Bad segments and bad epochs

Francois · August 3, 2020, 2:04pm

Hi Marc,

Indeed, this field is not much used in Brainstorm.
It is read from two file formats (EEGLAB .set and EGI .raw) for data that is already fully pre-processed and epoched. These files should not be imported as "raw continuous" but directly as epochs in Brainstorm (using menu "Import MEG/EEG" instead of "Review raw file"), because there is not much that can be done with them otherwise. Therefore I can't see any use case where it would useful for the function GetBadSegment to retreive this info...

When importing EEGLAB .set or EGI .raw files as epochs, the epoch(i).bad info is used to mark the imported trial as good or bad in the Brainstorm database:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_data.m#L151


      
          % Switch between file types

          switch lower(ImportOptions.ImportMode)

              % ===== EPOCHS =====

              case 'epoch'

                  % If all data sets have the same comment: consider them as trials

                  isTrials = (length(sFile.epochs) > 1) && all(strcmpi({sFile.epochs.label}, sFile.epochs(1).label));

                  % Loop on all epochs

                  for ieph = 1:length(ImportOptions.iEpochs)

                      % Get epoch number

                      iEpoch = ImportOptions.iEpochs(ieph);

                      % Import structure

                      BlocksToRead(end+1).iEpoch   = iEpoch;

                      BlocksToRead(end).Comment    = sFile.epochs(iEpoch).label;

                      BlocksToRead(end).TimeOffset = 0;

                      BlocksToRead(end).ImportTime = sFile.epochs(iEpoch).times;

                      % Copy optional fields

                      if isfield(sFile.epochs(iEpoch), 'bad') && (sFile.epochs(iEpoch).bad == 1)

                          BlocksToRead(end).isBad = 1;

                      end

                      if isfield(sFile.epochs(iEpoch), 'channelflag') && ~isempty(sFile.epochs(iEpoch).channelflag)

                          BlocksToRead(end).ChannelFlag = sFile.epochs(iEpoch).channelflag;

The CTF format has such bad epochs (in the file ClassFile.cls) and even bad segments (in the file bad.segments), but they are currently not read by Brainstorm. Is this something we want to do?

No one ever requested this, so I'm not sure it is worth investing time in it.
Do you have any clear use case in which there is some important information that is missing in the CTF recordings as currently processed by Brainstorm?