {{attachment:dipole_panel.png||height="420",width="300"}}
  * Data options: filter the available dipoles according the specific measurement.  For the GLSP, these are defined as:
   * '''Z-score''':
   * '''Goodness''':
   * '''Chi-square''':
   * '''Reduced Chi-square''':
   * '''Confvolume''':
  * Display options: these options allow for adjusting how the selected dipoles (according to the Data options) are displayed
   * '''Show max goodness''':  will show the dipole with the maximum goodness (within the constraints of the ''Data options'') at the time point selected.  If ''Show all time'' is selected, then this represents the maximum goodness over all time points.
   * '''Show all time''': plots all selected dipoles at all time points.  Unselecting this options will show only the current time point.
   * '''3D - Color dipoles according to Time''', Goodness of Fit, Z-score, Group: adjusts the colormap to reflect the measure.
 1. In the Dipoles panel, select ''Show max goodness of fit'', ''Show all time'', and color the dipoles according to ''Goodness of Fit''.  You should see the following display.  Explore the panel options to familiarize yourself with the capabilities.<<BR>><<BR>> {{attachment:max_GOF_cortex.png||height="200",width="260"}}
-Line 13:
+Line 38:
-.  In this window, you should select ''Expert Mode''.  You will see the following menu.  Select ''[Test] Mosher GLS''.  Click OK and use the default settings of the next menu and click OK.<<BR>><<BR>>
+=== Additional Example ===
Dipole scanning can also be restricted to a scout.  In this example, the scanning is restricted to a scout named '2' and colored according to ''Goodness of Fit''<<BR>><<BR>>
-Line 15:
+Line 41:
-{{attachment:.png}}  --- {{attachment:.png}}
+{{attachment:scanning_options_scouts.png||height="200",width="204"}} --- {{attachment:scan_dipoles_on_scout.png||height="250",width="285"}}
-Line 17:
+Line 43:
-.  Two results were added under the ERF: GLS and GLS-P. <<BR>><<BR>>
{{attachment:.png}}
+== Dipole models from Neuromag's Xfit and CTF's DipoleFit ==
Brainstorm can import dipoles that have been generated using external software:

'''Neuromag Source Modelling module, xfit:''' The .bdip format is described in [[attachment:bdip_format.pdf]]. For more information about xfit and the bdip format see Neuromag Software Manuals.

'''CTF DipoleFit:''' The DipoleFit software and the .dip format is described in the CTF Software Manuals.

'''To import'''

 1. Select the study where you want to import the dipole file
 1. Right click and select ‘Import dipoles’ (Figure 1)
 1. For Neuromag, you will be prompted to specify the number of subsets used for dipole fitting. '''In most cases, this will be one.''' If subsets are used, as defined in the text file $HOME/.meg_analysis/xfit_selections, then the number of subsets used needs to be input when prompted. (Figure 2)<<BR>><<BR>>

{{attachment:import.png||height="455",width="294"}} <<BR>><<BR>> Figure 1. Importing dipoles<<BR>><<BR>> {{attachment:dipoles_subsets_dialog.jpg}} <<BR>><<BR>> Figure 2. Neuromag option for channel subsets<<BR>><<BR>>

 * When displaying dipole files with multiple groups and/or subsets, the ''Loaded dipoles'' panel appears with a list of dipoles, grouped according to event (Group #1, Group#2, etc) and by channel subset, if used (Subset #1, Subset#2, etc.)
  * Select the Group(s) to plot
  * Clicking on a subset will select all Groups with that subset.  For example, selecting Subset #1 will select Group #1 (1), Group #2 (1), Group #3 (1), etc.

=== Examples ===
 * '''Example 1''' shows 5 subsets (channel groups of Left, Right, Anterior, Posterior, All Channels). When subset #2 is selected, dipoles fitted to the right channels are displayed.  In this case, ''Show all time'' is selected for the 4 Groups (events) and colored according to ''Goodness of Fit''<<BR>><<BR>>

{{attachment:subset_group_GOF.png||height="354",width="300"}}

 * '''Example 2''' shows all groups and subsets at one time point (0.3 ms), with goodness of fit greater than 80%, colored according to ''Group''.<<BR>><<BR>>

{{attachment:allgroups_allsubsets_1time.png||height="366",width="300"}}

<<EmbedContent(http://neuroimage.usc.edu/bst/get_feedback.php?Tutorials/TutDipScan)>>

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