@brainpilot/skills 0.0.6

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  1. package/dist/index.d.ts +6 -0
  2. package/dist/index.d.ts.map +1 -0
  3. package/dist/index.js +28 -0
  4. package/dist/index.js.map +1 -0
  5. package/package.json +35 -0
  6. package/skills/01_Meta-Skills/contribute-skill/SKILL.md +277 -0
  7. package/skills/01_Meta-Skills/contribute-skills-via-pr/SKILL.md +163 -0
  8. package/skills/01_Meta-Skills/paper-to-skill/SKILL.md +435 -0
  9. package/skills/01_Meta-Skills/paper-to-skill/references/extraction-guide.md +286 -0
  10. package/skills/01_Meta-Skills/paper-to-skill/references/skill-template.md +250 -0
  11. package/skills/01_Meta-Skills/repo-to-skill/SKILL.md +289 -0
  12. package/skills/01_Meta-Skills/share-case/SKILL.md +253 -0
  13. package/skills/01_Meta-Skills/share-usage/README.md +63 -0
  14. package/skills/01_Meta-Skills/share-usage/SKILL.md +395 -0
  15. package/skills/01_Meta-Skills/verify-skill/SKILL.md +331 -0
  16. package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/SKILL.md +194 -0
  17. package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/effect-sizes.md +352 -0
  18. package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/sample-size-guide.md +407 -0
  19. package/skills/02_Cross-Domain_Foundation/cogsci-statistics/SKILL.md +361 -0
  20. package/skills/02_Cross-Domain_Foundation/cogsci-statistics/references/common-analyses.md +517 -0
  21. package/skills/02_Cross-Domain_Foundation/cogsci-visualization/SKILL.md +292 -0
  22. package/skills/02_Cross-Domain_Foundation/cogsci-visualization/references/plot-recipes.md +709 -0
  23. package/skills/02_Cross-Domain_Foundation/research-literacy/SKILL.md +286 -0
  24. package/skills/02_Cross-Domain_Foundation/research-literacy/references/common-assumptions.md +320 -0
  25. package/skills/02_Cross-Domain_Foundation/research-literacy/references/planning-template.md +143 -0
  26. package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/SKILL.md +197 -0
  27. package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/references/instruction-templates.md +60 -0
  28. package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/SKILL.md +246 -0
  29. package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/classic-paradigms.md +435 -0
  30. package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/design-principles.md +256 -0
  31. package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/SKILL.md +270 -0
  32. package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/references/lavaan-templates.md +172 -0
  33. package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/SKILL.md +238 -0
  34. package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/references/scoring-rubric.md +143 -0
  35. package/skills/03_Cognitive_Psychology/drift-diffusion-model/SKILL.md +203 -0
  36. package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/fitting-guide.md +571 -0
  37. package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/model-variants.md +427 -0
  38. package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/SKILL.md +310 -0
  39. package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/references/ez-diffusion-formulas.md +137 -0
  40. package/skills/03_Cognitive_Psychology/signal-detection-analysis/SKILL.md +300 -0
  41. package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/application-guide.md +278 -0
  42. package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/sdt-formulas.md +318 -0
  43. package/skills/03_Cognitive_Psychology/visual-search-array-generator/SKILL.md +283 -0
  44. package/skills/03_Cognitive_Psychology/visual-search-array-generator/references/array-generation-parameters.yaml +111 -0
  45. package/skills/04_Psycholinguistics/reading-time-analysis/SKILL.md +301 -0
  46. package/skills/04_Psycholinguistics/reading-time-analysis/references/measure-computation-guide.md +195 -0
  47. package/skills/04_Psycholinguistics/self-paced-reading-designer/SKILL.md +257 -0
  48. package/skills/04_Psycholinguistics/self-paced-reading-designer/references/analysis-guide.md +356 -0
  49. package/skills/04_Psycholinguistics/self-paced-reading-designer/references/region-segmentation.md +266 -0
  50. package/skills/04_Psycholinguistics/sentence-stimulus-norming/SKILL.md +346 -0
  51. package/skills/04_Psycholinguistics/sentence-stimulus-norming/references/lexical-databases-guide.md +184 -0
  52. package/skills/05_EEG_ERP/eeg-paradigm-designer/SKILL.md +226 -0
  53. package/skills/05_EEG_ERP/eeg-paradigm-designer/references/component-paradigm-map.md +276 -0
  54. package/skills/05_EEG_ERP/eeg-paradigm-designer/references/timing-parameters.md +244 -0
  55. package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/SKILL.md +367 -0
