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Removing artefacts from TMS-EEG recordings using independent component analysis: Importance for assessing prefrontal and motor cortex network properties
Abstract
Introduction The combination of transcranial magnetic stimulation and electroencephalography (TMS-EEG) is emerging as a powerful tool for causally investigating cortical mechanisms and networks. However, various artefacts contaminate TMS-EEG recordings, particularly over regions such as the dorsolateral prefrontal cortex (DLPFC). The aim of this study was to substantiate removal of artefacts from TMS-EEG recordings following stimulation of the DLPFC and motor cortex using independent component analysis (ICA). Methods 36 healthy volunteers (30.8 ± 9 years, 9 female) received 75 single TMS pulses to the left DLPFC or left motor cortex while EEG was recorded from 57 electrodes. A subset of 9 volunteers also received 50 sham pulses. The large TMS artefact and early muscle activity (-2 to ~15 ms) were removed using interpolation and the remaining EEG signal was processed in two separate ICA runs using the FastICA algorithm. Five sub-types of TMS-related artefacts were manually identified: remaining muscle artefacts, decay artefacts, blink artefacts, auditory-evoked potentials and other noise-related artefacts. The cause of proposed blink and auditory-evoked potentials was assessed by concatenating known artefacts (i.e. voluntary blinks or auditory-evoked potentials resulting from sham TMS) to the TMS trials before ICA and evaluating grouping of resultant independent components (ICs). Finally, we assessed the effect of removing specific artefact types on TMS-evoked potentials (TEPs) and TMS-evoked oscillations. Results Over DLPFC, ICs from proposed muscle and decay artefacts correlated with TMS-evoked muscle activity size, whereas proposed TMS-evoked blink ICs combined with voluntary blinks and auditory ICs with auditory-evoked potentials from sham TMS. Individual artefact sub-types characteristically distorted each measure of DLPFC function across the scalp. When free of artefact, TEPs and TMS-evoked oscillations could be measured following DLPFC stimulation. Importantly, characteristic TEPs following motor cortex stimulation (N15, P30, N45, P60, N100) could be recovered from artefactual data, corroborating the reliability of ICA-based artefact correction. Conclusions Various different artefacts contaminate TMS-EEG recordings over the DLPFC and motor cortex. However, these artefacts can be removed with apparent minimal impact on neural activity using ICA, allowing the study of TMS-evoked cortical network properties.
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“During TMS-EEG, participants listened to white noise through intra-auricular earphones (Etymotic Research, ER3-14A, USA) to reduce the influence of auditory processing of the TMS click (Rogasch et al., 2014).”
From Investigation of neurobiological responses to theta burst stimulation during recovery from mild traumatic brain injury (mTBI) (2023) · cites this paper as Rogasch et al., 2014
In the citing paper
“Both rounds of component rejection following FastICA utilised a semiautomated artefact detection algorithm, based on previous research (Rogasch et al., 2014) and using TESA toolbox (Rogasch et al., 2017).”
From Investigation of neurobiological responses to theta burst stimulation during recovery from mild traumatic brain injury (mTBI) (2023) · cites this paper as Rogasch et al., 2014
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TMS measures explored by EEG recordings
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“Lastly, while our pre-processing follows the approach of Rogasch et al., 2014 [28 ], different pre-processing approaches exist in the literature [41 ] and future studies could explore the effects of different pre-processing methods on TEPs characterization.”
TMS-evoked potential propagation reflects effective brain connectivity
Daly, I. P., Williams, N., & Nasuto, S. J. (2024) · Journal of Neural Engineering · doi:10.1088/1741-2552/ad9ee0 · Cited by 2
“Various efforts have been made to develop signal processing pipelines to separate these different effects in the EEG, however they are not able to remove all artifacts and confounds optimally (Rogasch et al 2014, Biabani et al 2019).”
Varmaghani, S., Phlypo, R., Olivier David, A., Harquel, S., & Chauvin, A. (2025) · Journal of Neural Engineering · doi:10.1088/1741-2552/ae01d8 · Cited by 2
“In this study, we address these challenges by introducing a real-time TMS-EEG cleaning method designed for the purpose of closed-loop TMS-EEG, utilizing the widely adopted two-step ICA (Hamidi et al 2010, Rogasch et al 2014, Ross et al 2022) approach.”
InfluentialWang, L., Zang, X., Yang, H., Li, Q., Zhao, Y., Hong, H., He, H., Li, L., Shi, A., Hu, N., et al. (2025) · Brain Connectivity · doi:10.1177/21580014251392466 · Cited by 2
“Concurrent TMS-EEG recordings could provide insights into both cortical excitability and neural circuitry estimations (Casali et al., 2010; Che et al., 2019; Huang et al., 2025; Rogasch et al., 2014).”
