Raw continuous recording question + channel naming system

mcp0228 · July 28, 2022, 6:04am

Hello Brainstorm community,

I am trying to export the following preprocessed-raw-continuous recording consisting of 15 EEG channels, 2 EOG channels (EXG1 and EXG2) and 3 EMG channels (EXG3-5) into pdf pages of 30-sec epochs for sleep stage scoring and list some related questions. At the moment the EXG1-5 channels are classified within Brainstorm channel editing as EEG but they are actually EOG and EMG channels. This is so that EEG-EOG-EMG channels can be viewed on one page without opening a new window for each channel type.

I know that there is a way to specify channel type (as in EEG, EOG and EMG) using the following process "Import > Channel file > Set channels type".
However is there a Brainstorm process to change the NAME of the channel? I need to change the name of the EOG and EMG channels and was wondering if there is a fast way to do this (the EXG1-5 channels into something like left and right eye and chin muscle).
At the moment you will see at the top right-hand corner (circled in red) that the channels are being viewed at 51uV. Is there a way to specify this differently for each channel?
As in EEG channels get 50uV, EOG and EMG at 25 uV.
What would be the best way to export this continuous recording into 30-sec epochs?
I've tried "Import in database" specifying that the recording be split into 30-sec epochs.
This does not work fully as the epochs do not contain EOG and EMG (which I already specified to be EEG in the continuous recording). They do not appear because through the "Import in database" process, Brainstorm automatically reclassified them as EOG-NO-LOC.

Therefore how would you overcome this problem?
And subsequently, what would be the best way to export all 30-sec epochs into one file so that the end result is one file which I can flick through like a book so that each page equals a 30-sec epoch.

Many thanks in advance.

Francois · July 28, 2022, 9:33am

You could also correctly set the type EOG and EMG channels, and then create a custom montage in order to show the EEG + some non-EEG channels in the same view. Additionally, you'd be able to change the order of the channels, add colors, separators...
https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor#Custom_montage

However is there a Brainstorm process to change the NAME of the channel?

Edit the channel file, and change the names directly in the cells of the table:
https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Prepare_the_channel_file

At the moment you will see at the top right-hand corner (circled in red) that the channels are being viewed at 51uV. Is there a way to specify this differently for each channel?
As in EEG channels get 50uV, EOG and EMG at 25 uV.

With a custom montage, set the EEG channels to be "1 * channel_name" and the EOG/EMG channels to be "0.5 * channel_name".
https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor#Custom_montage

Then use the menus to set manually the amplitude scale, and disable the auto-scale when you change page:
https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Time_and_amplitude_resolution

I've tried "Import in database" specifying that the recording be split into 30-sec epochs.
This does not work fully as the epochs do not contain EOG and EMG (which I already specified to be EEG in the continuous recording). They do not appear because through the "Import in database" process, Brainstorm automatically reclassified them as EOG-NO-LOC.

The "Import to database" does not alter the channel file, it keeps it exactly identical to the original raw file.
If some channels renamed with a type "_NO_LOC", it is because you explicitly added 3D positions to the channel file with the menu "Add EEG positions". Follow carefully the EEG/Epilepsy tutorial:
https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Prepare_the_channel_file

pdf pages of 30-sec epochs
What would be the best way to export this continuous recording into 30-sec epochs?

If your goal is to save images, maybe you don't need to import the files, and could directly export images, either manually of from a script (see out_figure_image.m).
You can also set the current time point or the current page from a script. See tutorial_introduction.m.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/script/tutorial_introduction.m#L494


      
          hFigMeg1  = view_timeseries(sFilesAvg(1).FileName, 'MEG');

          hFigMeg2  = view_timeseries(sFilesAvg(2).FileName, 'MEG');

          hFigEeg1  = view_timeseries(sFilesAvg(1).FileName, 'Misc');

          hFigEeg2  = view_timeseries(sFilesAvg(2).FileName, 'Misc');

          hFigTopo1 = view_topography(sFilesAvg(1).FileName, 'MEG', '2DSensorCap');

          hFigTopo2 = view_topography(sFilesAvg(2).FileName, 'MEG', '2DSensorCap');

          hFigTp2   = view_topography(sFilesAvg(3).FileName, 'MEG', '3DSensorCap');

          hFigTp3   = view_topography(sFilesAvg(3).FileName, 'MEG', '2DDisc');

          hFigTp4   = view_topography(sFilesAvg(3).FileName, 'MEG', '2DLayout');

          % Set time: 90ms

          panel_time('SetCurrentTime', 0.090);

          % Set filters: 40Hz low-pass, no high-pass

          panel_filter('SetFilters', 1, 40, 0, [], 0, [], 0, 0);

          % View selected sensors

          SelectedChannels = {'MLC31', 'MLC32'};

          bst_figures('SetSelectedRows', SelectedChannels);

          view_timeseries(sFilesAvg(4).FileName, [], SelectedChannels);

          % Select time window

          figure_timeseries('SetTimeSelectionManual', hFigMeg1, [0.070, 0.130]);

          % Show sensors on 2DSensorCap topography

          isMarkers = 1;

If you scroll manually, you can use the shortcut F6 instead of F3, to scroll with no overlap with the previous page:
https://neuroimage.usc.edu/brainstorm/Tutorials/ReviewRaw#Mouse_and_keyboard_shortcuts

To score the sleep data in Brainstorm, create custom events shortcuts:
https://neuroimage.usc.edu/brainstorm/Tutorials/EventMarkers#Custom_shortcuts