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## page was renamed from MontageEditor | |
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=== Sensor selection === Let's switch to a nicer representation of the recordings time series: click on the "Display mode" button in the toolbar of the Record tab. |
''Authors: Francois Tadel, Martin Cousineau'' |
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{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawViewer?action=AttachFile&do=get&target=tsColumn.gif|tsColumn.gif|class="attachment"}} | <<TableOfContents(2,2)>> |
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Now the traces are displayed in columns, but all the channels are displayed in the same figure, which makes it unreadable. Select a subset of channels by right-clicking on the figure > '''Montages''', with the drop-down menu in the Record tab or with a keyboard shortcut ('''Shift+A, B, C'''...). Default groups of sensors are available for some MEG systems, but you can also create your own groups of sensors with the menu "Edit montages". | The display of the time series figures can be configured using montages of sensors. The term ''montage ''in the Brainstorm interface can refer to a simple sub-selection of data channels, or a linear recombination of these channels (eg. average reference or other EEG re-referecing montage). The selection of channels was already introduced in the tutorials [[http://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw#Montage_selection|Continuous recordings]] and [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Multiple_montages|EEG and epilepsy]]. This page illustrates how to use the montage editor to create custom displays. |
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{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutRawViewer?action=AttachFile&do=get&target=tsChannelSelection.gif|tsChannelSelection.gif|class="attachment"}} | == Pre-defined montages == The interface offers some pre-defined montages for standard acquisition systems: MEG (Elekta-Neuromag, CTF, Yokogawa, 4D), EEG (10-20 and 10-10 caps) and NIRS (overlay of multiple wavelengths). The montage menu is accessible from the Record tab or with the popup menu on the time series figures. |
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== Montages == A better way to review a large number of MEG/EEG signals at once is to display only a subset of them at once. This can be done using the "montage" interface. The term refers mainly to EEG, to define the referencing system used to display the values recorded on the electrodes: bipolar montages, custom reference electrodes, average reference. However, the same interface can be used in MEG to select only a subset of sensors in a given figure, using a predefined or custom set of channels. |
The keyboard shortcuts (Shift+A, Shift+B, etc), allow to jump quickly to a different montage (see [[https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor#Assigning_a_keyboard_shortcut|Assigning a keyboard shortcut]]). To display a second montage on the same recordings, open again the same file (right-click > Display time) and change the montage of the second window, as illustrated in the tutorial [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Multiple_montages|EEG and epilepsy]]. |
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* Use the drop-down menu in the Record tab to several predefined sets (ex. CTF LF = Group of left frontal sensors). Alternatively, right-click on the figure > Montage. You may need to decrease again the gain of the channels (use SHIFT+Mouse wheel) | . {{attachment:menu_popup.gif||height="293",width="689"}} |
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{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings?action=AttachFile&do=get&target=selectionsMenu.gif|selectionsMenu.gif|class="attachment"}} | == Edit montages == To edit/create your own montages, use the menu "Edit montages". By default, it shows only the montages that are relevant to the type of recordings you are currently looking at (in the example below: EEG 10-20). To see all the available options, click on the button "All". |
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* Note the keyboard shortcuts: '''SHIFT+letter'''. It makes it really easy to switch from a group of sensors to another (ex: Shift+A = all sensors, Shift+B = Left-frontal, Shift+C=Right-frontal...) | . {{attachment:all_montages.gif}} |
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* To edit/create your own selections, use the menu "Edit montages". You can edit the channels selection groups or the electrodes montages available for this installation of Brainstorm. By default, it shows only the ones that are relevant to the type of recordings you are currently looking at (in this case: CTF MEG recordings). To see all the available options, click on the button "All". | To create a new montage, click on the drop-down menu in the toolbar, the select the appropriate option (detailed in the following sections). |
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* Click on "New channel selection" to create a new selection Test1, and select a few channels in the list. | . {{attachment:new_montage.gif}} |
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{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings?action=AttachFile&do=get&target=selections.gif|selections.gif|class="attachment"}} | == Channel selection == To create a new selection of data channels, select the menu '''New channel selection''', enter a name for your montage, then select the channels you want to display in the list of available channels (hold the Shift or Ctrl/Command key to select multiple channels). |
