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marks.md
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[[_TOC_]] [[_TOC_]]
# Vised Marks Structure # Vised Marks Structure
Vised Marks is composed of a series of structures found in the EEG structure. The main structure is called **marks** but the basis is composed of three main structures. One for time, one for channels and one for components. Vised Marks is composed of a series of structures found within the EEG structure. The main structure is called **marks** but the basis is composed of three main structures. One for time, one for channels and one for components.
``` ```
>> EEG.marks >> EEG.marks
...@@ -14,14 +14,15 @@ ans = ...@@ -14,14 +14,15 @@ ans =
![markschartcorrectnums](/uploads/2b63ce2c7507b718b94e47edff23b7e6/markschartcorrectnums.png) ![markschartcorrectnums](/uploads/2b63ce2c7507b718b94e47edff23b7e6/markschartcorrectnums.png)
Each of the info structures also contains many sub structure for each set of marks criteria. Each of the info structures also contains many sub structures containing more information about each mark type.
# time.info # time.info
The time info structure is good for storing information on times of data which need to be removed or otherwise isolated. If removed this will create a time jump boundary and effects all of the channels during this time period. The visually annotation will appear as a coloured bar across the time windows that follow the criteria. The time info structure is good for storing information on times or periods of data which need to be removed or otherwise isolated. If removed this will create a time jump boundary and effects all of the channels during this time period. The visually annotation will appear as a coloured bar across the time windows that follow the criteria.
The time info structure contains the following fields: The time info structure contains the following fields:
* **Label**: The name of the mark structure, usually based off the criteria, or is the manual label. * **Label**: The name of the mark structure, usually based off the criteria, or is the manual label.
* **Color**: Color of the highlighted mark in the *visually edit in scroll plot* display. Described with [R G B]. * **Color**: Color of the highlighted mark in the *visually edit in scroll plot* display. Described with [R G B].
* **Flags**: The array containing a 0 or 1 for each point of time data. 1 indicating this point will be marked. * **Flags**: The array containing a 0 or 1 for each point of time data. 1 indicating this point will be marked.
An example flag would be to flag time before events start indicating pre-task time.
# chan.info # chan.info
The channel info structure is good for storing information on particular channels which need to be removed or otherwise isolated. The visually annotation changes the colour of the data plot line, and places a tag on the left side of the window by the channel name. The channel info structure is good for storing information on particular channels which need to be removed or otherwise isolated. The visually annotation changes the colour of the data plot line, and places a tag on the left side of the window by the channel name.
...@@ -31,7 +32,8 @@ The channel info structure contains the following fields: ...@@ -31,7 +32,8 @@ The channel info structure contains the following fields:
:so: Typically a lighter color to *"grey out"* bad channels :so: Typically a lighter color to *"grey out"* bad channels
* **Tag Color**: Color of channel tag located by the channel name in the *visually edit in scroll plot* display. Described with [R G B]. * **Tag Color**: Color of channel tag located by the channel name in the *visually edit in scroll plot* display. Described with [R G B].
* **Order** : ---__----___---__----___---___----__----___---___ * **Order** : ---__----___---__----___---___----__----___---___
* **Flags**: The array containing a 0 or 1 for each channel. 1 indicating this channel will be marked. * **Flags**: The array containing a 0 or 1 for each channel, 1 indicating this channel will be marked.
An example flag would be to find channels that share too much correlation, indicating a bridged pair.
# comp.info # comp.info
The component info structure is good for storing information on particular component which need to be removed or otherwise isolated. It works the same way as the channel info structure. The visually annotation changes the colour of the data plot line, and places a tag on the left side of the window by the component name. The component info structure is good for storing information on particular component which need to be removed or otherwise isolated. It works the same way as the channel info structure. The visually annotation changes the colour of the data plot line, and places a tag on the left side of the window by the component name.
...@@ -41,9 +43,14 @@ The component info structure contains the following fields: ...@@ -41,9 +43,14 @@ The component info structure contains the following fields:
:so: Typically a lighter color to *"grey out"* bad components. :so: Typically a lighter color to *"grey out"* bad components.
* **Tag Color**: Color of component tag located by the channel name in the *visually edit in scroll plot / ICA* display. Described with [R G B]. * **Tag Color**: Color of component tag located by the channel name in the *visually edit in scroll plot / ICA* display. Described with [R G B].
* **Order** : ---__----___---__----___---___----__----___---___ * **Order** : ---__----___---__----___---___----__----___---___
* **Flags**: The array containing a 0 or 1 for each component. 1 indicating this component will be marked. * **Flags**: The array containing a 0 or 1 for each component. 1 indicating this component will be marked.
An example flag would be to mark the components that do not replicate across parallel AMICA runs.
:so: :b: Sub structure 1 for each of the info structures is created with the *label* **manual**. This structure is usually a dependent array based off of the location of the other independent flag structures. See [Creating Marks by Script](https://git.sharcnet.ca/bucanl_eeglab_extensions/vised_marks/wikis/vised) to find the code that does this. # Manual Marks
:so: :b: Sub structure 1 for each of the info structures is created with the *label* **manual**. This structure is usually a dependent array based off of the indices of the other independent flag structures. See [Creating Marks by Script](https://git.sharcnet.ca/bucanl_eeglab_extensions/vised_marks/wikis/vised) to find the code that does this.
***
**Example of Time Flags** **Example of Time Flags**
...@@ -68,7 +75,7 @@ The component info structure contains the following fields: ...@@ -68,7 +75,7 @@ The component info structure contains the following fields:
| 10 | 1 | 1 | 1 | | 10 | 1 | 1 | 1 |
# Useful Commands # Useful Commands
Since all the marks structures are simply composed of 0's or 1's there are some useful commands that can be used to quickly isolate the marks. In the example below the *manual* faged channels will be removed from the data set. Since all the marks structures are simply composed of 0's or 1's there are some useful commands that can be used to quickly isolate the marks. In the example below the *manual* flaged channels will be removed from the data set.
**Find**: Will find all of the 1's in the array and return their indexes. **Find**: Will find all of the 1's in the array and return their indexes.
* eg. (x = find(EEG.marks.chan_info(1).flags)) to find out which channels will be removed. * eg. (x = find(EEG.marks.chan_info(1).flags)) to find out which channels will be removed.
...@@ -82,6 +89,7 @@ Since all the marks structures are simply composed of 0's or 1's there are some ...@@ -82,6 +89,7 @@ Since all the marks structures are simply composed of 0's or 1's there are some
**Find + Length**: Will find how many indices have been marked. **Find + Length**: Will find how many indices have been marked.
* eg. (x = length(find(EEG.marks.chan_info(1).flags))) to find out how many channels will be removed. * eg. (x = length(find(EEG.marks.chan_info(1).flags))) to find out how many channels will be removed.
You also have the ability in the function call marks_epochs2continuous to 'invert' 'on' and invert all of the 0s to 1s and 1s to 0s for the marks array. This can let you quickly isolate the channel or component in question. For example if you wanted to isolate a certain component like the you could mark it then invert the array to select and 'remove' 'on' to remove all the unwanted components.
*** ***
[ :house: **Return to Main Page**](https://git.sharcnet.ca/bucanl_eeglab_extensions/vised_marks/wikis/home) [ :house: **Return to Main Page**](https://git.sharcnet.ca/bucanl_eeglab_extensions/vised_marks/wikis/home)
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