EVALUATING THE EFFICACY OF NEUROREHABILITATION PROTOCOLS USING BRAIN CONNECTIVITY ANALYSIS /Heba Ali Abdelbary Ali

Supervisor: Prof. Walid Al-atabany

Thesis (M.A.)—Nile University, Egypt, 2024.

"Includes bibliographical references"

Contents:
CERTIFICATION OF APPROVAL i
CERTIFICATE OF ORIGINALITY ii
ACKNOWLEDGEMENTS iii
LIST OF FIGURES ix
LIST OF TABLES xi
ACRONYMS xiii
ABSTRACT xiv
1 INTRODUCTION 1
1.1 Motivation.................................................................................................................. 1
1.1.1 The importance of brain networks in humans ................................................. 1
1.1.2 The Significance of Brain Connectivity in Stroke Patient Recovery .............. 2
1.2 Problem Statement and Objectives ............................................................................... 5
1.2.1 Problem Definition......................................................................................... 5
1.2.2 Objectives and Contribution........................................................................... 5
1.3 Thesis Structure ......................................................................................................... 6
2 BACKGROUND AND LITERATURE REVIEW 8
v
2.1 Electroencephalography (EEG)................................................................................... 9
2.2 Connectivity of Brain Regions ..................................................................................10
2.2.1 Types of Brain Connectivity .........................................................................11
2.2.2 Difference between Intra and Inter-Brain Connectivity..................................12
2.2.3 Brain Connectivity Identification Techniques................................................14
2.3 Human Connectome Project (HCP)............................................................................17
2.4 Connectivity and Brain Diseases...............................................................................20
2.5 Neural OscillationNetwork......................................................................................21
2.6 Plasticity and Brain Repair........................................................................................22
2.7 Static and Dynamic Functional Connectivity ............................................................24
3 METHODOLOGY 26
3.1 Approach Overview..................................................................................................26
3.2 Datasets....................................................................................................................26
3.2.1 Phase 1 datasets:..........................................................................................28
3.2.2 Phase 2 Dataset: g.tec dataset......................................................................30
3.2.3 Phase 3 Dataset: Aphasia dataset.................................................................33
3.3 Data-Preprocessing ...................................................................................................33
3.3.1 Independent Component Analysis (ICA)........................................................34
3.3.2 Preprocessing of NMT Dataset....................................................................35
3.3.3 Preprocessing of TUH Dataset.....................................................................37
3.3.4 Preprocessing of g.tec Dataset......................................................................37
3.3.5 Preprocessing of Aphasia Dataset................................................................39
3.4 Functional connectivity measurement .......................................................................41
3.4.1 Pearson Correlation.....................................................................................41
3.4.2 Mutual Information .....................................................................................42
3.5 Similarity Measurement of Functional Connectivity Matrix .....................................42
3.6 Graph Representation..............................................................................................43
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4 RESULTS 45
4.1 Phase 1: Differentiation between healthy and pathological Functional Brain
Connectivity ............................................................................................................. 45
4.2 Phase-2: Functional Brain Connectivity for Assessing Post-Stroke Rehabilitation Recovery............................................................................................................. 47
4.2.1 Inter and Intra Functional Connectivity.......................................................... 49
4.2.2 Linear and Nonlinear Techniques for Functional Connectivity ...................... 51
4.2.3 Neural Oscillation Analysis .......................................................................... 53
4.2.4 Graph Representation for Functional Connectivity ........................................ 56
4.3 Phase 3: Post-Stroke Aphasia.................................................................................... 57
5 DISCUSSION 68
5.1 Phase 1: Differentiation between Normal and Abnormal Functional Connectivity Patterns ............................................................................................................... 68
5.2 Phase 2: Functional Brain Connectivity for Assessing Post-Stroke Rehabilitation 69
5.2.1 I: Inter and Intra- Functional Connectivity matrices..................................... 70
5.2.2 II: Frequency Bands and Inter-neuron Networks ........................................... 72
5.2.3 Graph Representation for Brain Functional Connectivity .............................. 74
5.3 Phase 3: Post-Stroke Aphasia Analysis ..................................................................... 77
5.4 Strengths and Limitations........................................................................................... 78
6 CONCLUSION AND FUTURE WORK 79
6.1 Conclusion................................................................................................................ 79
6.2 Future Work.............................................................................................................. 80
A ACHIEVEMENTS 97
A.1 Publications.............................................................................................................. 97
A.2 Awards...................................................................................................................... 97

Abstract:
Stroke is the primary factor behind enduring disabilities, leading to motor and cognitive impairment. Despite receiving standard stroke therapy, most patients remain disabled when
entering the chronic phase. Researchers are exploring alternative approaches to enhance brain
plasticity and connectivity, utilizing effective biomarkers to improve recovery chances.
Enhanced neu- ral activity has been identified as a sign of improved functional recovery.
This work utilizes the functional brain connectivity network to assess the rehabilitation
protocols for post-stroke recovery in two case studies: patients with aphasia and those
with motor deficits. The study demonstrates the success of the primary objective through
three comprehensive research phases that utilized linear and nonlinear techniques for
measuring static and dynamic functional con- nectivity. Our study reveals a consistent
brain connectivity pattern observed in healthy cases, with a prevalence rate of 96% among
all participants. Meanwhile, pathological cases exhibit distinct patterns depending on the
type of abnormality. Furthermore, our results confirm the effectiveness of the rehabilitation
strategies utilized with these patients using functional connec- tivity as a biomarker for
recovery. Additionally, employing functional connectivity can lead to the identification of
hemisphere dominance which helps the neurologist to customize the treatment.
Keywords
Neurorehabilitation, Brain Computer Interface, Functional Brain Connectivity,
Neuroplasticity, Brain Network

Text in English, abstracts in English and Arabic