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Selecting Marks

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Mike Cichonski edited this page Mar 13, 2019 · 2 revisions

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Selecting Marks

The select marks tool is available in order to select the EEG.data that is or is not currently selected by particular marks. In EEGLAB go to:
Tools -> Marks-> Select Data markwindow

selectmarks This user interface allows you to select the marks that you have added into the data. Simply choose the name of the marks you would like to select by using the| ... | button. The field below should then auto populate with all of the indexes that have been selected for that mark.

To remove marked data select the Remove these indexes button, and click | Ok |. EEGLAB will then prompt you to save the new data file.

This same process can be used when selecting and removing components. Visually identify the unwanted components such as blinks and heartbeats, mark them, then use this tool to remove them from the component data. You can also type the components directly into the user interface.

If you do not select Remove these indexes, then you will be removing all data that does not match the selected indexes.

Editing Marks

This section contains some more information on creating, editing and selecting marks in ways that would be frustratingly difficult by hand. The editing marks section allows you to preform things such as automatically searching for event breaks or flag breaks. You can also add, combine, and delete your marks using the pop up GUIs.

markseditmarks

Collect Reject Structure into Marks Structure

When selecting this option, it will combine the rejected marks from the EEG.reject structure native to EEGLAB into the 'manual' mark in the EEG.marks structure. you will be prompted for the new save name of the data set.

Mark Flag Gaps

This tool can be used to find areas in data where there are no other flags.

  • Mark Labels to Consider:
    You will have to specify what flags you are looking for the absence of. For example if you wanted to mark all the time containing good data, you would list all of the flags that are in bad data.
  • Exact Label: Check this box if the time mark names to consider must be exactly as typed. Uncheck this box to match any time mark that includes a particular string.
  • Critical inter-flag gap:
    This is the minimum gap needed between marks to be considered. The default is set to 3 seconds so good data in a segment of less than 3 seconds will not be considered. This will ensure you are not looking at tiny slivers of time if they are surrounded by bad data.
  • Gap Marks Reference Points:
    • first: use only the onsets of each selected time mark as a boundary
    • second: use only the offsets of each selected time mark as a boundary
    • both: use both onsets and offsets of each selected time mark as a boundary
  • Offset:
    This modifies the gaps by either adding or subtracting from the amount of flagged time points in each gap in either direction. For example, if a 3000ms gap is marked from time points 1001 to 4000 (assuming a sample rate of 1000Hz), and we set the offset to [1000 -500], it will adjust the gap to only cover time points 2001 to 3500.
  • Invert Flags: This option currently has no effect.
  • New Mark Label: Select a name for your new mark!
  • New Mark Color: Select a color for your new mark! These are RGB values normalized from 0 to 1 (e.g. .2 .2 .2)

flaggap

Mark Event Gaps

This tool can be used to mark areas in data around and between specified events.

  • Event Types to Consider:
    You will have to specify what events you are looking for. For example, if you want to mark all the time that is out of task, such as a break, then you would select all of the tasks to consider, and mark those as in_task, or conversely, mark all time points that don't include the selected events as out_task using the invert flags checkbox.
  • {start stop} Interval Event Types Select one or two events to treat as a start and stop marker for marking time periods.
  • Critical inter-flag gap: This is the minimum/maximum gap needed between events to be considered. The default is set to 3 seconds so the mark will only highlight when the wait time between the events is longer than 3 seconds for minimum. If you use the maximum option than you could mark the event gaps that are shorter than your time if you wanted.
  • Gap Marks Reference Points:
    NOTE: Only the 'both' option currently works.
  • Offset:
    This modifies the gaps by either adding or subtracting from the amount of flagged time points in each gap in either direction. For example, if a 3000ms gap is marked from time points 1001 to 4000 (assuming a sample rate of 1000Hz), and we set the offset to [1000 -500], it will adjust the gap to only cover time points 2001 to 3500.
  • New Mark Label: Select a name for your new mark!
  • New Mark Color: Select a color for your new mark! These are RGB values normalized from 0 to 1 (e.g. .2 .2 .2)

eventgap

Combine Flag Types

This tool combines two marks structure into one.

  • Info Type:
    Select the type of mark you are going to edit from the drop down box.
  • Merge:
    This is the mark(s) that is/are going to be merged.
  • Merge Into:
    This is the mark that is going to receive the mark information from the mark(s) selected above. It will contain all of its old indices marked, plus any indices that were unique to the merging marks. This is the function used to combined marks into manual see Manual Marks for reference.
    For both of these fields you can use the | ... | button to select from you list of created marks.

comobomarks

Add/Remove/Clear Marks Flag Type

In this GUI you can add, clear or delete you marks.

  • Action to Perform: select add, clear or delete from the drop down box.
  • Information Type: Select the type of mark you are going to edit from the drop down box.
  • Mark Label: Select the mark that you wish to change. Or type in the name of the new mark you are creating.
  • New Time Mark Color: If you are adding, chose the color of the mark for vised display.
  • Line and Tag Color: If you are adding, chose the color of the line and the color of the tag for vised display.
  • Mark Order: When plotting the scalp channels/components with the vised scroll plot, this determines the Z-axis location of the trace. Values below 0 appear behind the time marks and values above 0 appear in front of the time marks. This is used to determine which type of channel/component marks appear in front of others in the scroll plot. If a particular channel or component is marked for multiple reasons, the mark with the highest order value will be drawn last, which means only the color for the highest ranked mark will be visible.

addsubmarks

These GUIs are very helpful when manually editing files or if you are just getting started. Once you understand how the functions work you can incorporate these actions as function calls and place them in your scripts.

Updated/Verified by Mike Cichonski on 2019-03-13

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