  56. package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/references/parameter-lookup-tables.md +138 -0
  57. package/skills/05_EEG_ERP/erp-analysis/SKILL.md +185 -0
  58. package/skills/05_EEG_ERP/erp-analysis/references/erp-components.md +447 -0
  59. package/skills/05_EEG_ERP/erp-analysis/references/preprocessing-pipeline.md +277 -0
  60. package/skills/05_EEG_ERP/erp-analysis/references/statistical-approaches.md +351 -0
  61. package/skills/05_EEG_ERP/mne-python-guide/SKILL.md +174 -0
  62. package/skills/05_EEG_ERP/mne-python-guide/references/decoding.md +178 -0
  63. package/skills/05_EEG_ERP/mne-python-guide/references/io_formats.md +160 -0
  64. package/skills/05_EEG_ERP/mne-python-guide/references/preprocessing.md +259 -0
  65. package/skills/05_EEG_ERP/mne-python-guide/references/simulation.md +173 -0
  66. package/skills/05_EEG_ERP/mne-python-guide/references/source_localization.md +234 -0
  67. package/skills/05_EEG_ERP/mne-python-guide/references/statistics.md +196 -0
  68. package/skills/05_EEG_ERP/mne-python-guide/references/time_frequency.md +165 -0
  69. package/skills/05_EEG_ERP/mne-python-guide/references/visualization.md +175 -0
  70. package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/SKILL.md +317 -0
  71. package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
  72. package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/SKILL.md +296 -0
  73. package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/design-matrix-guide.md +214 -0
  74. package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/statistical-inference.md +288 -0
  75. package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/SKILL.md +274 -0
  76. package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/quality-control.md +336 -0
  77. package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/step-by-step-pipeline.md +380 -0
  78. package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/SKILL.md +264 -0
  79. package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/references/design-optimization-examples.md +114 -0
  80. package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/SKILL.md +273 -0
  81. package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/decoding-methods.md +170 -0
  82. package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/rsa-guide.md +266 -0
  83. package/skills/06_fMRI_Neuroimaging/pycortex-guide/SKILL.md +123 -0
  84. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/database-subjects.md +179 -0
  85. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/dataset-types.md +208 -0
  86. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/freesurfer-fmriprep.md +162 -0
  87. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mapping-transforms.md +181 -0
  88. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mni-utils.md +207 -0
  89. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/surface-analysis.md +219 -0
  90. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/visualization.md +251 -0
  91. package/skills/07_Computational_Modeling/act-r-model-builder/SKILL.md +297 -0
  92. package/skills/07_Computational_Modeling/act-r-model-builder/references/model-patterns.md +197 -0
  93. package/skills/07_Computational_Modeling/act-r-model-builder/references/parameter-table.yaml +204 -0
  94. package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/SKILL.md +294 -0
  95. package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/diagnostics-checklist.md +351 -0
  96. package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/prior-selection-guide.md +241 -0
  97. package/skills/07_Computational_Modeling/parameter-recovery-checker/SKILL.md +269 -0
  98. package/skills/07_Computational_Modeling/parameter-recovery-checker/references/recovery-diagnostics.md +207 -0
  99. package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/SKILL.md +317 -0
  100. package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
  101. package/skills/08_Computational_Neuroscience/neural-decoding-analysis/SKILL.md +273 -0
  102. package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/decoding-methods.md +170 -0
  103. package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/rsa-guide.md +266 -0
  104. package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/SKILL.md +305 -0
  105. package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/data-requirements.md +60 -0
  106. package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/method-comparison.md +151 -0
  107. package/skills/08_Computational_Neuroscience/spiking-network-model-builder/SKILL.md +376 -0
  108. package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/hh-parameters.md +117 -0
  109. package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/network-regimes.md +130 -0