Tăuţan, A.-M., Casula, E. P., Borghi, I., Maiella, M., Bonnı̀, S., Minei, M., Assogna, M., Ionescu, B. E., Koch, G., & Santarnecchi, E. (2022) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/embc48229.2022.9871043 · Cited by 2
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Reduced auditory perception and brain response with quiet TMS coil
Murphy, D. L. K., Koponen, L. M., Wood, E. A., Li, Y., Bukhari‐Parlakturk, N., Goetz, S. M., & Peterchev, A. V. (2024) · Brain stimulation · doi:10.1016/j.brs.2024.10.003 · Cited by 2
“The first three TEP components have been frequently identified as the N15-P30-N45 complex: N15 at the stimulation site, more central P30, and parietal N45 [22,46].”
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Alam, M. T., Farooq, H., Khalid, M. N., Kumar, T., & Rasheed, K. (2019) · Communications in computer and information science · doi:10.1007/978-981-13-6052-7_65 · Cited by 2
Towards a causal role of Broca's area in language: A TMS-EEG study on syntactic prediction
Maran, M., Numssen, O., Hartwigsen, G., Friederici, A. D., & Zaccarella, E. (2021) · Cited by 2
Coyle, H. L., Bailey, N. W., Ponsford, J. L., & Hoy, K. E. (2022) · medRxiv · doi:10.1101/2022.06.05.22275980 · Cited by 2
“TEP analysis focussed on four separate peaks known to occur following stimulation of the prefrontal cortex, the N45, P60, N100 and P200 (Rogasch et al. 2015; Rogasch et al. 2014).”
BackgroundMethodSelf-citationEvaluation of GABA A R-mediated inhibition in the human brain using TMS-evoked potentialsPreprint
Šulcová, D., Salatino, A., Ivanoiu, A., & Mouraux, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.31.514225 · Cited by 3
“Data pre-processing generally followed a previously established pipeline [41].”
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“Specific components of the TMS-evoked potential (TEP) and induced oscillatory activity serve as indirect proxies of cortical excitation-inhibition (E/I) balance 14,15 , which appears disrupted in MDD 16 .”
Self-citationThe Past, Current and Future Research in Cerebellar TMS Evoked Responses—A Narrative Review
Fong, P., Rothwell, J. C., & Rocchi, L. (2024) · Brain Sciences · doi:10.3390/brainsci14050432 · Cited by 1
“This procedure has been applied in some reports to reduce vertex potentials evoked by auditory stimulation [70,85,86] and may theoretically be effective in reducing somatosensory responses as well, due to their spatial and temporal overlap [81]; however, further validation is needed before…”
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Cortical dynamics of motivational salience: TMS-EEG and ERP integration in a food cue paradigm
King, F. C., Ismail, F., Statsenko, Y. A., Baylis, G. C., & Ljubisavljević, M. (2025) · NeuroImage · doi:10.1016/j.neuroimage.2025.121679 · Cited by 1
Real-Time Brain-State-Coupled Corticocortical Paired Associative Stimulation of Cognitive Networks
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Mapping human cortical excitability through coupling between robotized TMS and EEG
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“EEG signal processing The EEG preprocessing was performed using the Fieldtrip toolbox for Matlab, and following the methodology described in [3], using two rounds of ICA.”
MethodTask Modulated Cortical Response During Emotion Regulation: A TMS Evoked Potential Study
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MEG/EEG in the Study of Brain Function
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Transcranial Magnetic Stimulation in Speech and Language Research
D’Ausilio, A., Pellicciari, M. C., Casula, E. P., & Fadiga, L. (2023) · Neuromethods · doi:10.1007/978-1-0716-3263-5_10 · Cited by 2
Cortical inhibition on TMS-EEG: interstimulus interval effect on short-interval paired-pulse *
Mijancos-Martínez, G., Bachiller, A., Fernández‐Linsenbarth, I., Romero, S., Alonso, J. F., Molina, V., & Mañanas, M. Á. (2023) · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) · doi:10.1109/embc40787.2023.10340654 · Cited by 1
“The TMS artifact was deleted and interpolated [28].”
MethodSpectral F Test for detecting TMS/EEG responses
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Exploring the properties of the left angular gyrus using TMS-evoked potentialsPreprint
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“One major concern when interpreting TEPs is the inevitable contamination by peripherally evoked sensory potentials (PEPs) (Biabani, Fornito, Mutanen, Morrow, & Rogasch, 2019; Conde et al., 2019).”