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* Click on Save. Back to the time series figure. Look in the popup menu again, you can see your new selection in the menu: Test1. You can now use the time series view with those predefined selections of sensors. | In the figure, the channels are displayed in the same order as they are defined in the channel file. If you want to change the display order of the channels, you need to create a custom montage. |
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* To display several montages at the same time, or with different different display options, you need to open twice the same file and then set the parameters differently. You have two option to clone the figure: * Do twice: Right-click on the file in the database explorer > MEG > Display time series |
. {{attachment:selection.gif}} |
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* Right-click on a figure > Figure > Clone figure | == Custom montage == All the other types of montages that you can edit are '''custom montages'''. They let you define line by line what to display in the time series figures. A montage is represented as a short text file, with one line of text per signal to display. A signal is a linear combination of one or more channels of data. The generic syntax to represent the sum of N channels ''ch,,i,,'' with individual weights ''w,,i,,'' is: |
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* To have the same scale in both figures, use the buttons "..." in the figures | {{{ label|color : w1*ch1, w2*ch2, ..., wN*chN }}} The screen capture below illustrates a few examples. |
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{{http://neuroimage.usc.edu/brainstorm/Tutorials/TutExploreRecodings?action=AttachFile&do=get&target=figClone.gif|figClone.gif|class="attachment"}} | * '''Line1''': Channel F7. * '''Line2''': Channel F8. * '''Line3''': Subtraction (F7 - F8). * '''Line4''': Subtraction (F7 - F8), displayed in green. * '''Color''': Indicated in hexadecimal notation RRGGBB, use any [[http://www.w3schools.com/colors/colors_picker.asp|HTML color picker]] for help. * '''Line5''': Channel F7 in red and channel F8 in blue ('''overlay''' signals by giving them the same label). * '''Line6''': Computes "FC1 - 0.5*F7 - 0.5*F8" (typical syntax for a linked re-referencing). * '''Separator''': A line that contains only ":" * '''Line7''': Channel ECG, with a fixed scaling factor 0.05 (so that it can be displayed in the same figure).<<BR>><<BR>> {{attachment:custom.gif}} == Re-referencing montage == The menus '''New re-referencing montage (single ref)''' or '''(linked ref)''' are shortcuts to create custom montages that subtract the values of one or two channels to all the other channels. . {{attachment:ref_montage.gif}} Every time you select one of these menus, you get the warning below. The montages are not applied to the recordings, they are for visualization only. To re-reference correctly your EEG recordings, use the process "Standardize > Re-reference EEG". . {{attachment:ref_warning.gif}} == Average reference == A special type of montage is available for re-referencing the EEG/SEEG/ECoG recordings to an average reference. It subtracts from each channel the average of all the channels. It cannot be edited and is displayed as a matrix with (1-1/N,,chan,,) on the diagonal and (-1/(N,,chan,,-1)) everywhere else. . {{attachment:avgref.gif}} For ECoG and sEEG recordings, the average reference is computed separately for each '''group of contacts''', typically each grid/strip or depth electrode. The groups of channels are defined with the field Group in the channel file, and can be edited with the channel editor (right-click on the channel file > Edit channel file). {{attachment:avgref_seeg.gif}} == Apply a montage to the recordings == The montage selection is only a visualization option, it never modifies the recordings. If you want to apply a specific montage to the recordings, you can use two processes: * '''Standardize > Re-reference EEG''': Only available for continuous recordings, see [[http://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Average_reference|EEG and Epilepsy]]. * '''Standardize > Apply montage''': Only available for imported epochs, usually not recommended. == Assigning a keyboard shortcut == You can easily switch between montages directly from figures by assigning a keyboard shortcut to a montage (Shift+A to Shift+Z). Shift + A is reserved for All channels, but you are free to assign any other letter to the montage of your choice. In order to do so, select your montage of interest in the Montage editor and click on the keyboard icon. . {{attachment:montage_keyboard.png}} You will then be prompted to enter a letter key (B to Z). . {{attachment:montage_hotkey.png}} If a valid letter is entered, the shortcut will be automatically be saved and appear next to the chosen montage. If another montage had the same shortcut, it will be overwritten. . {{attachment:montage_hotkey_chosen.png}} . <<EmbedContent(http://neuroimage.usc.edu/bst/get_feedback.php?Tutorials/MontageEditor)>> |
Montage editor
Authors: Francois Tadel, Martin Cousineau
Contents
The display of the time series figures can be configured using montages of sensors. The term montage in the Brainstorm interface can refer to a simple sub-selection of data channels, or a linear recombination of these channels (eg. average reference or other EEG re-referecing montage). The selection of channels was already introduced in the tutorials Continuous recordings and EEG and epilepsy. This page illustrates how to use the montage editor to create custom displays.
