Bad channels and bad segments
Authors: Francois Tadel, Elizabeth Bock
Contents
From auditory
Bad channels
- During the visual exploration, some channels appeared generally noisier than the others. Example:
Right-click on Run01 > Good/bad channels > Mark some channels as bad
> MRT51, MLO52
Right-click on Run02 > Good/bad channels > Mark some channels as bad
> MRT51, MLO52, MLO42, MLO43
From CTF
Bad channels
If you find out that a sensor has unexpected values, that are not coherent with the other surrounding sensors, you can choose to ignore it in the displays and in the source estimation process. In the channel file, each channel has a flag which indicates if it is good or bad. You may also import recordings files that already have some bad channels defined.
Select a few channels with one of the method described above: click on the time series, click on the sensors dots, right-click and move to select a group of sensors. Then right-click in one of the figures and check out the Channels sub-menu:
View selected: Show the time series of the selected sensors
Mark selected as bad: Remove sensors from the display and all the further computations
Mark non-selected as bad: Keep only the selected channels
Reset selection: Unselect all the selected sensors
Mark all channels as good: Brings back all the channels to display
Edit good/bad channels: Opens an interface that looks like the channel editor, but with one extra column to edit the status (good or bad) of each channel.
Mark channels as bad: Right-click > Channels > Mark selected as bad, or press Delete key. The sensors should disappear in all figures, and the topography view (2D sensors cap) is updated so that the interpolation on the 2D surface now ignores the bad channels.
Get the channels back: two options
Right-click on figure > Channels > Mark all channels as good
Right-click on figure > Channels > Edit good/bad channels... : this menu open a window very similar to the Channel Editor window introduced in previous tutorials, but without the annoying location and orientation values, and with green and red dots. Click on the dots to mark a channel as good or bad.
- Note that if you click on a row in this window, it will select the corresponding channel in the time series and topography figures.
- Close this window to save the changes.
Batching this from the database explorer:
- You will find a "Channels" menu for any node in the tree that contains recordings.
- If you do this on the level of a node, the operation will be applied recursively to all the recordings contained in the node. This way, you can quickly set that the channel 63 is always bad, or that electrode 43 is not working for subject #12, without having to visualize all the recordings one after the other.
The View all bad channels command displays the list of all the bad channels in all the files in the Messages tab, in main Brainstorm window.
Important notes:
The good/bad channel flags are stored in the recordings files, not in the channel files. So if you marked some channels as bad in the ERF data file, there are still considered as good in the Std data file.
ADD BAD CHANNEL MONTAGE
From auditory
Bad segments
- At this point, you should review the entire files, by pages of a few seconds scrolling with the F3 key, to identify all the bad channels and the noisy segments of recordings. Do this with the the EOG channel open at the same time to identify saccades or blinks that were not completely corrected with the SSP projectors. As this is a complicated task that requires some expertise, we have prepared a list of bad segments for these datasets.
Open Run01. In the Record tab, select File > Add events from file:
File name: sample_auditory/data/S01_AEF_20131218_01_notch/events_bad_01.mat
- File type: Brainstorm (events*.mat)
It adds 12 bad segments to the file.
Open Run02. In the Record tab, select File > Add events from file:
File name: sample_auditory/data/S01_AEF_20131218_02_notch/events_bad_02.mat
- File type: Brainstorm (events*.mat)
It adds 9 bad segments and 16 saccades to the file.