@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

package/bin/skills/neurokit2/references/eog.md

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+# Electrooculography (EOG) Analysis
+
+## Overview
+
+Electrooculography (EOG) measures eye movements and blinks by detecting electrical potential differences generated by eye position changes. EOG is used in sleep studies, attention research, reading analysis, and artifact correction for EEG.
+
+## Main Processing Pipeline
+
+### eog_process()
+
+Automated EOG signal processing pipeline.
+
+```python
+signals, info = nk.eog_process(eog_signal, sampling_rate=500, method='neurokit')
+```
+
+**Pipeline steps:**
+1. Signal cleaning (filtering)
+2. Blink detection
+3. Blink rate calculation
+
+**Returns:**
+- `signals`: DataFrame with:
+  - `EOG_Clean`: Filtered EOG signal
+  - `EOG_Blinks`: Binary blink markers (0/1)
+  - `EOG_Rate`: Instantaneous blink rate (blinks/min)
+- `info`: Dictionary with blink indices and parameters
+
+**Methods:**
+- `'neurokit'`: NeuroKit2 optimized approach (default)
+- `'agarwal2019'`: Agarwal et al. (2019) algorithm
+- `'mne'`: MNE-Python method
+- `'brainstorm'`: Brainstorm toolbox approach
+- `'kong1998'`: Kong et al. (1998) method
+
+## Preprocessing Functions
+
+### eog_clean()
+
+Prepare raw EOG signal for blink detection.
+
+```python
+cleaned_eog = nk.eog_clean(eog_signal, sampling_rate=500, method='neurokit')
+```
+
+**Methods:**
+- `'neurokit'`: Butterworth filtering optimized for EOG
+- `'agarwal2019'`: Alternative filtering
+- `'mne'`: MNE-Python preprocessing
+- `'brainstorm'`: Brainstorm approach
+- `'kong1998'`: Kong's method
+
+**Typical filtering:**
+- Low-pass: 10-20 Hz (remove high-frequency noise)
+- High-pass: 0.1-1 Hz (remove DC drift)
+- Preserves blink waveform (typical duration 100-400 ms)
+
+**EOG signal characteristics:**
+- **Blinks**: Large amplitude, stereotyped waveform (200-400 ms)
+- **Saccades**: Rapid step-like deflections (20-80 ms)
+- **Smooth pursuit**: Slow ramp-like changes
+- **Baseline**: Stable when eyes fixated
+
+## Blink Detection
+
+### eog_peaks()
+
+Detect eye blinks in EOG signal.
+
+```python
+blinks, info = nk.eog_peaks(cleaned_eog, sampling_rate=500, method='neurokit',
+                            threshold=0.33)
+```
+
+**Methods:**
+- `'neurokit'`: Amplitude and duration criteria (default)
+- `'mne'`: MNE-Python blink detection
+- `'brainstorm'`: Brainstorm approach
+- `'blinker'`: BLINKER algorithm (Kleifges et al., 2017)
+
+**Key parameters:**
+- `threshold`: Amplitude threshold (fraction of max amplitude)
+  - Typical: 0.2-0.5
+  - Lower: more sensitive (may include false positives)
+  - Higher: more conservative (may miss small blinks)
+
+**Returns:**
+- Dictionary with `'EOG_Blinks'` key containing blink peak indices
+
+**Blink characteristics:**
+- **Frequency**: 15-20 blinks/min (resting, comfortable)
+- **Duration**: 100-400 ms (mean ~200 ms)
+- **Amplitude**: Varies with electrode placement and individual factors
+- **Waveform**: Biphasic or triphasic
+
+### eog_findpeaks()
+
+Low-level blink detection with multiple algorithms.
+
+```python
+blinks_dict = nk.eog_findpeaks(cleaned_eog, sampling_rate=500, method='neurokit')
+```
+
+**Use cases:**
+- Custom parameter tuning
+- Algorithm comparison
+- Research method development
+
+## Feature Extraction
+
+### eog_features()
+
+Extract characteristics of individual blinks.
+
+```python
+features = nk.eog_features(signals, sampling_rate=500)
+```
+
+**Computed features:**
+- **Amplitude velocity ratio (AVR)**: Peak velocity / amplitude
+  - Discriminates blinks from artifacts
+- **Blink-amplitude ratio**: Consistency of blink amplitudes
+- **Duration metrics**: Blink duration statistics (mean, SD)
+- **Peak amplitude**: Maximum deflection
+- **Peak velocity**: Maximum rate of change
+
+**Use cases:**
+- Blink quality assessment
+- Drowsiness detection (blink duration increases when sleepy)
+- Neurological assessment (altered blink dynamics in disease)
+
+### eog_rate()
+
+Compute blink frequency (blinks per minute).