  110. package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/SKILL.md +258 -0
  111. package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/indicator-parameters.md +242 -0
  112. package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/pipeline-details.md +211 -0
  113. package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/SKILL.md +261 -0
  114. package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/opsin-catalog.md +124 -0
  115. package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/stimulation-parameters.md +304 -0
  116. package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/SKILL.md +367 -0
  117. package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/disconnection-guide.md +152 -0
  118. package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/vlsm-pipeline.md +182 -0
  119. package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/SKILL.md +250 -0
  120. package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/deficit-profiles.md +302 -0
  121. package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/test-catalog.md +304 -0
  122. package/skills/11_Developmental_Cognition/infant-looking-time-designer/SKILL.md +345 -0
  123. package/skills/11_Developmental_Cognition/infant-looking-time-designer/references/age-parameters.yaml +186 -0
  124. package/skills/12_Social_Cognition/tom-task-selector/SKILL.md +379 -0
  125. package/skills/12_Social_Cognition/tom-task-selector/references/task-database.md +317 -0
  126. package/skills/13_Visualization/nature-figure/README.md +442 -0
  127. package/skills/13_Visualization/nature-figure/SKILL.md +60 -0
  128. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-01-bar-charts.png +0 -0
  129. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-02-line-trends.png +0 -0
  130. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-03-heatmaps.png +0 -0
  131. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-04-scatter-bubble.png +0 -0
  132. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-05-radar-polar.png +0 -0
  133. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-06-distributions.png +0 -0
  134. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-07-forest-interval.png +0 -0
  135. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-08-area-stacked.png +0 -0
  136. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-09-image-plates.png +0 -0
  137. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-10-network-matrix.png +0 -0
  138. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_motivation.png +0 -0
  139. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation.png +0 -0
  140. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation_distillation.png +0 -0
  141. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_contrastive.png +0 -0
  142. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_CEDAR.png +0 -0
  143. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_IEDB.png +0 -0
  144. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_schematic.png +0 -0
  145. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/RNAGenScape_schematic.png +0 -0
  146. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/ablation.png +0 -0
  147. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/comparison.png +0 -0
  148. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_ablation.py +86 -0
  149. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_comparison.py +109 -0
  150. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/diffusion_swiss_roll.py +97 -0
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  152. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.pdf +0 -0
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  158. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Ablation.py +64 -0
  159. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_GeneRegulatory.py +74 -0
  160. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Trajectory.py +74 -0
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  167. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_ablation_Cancer.png +0 -0
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  172. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/raw_data.py +125 -0
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  179. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_hole_manifold.py +82 -0
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+ # Lexical Databases Guide
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+
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+ This reference file supplements the main `SKILL.md` with detailed instructions for accessing and querying the lexical control databases needed for stimulus norming.
