Brain–computer interfaces (BCIs) measure brain activity and translate it to control computer programs or external devices. However, the activity generated by the BCI makes measurements for objective fatigue evaluation very difficult, and the situation is further complicated due to different movement artefacts. The BCI performance could be increased if an online method existed to measure the fatigue objectively and accurately. While BCI-users are moving, a novel automatic online artefact removal technique is used to filter out these movement artefacts. The effects of this filter on BCI performance and mainly on peak frequency detection during BCI use were investigated in this paper. A successful peak alpha frequency measurement can lead to more accurately determining objective user fatigue. Fifteen subjects performed various imaginary and actual movements in separate tasks, while fourteen electroencephalography (EEG) electrodes were used. Afterwards, a steady-state visual evoked potential (SSVEP)-based BCI speller was used, and the users were instructed to perform various movements. An offline curve fitting method was used for alpha peak detection to assess the effect of the artefact filtering. Peak detection was improved by the filter, by finding 10.91% and 9.68% more alpha peaks during simple EEG recordings and BCI use, respectively. As expected, BCI performance deteriorated from movements, and also from artefact removal. Average information transfer rates (ITRs) were 20.27 bit/min, 16.96 bit/min, and 14.14 bit/min for the (1) movement-free, (2) the moving and unfiltered, and (3) the moving and filtered scenarios, respectively.
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