+
+```python
+blink_rate = nk.eog_rate(blinks, sampling_rate=500, desired_length=None)
+```
+
+**Method:**
+- Calculate inter-blink intervals
+- Convert to blinks per minute
+- Interpolate to match signal length
+
+**Typical blink rates:**
+- **Resting**: 15-20 blinks/min
+- **Reading/visual tasks**: 5-10 blinks/min (suppressed)
+- **Conversation**: 20-30 blinks/min
+- **Stress/dry eyes**: >30 blinks/min
+- **Drowsiness**: Variable, longer blinks
+
+## Analysis Functions
+
+### eog_analyze()
+
+Automatically select event-related or interval-related analysis.
+
+```python
+analysis = nk.eog_analyze(signals, sampling_rate=500)
+```
+
+**Mode selection:**
+- Duration < 10 seconds → event-related
+- Duration ≥ 10 seconds → interval-related
+
+### eog_eventrelated()
+
+Analyze blink patterns relative to specific events.
+
+```python
+results = nk.eog_eventrelated(epochs)
+```
+
+**Computed metrics (per epoch):**
+- `EOG_Blinks_N`: Number of blinks during epoch
+- `EOG_Rate_Mean`: Average blink rate
+- `EOG_Blink_Presence`: Binary (any blinks occurred)
+- Temporal distribution of blinks across epoch
+
+**Use cases:**
+- Blink-locked ERP contamination assessment
+- Attention and engagement during stimuli
+- Visual task difficulty (suppressed blinks during demanding tasks)
+- Spontaneous blinks after stimulus offset
+
+### eog_intervalrelated()
+
+Analyze blink patterns over extended periods.
+
+```python
+results = nk.eog_intervalrelated(signals, sampling_rate=500)
+```
+
+**Computed metrics:**
+- `EOG_Blinks_N`: Total number of blinks
+- `EOG_Rate_Mean`: Average blink rate (blinks/min)
+- `EOG_Rate_SD`: Blink rate variability
+- `EOG_Duration_Mean`: Average blink duration (if available)
+- `EOG_Amplitude_Mean`: Average blink amplitude (if available)
+
+**Use cases:**
+- Resting state blink patterns
+- Drowsiness or fatigue monitoring (increased duration)
+- Sustained attention tasks (suppressed rate)
+- Dry eye assessment (increased rate, incomplete blinks)
+
+## Simulation and Visualization
+
+### eog_plot()
+
+Visualize processed EOG signal and detected blinks.
+
+```python
+nk.eog_plot(signals, info)
+```
+
+**Displays:**
+- Raw and cleaned EOG signal
+- Detected blink markers
+- Blink rate time course
+
+## Practical Considerations
+
+### Sampling Rate Recommendations
+- **Minimum**: 100 Hz (basic blink detection)
+- **Standard**: 250-500 Hz (research applications)
+- **High-resolution**: 1000 Hz (detailed waveform analysis, saccades)
+- **Sleep studies**: 200-250 Hz typical
+
+### Recording Duration
+- **Blink detection**: Any duration (≥1 blink)
+- **Blink rate estimation**: ≥60 seconds for stable estimate
+- **Event-related**: Depends on paradigm (seconds per trial)
+- **Sleep EOG**: Hours (full night)
+
+### Electrode Placement
+
+**Standard configurations:**
+
+**Horizontal EOG (HEOG):**
+- Two electrodes: lateral canthi (outer corners) of left and right eyes
+- Measures horizontal eye movements (saccades, smooth pursuit)
+- Bipolar recording (left - right)
+
+**Vertical EOG (VEOG):**
+- Two electrodes: above and below one eye (typically right)
+- Measures vertical eye movements and blinks
+- Bipolar recording (above - below)
+
+**Sleep EOG:**
+- Often uses slightly different placement (temple area)
+- E1: 1 cm lateral and 1 cm below outer canthus of left eye
+- E2: 1 cm lateral and 1 cm above outer canthus of right eye
+- Captures both horizontal and vertical movements
+
+**EEG contamination removal:**
+- Frontal electrodes (Fp1, Fp2) can serve as EOG proxies
+- ICA-based EOG artifact removal common in EEG preprocessing
+
+### Common Issues and Solutions
+
+**Electrode issues:**
+- Poor contact: low amplitude, noise
+- Skin preparation: clean, light abrasion
+- Conductive gel: ensure good contact
+
+**Artifacts:**
+- Muscle activity (especially frontalis): high-frequency noise
+- Movement: cable artifacts, head motion
+- Electrical noise: 50/60 Hz hum (ground properly)
+
+**Saturation:**
+- Large saccades may saturate amplifier
+- Adjust gain or voltage range
+- More common with low-resolution systems
+
+### Best Practices
+
+**Standard workflow:**
+```python
+# 1. Clean signal
+cleaned = nk.eog_clean(eog_raw, sampling_rate=500, method='neurokit')
+
+# 2. Detect blinks
+blinks, info = nk.eog_peaks(cleaned, sampling_rate=500, method='neurokit')
+
+# 3. Extract features