Pre-defined montages
The interface offers some pre-defined montages for standard acquisition systems: MEG (Elekta-Neuromag, CTF, Yokogawa, 4D), EEG (10-20 and 10-10 caps) and NIRS (overlay of multiple wavelengths). The montage menu is accessible from the Record tab or with the popup menu on the time series figures.
The keyboard shortcuts (Shift+A, Shift+B, etc), allow to jump quickly to a different montage (see Assigning a keyboard shortcut). To display a second montage on the same recordings, open again the same file (right-click > Display time) and change the montage of the second window, as illustrated in the tutorial EEG and epilepsy.
Edit montages
To edit/create your own montages, use the menu "Edit montages". By default, it shows only the montages that are relevant to the type of recordings you are currently looking at (in the example below: EEG 10-20). To see all the available options, click on the button "All".
To create a new montage, click on the drop-down menu in the toolbar, the select the appropriate option (detailed in the following sections).
Channel selection
To create a new selection of data channels, select the menu New channel selection, enter a name for your montage, then select the channels you want to display in the list of available channels (hold the Shift or Ctrl/Command key to select multiple channels).
In the figure, the channels are displayed in the same order as they are defined in the channel file. If you want to change the display order of the channels, you need to create a custom montage.
Custom montage
All the other types of montages that you can edit are custom montages. They let you define line by line what to display in the time series figures. A montage is represented as a short text file, with one line of text per signal to display. A signal is a linear combination of one or more channels of data. The generic syntax to represent the sum of N channels chi with individual weights wi is:
label|color : w1*ch1, w2*ch2, ..., wN*chN
The screen capture below illustrates a few examples.
Line1: Channel F7.
Line2: Channel F8.
Line3: Subtraction (F7 - F8).
Line4: Subtraction (F7 - F8), displayed in green.
Color: Indicated in hexadecimal notation RRGGBB, use any HTML color picker for help.
Line5: Channel F7 in red and channel F8 in blue (overlay signals by giving them the same label).
Line6: Computes "FC1 - 0.5*F7 - 0.5*F8" (typical syntax for a linked re-referencing).
Separator: A line that contains only ":"
Line7: Channel ECG, with a fixed scaling factor 0.05 (so that it can be displayed in the same figure).
Re-referencing montage
The menus New re-referencing montage (single ref) or (linked ref) are shortcuts to create custom montages that subtract the values of one or two channels to all the other channels.
Every time you select one of these menus, you get the warning below. The montages are not applied to the recordings, they are for visualization only. To re-reference correctly your EEG recordings, use the process "Standardize > Re-reference EEG".
Average reference
A special type of montage is available for re-referencing the EEG/SEEG/ECoG recordings to an average reference. It subtracts from each channel the average of all the channels. It cannot be edited and is displayed as a matrix with (1-1/Nchan) on the diagonal and (-1/(Nchan-1)) everywhere else.
For ECoG and sEEG recordings, the average reference is computed separately for each group of contacts, typically each grid/strip or depth electrode. The groups of channels are defined with the field Group in the channel file, and can be edited with the channel editor (right-click on the channel file > Edit channel file).
Apply a montage to the recordings
The montage selection is only a visualization option, it never modifies the recordings. If you want to apply a specific montage to the recordings, you can use two processes:
Standardize > Re-reference EEG: Only available for continuous recordings, see EEG and Epilepsy.
Standardize > Apply montage: Only available for imported epochs, usually not recommended.
Assigning a keyboard shortcut
You can easily switch between montages directly from figures by assigning a keyboard shortcut to a montage (Shift+A to Shift+Z). Shift + A is reserved for All channels, but you are free to assign any other letter to the montage of your choice. In order to do so, select your montage of interest in the Montage editor and click on the keyboard icon.
You will then be prompted to enter a letter key (B to Z).
If a valid letter is entered, the shortcut will be automatically be saved and appear next to the chosen montage. If another montage had the same shortcut, it will be overwritten.