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“Referring to previously reported methods [ 33 , 50 , 51 ], the following procedure was used to remove TMS artifacts and noisy epochs: First, a period of the TMS onset to 20 ms was linearly interpolated, as this is the time frame during which the ringing artifact can be visually observed.”
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“Two rounds of independent component analysis (fastICA [36,37]) removed residual artefacts.”
Theta Burst Stimulation of the Human Cerebellum
Harrington, A. (2015) · Otago University Research Archive (University of Otago)
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Radhu, N. (2015) · TSpace (University of Toronto)
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RETRACTED CHAPTER: Artifact Rejection for Concurrent TMS-EEG Data
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“EEG data processing and analysis EEG data were preprocessed and analyzed offline using Brain Vision Analyzer (Brain Products, Inc.) and Matlab (Mathworks, Natick, MA, USA), in a manner modeled after Rogasch et al. (2014).”
MethodSun, Y. (2017) · TSpace (University of Toronto)
Hui, J. (2019) · TSpace (University of Toronto)
Cortical oscillations to measure anti-epileptic drug activity in clinical trialsPreprint
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Towards a causal role of Broca’s area in language: A TMS-EEG study on syntactic predictionPreprint
Maran, M., Numssen, O., Hartwigsen, G., Friederici, A. D., & Zaccarella, E. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.14.439631
“Electromagnetic artifacts are commonly observed following each TMS pulse (Ilmoniemi & Kičić, 2010; Rogasch et al., 2013, 2014; Veniero et al., 2009), and depending on the target location additional large cranial muscular activity can contaminate the EEG signal.”
BackgroundTMS-Evoked EEG Response in Neuropsychiatric Disorders
Gordon, P. C., & Ziemann, U. (2021) · Springer eBooks · doi:10.1007/978-3-030-76136-3_6
Stengel, C., Amengual, J. L., Moreau, T., & Valero‐Cabré, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.22.469553
“Artefact components were identified based on the guidelines by Rogasch et al. (2014).”
MethodMosayebi-Samani, M., Agboada, D., Mutanen, T. P., Haueisen, J., Kuo, M., & Nitsche, M. A. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4173661
MEG/EEG Combined with Other Brain Imaging Methods
Hari, R., & Puce, A. (2023) · doi:10.1093/med/9780197542187.003.0021
Zapata, I. A., Li, Y., & Wen, P. P. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4693533
Fernández‐Linsenbarth, I. (2023) · UVaDOC UVaDOC University of Valladolid Documentary Repository (University of Valladolid) · doi:10.35376/10324/66288
Stroke-induced slow oscillations in dynamic brain organizationPreprint
Tscherpel, C., Mustin, M., Rosjat, N., Ziemann, U., Fink, G. R., Daun, S., & Grefkes, C. (2024) · medRxiv · doi:10.1101/2024.04.07.24305437
Oscillatory TMS-EEG-Responses induced by repetitive transcranial magnetic stimulation
Chen, C., Yang, P., & Zhang, Z. (2024) · International Conference on Computing and Pattern Recognition (ICCPR) · doi:10.1145/3704323.3704352
“The EEG preprocessing followed the general guidelines of earlier studies [32, 33] and TMS-EEG [34–36] processing.”
Corominas-Teruel, X., Bracco, M., Lohof, A. M., Sherrard, R. M., Colomina, M. T., Mahon, S., Charpier, S., & Valero‐Cabré, A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.04.636500
“Eye movements and continuous muscle artifacts were removed through Independent Component Analysis (ICA; 60 ), while the SOUND algorithm was used to suppress recording noise, and the SSP-SIR filter to remove time-locked TMS-evoked muscle artifacts 61,62 if present.”
Bonfanti, D., Bertacco, E., Parra, L. C., Mazzi, C., & Savazzi, S. (2025) · Clinical Neurophysiology · doi:10.1016/j.clinph.2025.03.041
“Independent component analysis (ICA) (Delorme et al., 2007) was then used to remove the tail-end of the muscle artifact due to the TMS pulse (Rogasch et al., 2014, Rogasch et al., 2017).”