+features = nk.eog_features(signals, sampling_rate=500)
+
+# 4. Comprehensive processing (alternative)
+signals, info = nk.eog_process(eog_raw, sampling_rate=500)
+
+# 5. Analyze
+analysis = nk.eog_analyze(signals, sampling_rate=500)
+```
+
+**EEG artifact correction workflow:**
+```python
+# Option 1: Regression-based removal
+# Identify EOG components from cleaned EOG signal
+# Regress out EOG from EEG channels
+
+# Option 2: ICA-based removal (preferred)
+# 1. Run ICA on EEG data including EOG channels
+# 2. Identify ICA components correlated with EOG
+# 3. Remove EOG components from EEG data
+# NeuroKit2 integrates with MNE for this workflow
+```
+
+## Clinical and Research Applications
+
+**EEG artifact correction:**
+- Blinks contaminate frontal EEG channels
+- ICA or regression methods remove EOG artifacts
+- Essential for ERP studies
+
+**Sleep staging:**
+- Rapid eye movements (REMs) during REM sleep
+- Slow rolling eye movements during drowsiness
+- Sleep onset and stage transitions
+
+**Attention and cognitive load:**
+- Blink rate suppressed during demanding tasks
+- Blinks cluster at task boundaries (natural breakpoints)
+- Spontaneous blink as indicator of attention shifts
+
+**Fatigue and drowsiness monitoring:**
+- Increased blink duration when sleepy
+- Slower eyelid closures
+- Partial or incomplete blinks
+- Driver monitoring applications
+
+**Reading and visual processing:**
+- Blinks suppressed during reading
+- Eye movements during saccades (line changes)
+- Fatigue effects on reading efficiency
+
+**Neurological disorders:**
+- **Parkinson's disease**: Reduced spontaneous blink rate
+- **Schizophrenia**: Increased blink rate
+- **Tourette syndrome**: Excessive blinking (tics)
+- **Dry eye syndrome**: Increased, incomplete blinks
+
+**Affective and social cognition:**
+- Blink synchrony in social interaction
+- Emotional modulation of blink rate
+- Blink-related potentials in ERPs
+
+**Human-computer interaction:**
+- Gaze tracking preprocessing
+- Attention monitoring
+- User engagement assessment
+
+## Eye Movement Types Detectable with EOG
+
+**Blinks:**
+- Large amplitude, brief duration (100-400 ms)
+- NeuroKit2 primary focus
+- Vertical EOG most sensitive
+
+**Saccades:**
+- Rapid, ballistic eye movements (20-80 ms)
+- Step-like voltage deflections
+- Horizontal or vertical
+- Require higher sampling rates for detailed analysis
+
+**Smooth pursuit:**
+- Slow tracking of moving objects
+- Ramp-like voltage changes
+- Lower amplitude than saccades
+
+**Fixations:**
+- Stable gaze
+- Baseline EOG with small oscillations
+- Duration varies (200-600 ms typical in reading)
+
+**Note:** Detailed saccade/fixation analysis typically requires eye tracking (infrared, video-based). EOG useful for blinks and gross eye movements.
+
+## Interpretation Guidelines
+
+**Blink rate:**
+- **Normal resting**: 15-20 blinks/min
+- **<10 blinks/min**: Visual task engagement, concentration
+- **>30 blinks/min**: Stress, dry eyes, fatigue
+- **Context-dependent**: Task demands, lighting, screen use
+
+**Blink duration:**
+- **Normal**: 100-400 ms (mean ~200 ms)
+- **Prolonged**: Drowsiness, fatigue (>500 ms)
+- **Short**: Normal alertness
+
+**Blink amplitude:**
+- Varies with electrode placement and individuals
+- Within-subject comparisons most reliable
+- Incomplete blinks: reduced amplitude (dry eye, fatigue)
+
+**Temporal patterns:**
+- **Clustered blinks**: Transitions between tasks or cognitive states
+- **Suppressed blinks**: Active visual processing, sustained attention
+- **Post-stimulus blinks**: After completing visual processing
+
+## References
+
+- Kleifges, K., Bigdely-Shamlo, N., Kerick, S. E., & Robbins, K. A. (2017). BLINKER: Automated extraction of ocular indices from EEG enabling large-scale analysis. Frontiers in Neuroscience, 11, 12.
+- Agarwal, M., & Sivakumar, R. (2019). Blink: A fully automated unsupervised algorithm for eye-blink detection in EEG signals. In 2019 57th Annual Allerton Conference on Communication, Control, and Computing (pp. 1113-1121). IEEE.
+- Kong, X., & Wilson, G. F. (1998). A new EOG-based eyeblink detection algorithm. Behavior Research Methods, Instruments, & Computers, 30(4), 713-719.
+- Schleicher, R., Galley, N., Briest, S., & Galley, L. (2008). Blinks and saccades as indicators of fatigue in sleepiness warnings: Looking tired? Ergonomics, 51(7), 982-1010.