... | ... | @@ -120,15 +120,44 @@ Adjust the matrix that is displayed at the bottom until you find the right fit a |
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:so: After doing you first file by manually warping, you will be able to see the transformation matrix that will be used. You can use this matrix to help you get a *head start* ( :smile: ) on the next file, or use this in the config to morph all of the files the same way.
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![warp4](/uploads/0ffd5834f3356d22aae23e0861fe6ff0/warp4.png)
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***
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# Event and Marks Variables
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The pipeline proceeding this script needs to be contain specific events that indicate in-task time and out of task time. This is because ICA analysis is sensitive to messy task time that could contain movement artifacts or non-stationary so we only want to submit the essential data to ICA. To do this the out of task time is flagged using our Out/On/In events to create removal marks. This system uses the [Vised Marks plugin](https://git.sharcnet.ca/bucanl_eeglab_extensions/vised_marks/wikis/home) to do the data flagging.
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:so: If you are building your own ESS capsule or you are lucky these events can be built into the capsule already. Use the HED tags:
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* Custom/Marks/RecStart
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* Custom/Marks/RecStop
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* Custom/Marks/In
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These tags will be identified and used as your On/Off/In events respectively.
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**Onevents/Offevents/Inevents**
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To tell the script where to flag, you need to give it Onevents and Offevents **OR** Inevents.
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* **In events** are events that need to be surrounded in In task time. Any time that is not within 3 sec of an Inevent is considered out of task. This is ideal for studies with many repeated tasks that are within a few seconds of each other.
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* Config Example: A Go/NoGo task with 1 as Go and 2 as NoGo with one or the other every 2 seconds. This task has many short breaks between the sessions. Inevents would be ideal as you could specify ```[Inevent], 1 2```and that would ensure that all of the Go and NoGo tasks are included for ICA, while the breaks and lead up times would be removed.
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* **On/Off events** can also be thought of as *Record On* and *Record Off*. They are specified in pairs to act as boundaries for in task time. Any time on the outside of these events will be marked black and out of task.
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* Config Example: A study where participants are asked to clear their mind for 5 min. The start of this task is event 11 and the end is 22. In this case Inevents would not work, as they would only gather 6sec of the task. Instead if you specify ```[Onevent], 11```and ```[Offevent], 22``` that would ensure that the whole 5min is set as in task recording. Notice how 11 and 22 are a paired set. If 11 was always on but off alternated between 22 and 33, then you would specify the following in the config:```[Onevent], 11 11```and ```[Offevent], 22 33```. 11 is recorded twice but each time it has a different stop indicator. You also have to be weary about the number of events of each type you have in the file. **For every On there must be an Off**, since the marking function uses intervals.
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If you do not have the prebuilt ESS and you don not fill out the config file you will prompted with the following GUI that asks for the same information.
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Depending on which method you are using simply type in the event numbers separated by spaces. If your study does not contain events that suit either of these methods you can manually add *Recording Start* and *Recording Stop* marks. To do this select the *Manual Mode* checkbox.
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**Onevents/Offevents/Inevents**
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![events](/uploads/38fbc765ee402361dffbc6e0f34c0795/events.png)
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If you selected *Manual Mode* then this little GUI will pop up. This GUI simply warns you that you are entering the Vised-Marks editor and that any annotations you use will be added to the marks structure. The two commands you will be using are:
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* ```a``` to drop a RecStart event at your cursor
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* ```b``` to drop a RecStop event at your cursor
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See the example below where we placed events before and after each block of tasks.
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![events2](/uploads/ed4a00ef37fd4d59ed7a979d5f7078c3/events2.png)
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![vised3](/uploads/fcc6034816cd3f29dc38781760c4ea8f/vised3.png)
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After you click *Update Marks Structure* the events that you dropped into the data will be saved into the events information structure. Vised Marks will then proceed to place *Out of task Marks* everywhere outside your boundaries. Below is a example of what the final result will look like if you were to plot the data afterwards.
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![events5](/uploads/8e0c5b4c3044b2c85479bfe184a4f9a4/events5.png)
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These methods may seem like a lot of work but they can easily be simplified by using the events that already exist in the experiment. For the example above if we used Inevents we could have listed all of the event types in the experiment in the config file. We would get the same result as there were no events during the break times. That method would have run automatically and would have saved bunch of time. Consider your experiment when choosing a marking method.
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***
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