====== EEG Remarking Status Channel ======

"Remarking" is part of the preprocessing pipeline. For more see [[:tools:eeg_7t_preprocessingpipeline|EEG Preprocessing Pipeline for 7T/BrainMechR01]]

===== Why =====

The BioSemi device used in [[:tools:loefeeg]] records in [[https://www.biosemi.com/faq/file_format.htm|24-bits]] on the [[https://www.biosemi.com/faq/trigger_signals.htm|Status Channel (16 available for task)]]. Matlab and python read in 32-bits. Task "trigger"/"TTL" values in the ''Status'' channel are read in offset from what is sent/intended-to-be-recorded. More info about the BDF format on [[https://www.fieldtriptoolbox.org/getting_started/biosemi/#the-bdf-fileformat|fieldtriptoolbox's page]], and for more on bit masking, see mne python's [[https://mne.tools/dev/generated/mne.io.read_raw_bdf.html#:~:text=to%20retrieve%20correct%20event%20values%20(bits%201-16)%2C%20one%20could%20do|read_bdf documentation]]. Also see [[https://wiki.besa.de/index.php?title=Reading_BioSemi_data_with_BESA|BESA's note on "negative logic"]] (maybe why our status channel has negative values).

Additionally, tasks may send more information than desired for analsyis. E.g. we may want to group all prep events into a single type but the task sends different triggers for various types of prep events. Remarking would collapse all of these (say values 100-150) into a single event code (say 100). 

===== Code =====

TODO: example matlab code? link to github functions (fix_stim_channel).