Aging alters face expressions processing and recognition: insights on possible neural mechanisms
Ginatempo, F., Loi, N., Zeroual, M., Cadoni, M. I., Fadda, M., Lagorio, A., & Deriu, F. (2025) · Journal of Neurophysiology · doi:10.1152/jn.00237.2024
Electromagnetic interference suppression in combined tACS-rTMS therapy
Wu, N., Li, J., Wu, Z., Wang, P., Zhang, C., Wu, C., Huo, X., & Zhang, G. (2025) · Biomedical Physics & Engineering Express · doi:10.1088/2057-1976/adf4ed
Effect of transcranial magnetic pulses on cortical network connectivity in schizophrenia
Molina, V., Ruiz-Gómez, S. J., Fernández‐Linsenbarth, I., Beño‐Ruiz‐de‐la‐Sierra, R. M., Osorio, E., Roig, A., Mijancos-Martínez, G., Rodríguez-Valbuena, C., Bachiller, A., Mañanas, M. Á., et al. (2025) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2025.111471
Han, Y., Huang, Z., Wang, Y., Liu, Y., He, J., Gao, Z., Fitzgerald, P. B., Daskalakis, Z. J., & Che, X. (2025) · Cerebral Cortex · doi:10.1093/cercor/bhaf310 · Cited by 1
Self-citationSleep-like slow waves in wakefulness index post-stroke behavioural alterations
Pearce, D. J., Biabani, M., Brosnan, M. B., Chong, T. T. ‐., Demeyere, N., Loughnane, G. M., Mattingley, J. B., Moore, M. J., New, P. W., Rangelov, D., et al. (2026) · Journal of Neurophysiology · doi:10.1101/2025.11.24.689850
“Finally, using FastICA we applied an automated Independent Component Analysis (ICA) procedure to remove artifacts related to ocular and muscular movement (Hyvärinen & Oja, 2000; Rogasch et al., 2014).”
Murphy, N., Tomasevic, L., Graziadio, S., Peraza, L. R., Rochester, L., & Taylor, J. (2015) · doi:10.13140/rg.2.1.3580.8805
Mijancos-Martínez, G., Fernández‐Linsenbarth, I., Bachiller, A., Beño‐Ruiz‐de‐la‐Sierra, R. M., Osorio-Iriarte, E., Roig-Herrero, A., Rodríguez-Valbuena, C., Talavera, J. C. F., Ruiz-Gómez, S. J., Mancha, R. D., et al. (2025) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2025.111593
Jan-Cordón, D. E. (2025) · Neuroscience Informatics · doi:10.1016/j.neuri.2025.100254
Assessing SICI Cortical Inhibition With DLPFC TMS‐EEG Using Different ISI Values
Mijancos-Martínez, G., Bachiller, A., Fernández‐Linsenbarth, I., Ruiz-Gómez, S. J., Romero, S., Molina, V., & Mañanas, M. A. (2026) · Psychophysiology · doi:10.1111/psyp.70229
“Different TMS protocols exist to assess cortical excitability/inhibition, plasticity, or connectivity variations (Kropotov 2016; Ilmoniemi and Kičić 2010; Cao et al. 2021; Rogasch et al. 2014; Kallioniemi et al. 2022).”
Huntington, H. R., Phelps, C. E., Lehmann, T., Büchel, D., Khurana, A., Wang, L., Patel, A. A., Olshausen, C. E., Kayali, L. J., Boluordi, T., et al. (2026) · Brain Sciences · doi:10.3390/brainsci16020156
“Based on the fastICA decomposition, the pop_tesa_compselect function was used to remove components containing TMS-induced muscle artifacts, ocular artifacts, muscle activity, and electrical noise, following the approach described by Rogasch et al. [43,45].”
The effect of EEG lead configuration on early TMS–EEG artifactsPreprint
Lankinen, K., Fadel, G., Nummenmaa, A. R., Ilmoniemi, R. J., & Raij, T. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.10.705170
“…developed software means for modeling (Freche et al., 2018) and removing the decay artifact and other TMS–EEG artifacts (Mäki and Ilmoniemi, 2011; Rogasch et al., 2014; Mutanen et al., 2016; Casula et al., 2017; Wu et al., 2018; Mutanen et al., 2020; Rogasch et al., 2022; Metsomaa et al., 2024;…”
Abedi, A., Moradi, G. H., Shirazi, R. S., & Jahed, M. (2025) · National and International Iranian Conference on Biomedical Engineering (ICBME) · doi:10.1109/icbme68496.2025.11392443
“Independent Component Analysis was applied to remove eye and muscle artifacts [46,52].”
Personalizing neuromodulation for chronic pain: A connectivity-guided randomized trialPreprint
Martino, E. D., Bach, M. M., Couto, B. A., Jakobsen, A., Martins, P. N., Ingemann-Molden, S., Casali, A. G., Graven‐Nielsen, T., & de Andrade, D. C. (2026) · medRxiv · doi:10.64898/2026.03.02.26347430
Hao, W., Ding, X., Ren, K., Cui, C., Zhang, Y., He, J., Guo, X., Wang, Y., Ju, H., & Lin, Y. (2026) · BMC Psychiatry · doi:10.1186/s12888-026-07978-2
“Independent component analysis (ICA) was used to remove artifacts, including eye movement (EOG), muscle (EMG) and TMS-induced artifacts (TMS pulse artifacts were removed by TESA’s built-in artifact subtraction algorithm) [18].”
Applications of robotized cortical stimulation mapping
Passera, B. (2021) · theses.fr (ABES) · doi:10.70675/06abbd79z4119z4be5z9b98z2fe1e2bebce3
Integrated Noninvasive Brain Imaging Advancements: A Multimodal Approach
Balasubramanian, S., Patel, P., Kathi, S., Joseph, R., & Annavarapu, R. N. (2026) · IEEE Journal of Selected Areas in Sensors · doi:10.1109/jsas.2026.3685662
“These are removed by various filters [78] and by computational methods, such as independent component analysis [79].”
Cognitive load modulates cortical excitability in the human prefrontal cortexPreprint
Hassan, U., Forman, L., Hartford, J. D., Lee, H., Parmigiani, S., Chen, N.-F., Ross, J. M., Solomon, E. A., Gogulski, J., Kim, N., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.25.720856
Lin, H.-S., Lee, C.-M., Ye, L.-X., Chen, S.-H., Chiu, P., Huang, C.-H., Hsieh, C.-Y., Chen, H.-S., & Wu, T. (2026) · Research Square · doi:10.21203/rs.3.rs-9667442/v1
Different modulation patterns of theta and gamma dual-site HD-tACS on cognitive impairment
Hao, W., Yu, X., Zhou, Q., Jia, Y., Su, X., Yu, Y., Wang, Y., Wang, J., & Liu, C. (2026) · iScience · doi:10.1016/j.isci.2026.116138
Sayalı, C., Gogulski, J., Granö, I., Jaro, D., Weisman, E., Lofland, G., Lioumis, P., & Barrett, F. S. (2026) · Clinical Neurophysiology · doi:10.1016/j.clinph.2026.2112327
Zhang, Q., Zhang, D., Alimu, G., Guragai, B., Li, W., Zhang, J., Jin, Z., & Li, L. (2026) · Neuroscience · doi:10.1016/j.neuroscience.2026.07.011
Metadata
- Authors
- Rogasch, N. C., Thomson, R. H., Farzan, F., Fitzgibbon, B. M., Bailey, N. W., Hernandez-Pavon, J. C., Daskalakis, Z. J., & Fitzgerald, P. B.
- Affiliations
- The Alfred Hospital (AU)
- Centre for Addiction and Mental Health (CA)
- Aalto University (FI)
- Corresponding author
- Rogasch, Nigel C.
- ORCID
- Venue
- NeuroImage
- Publisher
- Elsevier BV
- Published
- 2014-11
- Volume
- 101
- Pages
- 425-439
- ISSN
- 1053-8119 (ISSN-L)
- OpenAlex
- W1969040087
- Cited by
- 309
- References
- 77
- Citations by year
- 2026: 34 · 2025: 28 · 2024: 25 · 2023: 33 · 2022: 36 · 2021: 34 · 2020: 18 · 2019: 26 · 2018: 26 · 2017: 22 · 2016: 19 · 2015: 7 · 2014: 1
- FWCI
- 7.89
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- NeuroImage (publishedVersion)
- PubMed (publishedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Funders
- Pfizer
- BrainsWay
- National Health and Medical Research Council
- National Medical Research Council
- Topics
- Life Sciences › Neuroscience › Neurology › Transcranial Magnetic Stimulation Studies
- Life Sciences › Neuroscience › Cognitive Neuroscience › EEG and Brain-Computer Interfaces
- Physical Sciences › Computer Science › Signal Processing › Blind Source Separation Techniques
- Keywords
- TMS-EEG, artifact removal, independent component analysis, TMS-evoked potentials, dorsolateral prefrontal cortex, motor cortex, auditory evoked potentials, FastICA, EEG signal processing
- MeSH terms
- Adult, Data Interpretation, Statistical, Electroencephalography, Evoked Potentials, Female, Humans, Male, Motor Cortex, Artifacts, Prefrontal Cortex, Transcranial Magnetic Stimulation, Young Adult
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