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+
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+ ## 1. Word Frequency Databases
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+
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+ ### 1.1 SUBTLEX-US (Recommended)
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+
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+ **Source**: Brysbaert & New (2009)
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+ **URL**: https://www.ugent.be/pp/experimentele-psychologie/en/research/documents/subtlexus
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+ **Corpus**: American English subtitles (~51 million words from 8,388 films/TV episodes)
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+
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+ **Key columns**:
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+ | Column | Description | Use |
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+ |--------|-------------|-----|
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+ | `FREQcount` | Raw frequency count | For computing custom metrics |
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+ | `CDcount` | Contextual diversity (number of films/episodes containing the word) | Better predictor than raw frequency for some tasks (Adelman et al., 2006) |
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+ | `Lg10WF` | Log10(frequency per million + 1) | **Primary frequency measure** -- use this for matching |
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+ | `Lg10CD` | Log10(contextual diversity per million + 1) | Alternative to Lg10WF |
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+ | `SUBTLWF` | Frequency per million words | For reporting and interpretability |
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+
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+ **How to use**:
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+ 1. Download the Excel file from the URL above
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+ 2. Look up each critical word
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+ 3. Extract `Lg10WF` for each word
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+ 4. Compare condition means; ensure no significant difference (p > 0.20)
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+
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+ **Typical values**:
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+ - Very high frequency (the, is, and): Lg10WF > **4.0**
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+ - High frequency (house, water, know): Lg10WF ~ **3.0-4.0**
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+ - Medium frequency (sword, puzzle, brave): Lg10WF ~ **2.0-3.0**
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+ - Low frequency (abacus, fjord, plinth): Lg10WF < **2.0**
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+ - Very low frequency / unknown: Lg10WF < **1.0** or absent from database
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+
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+ ### 1.2 SUBTLEX-UK
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+
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+ **Source**: van Heuven et al. (2014)
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+ **URL**: http://crr.ugent.be/archives/1423
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+ **Use**: For British English materials; same structure as SUBTLEX-US
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+
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+ ### 1.3 Other Language Versions
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+
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+ SUBTLEX databases exist for: Dutch, Chinese, German, Spanish, French, Greek, and others. Use the version matching your experimental language.
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+
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+ ## 2. Concreteness Ratings
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+
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+ ### Brysbaert et al. (2014)
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+
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+ **Source**: Brysbaert, Warriner, & Kuperman (2014)
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+ **URL**: http://crr.ugent.be/archives/1330
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+ **Coverage**: ~40,000 English word lemmas
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+ **Scale**: 1 (abstract) to 5 (concrete), collected via crowdsourcing (N ~ 30 raters per word)
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+
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+ **Key columns**:
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+ | Column | Description |
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+ |--------|-------------|
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+ | `Conc.M` | Mean concreteness rating (1-5) |
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+ | `Conc.SD` | Standard deviation of ratings |
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+
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+ **Typical values**:
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+ - Very concrete (table, dog, hammer): > **4.5**
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+ - Concrete (forest, music, bread): **3.5-4.5**
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+ - Medium (justice, freedom, idea): **2.5-3.5**
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+ - Abstract (truth, hope, theory): **1.5-2.5**
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+ - Very abstract (essence, entropy): < **1.5**
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+
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+ ## 3. Age of Acquisition (AoA) Ratings
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+
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+ ### Kuperman et al. (2012)
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+
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+ **Source**: Kuperman, Stadthagen-Gonzalez, & Brysbaert (2012)
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+ **URL**: http://crr.ugent.be/archives/806
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+ **Coverage**: ~30,000 English words
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+ **Scale**: Estimated age (in years) at which the word was learned
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+
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+ **Key columns**:
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+ | Column | Description |
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+ |--------|-------------|
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+ | `Rating.Mean` | Mean estimated AoA in years |
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+ | `Rating.SD` | Standard deviation |
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+
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+ **Typical values**:
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+ - Early acquired (dog, water, happy): **2-4 years**
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+ - Medium acquisition (bicycle, important, discover): **5-8 years**
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+ - Late acquired (mortgage, rhetoric, hypothesis): **10+ years**
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+
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+ ## 4. Emotional Valence and Arousal
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+
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+ ### Warriner et al. (2013)
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+
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+ **Source**: Warriner, Kuperman, & Brysbaert (2013)
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+ **URL**: http://crr.ugent.be/archives/1003
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+ **Coverage**: ~14,000 English words
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+ **Scale**: 1-9 for valence (unhappy-happy), arousal (calm-excited), and dominance (controlled-in control)
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+
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+ **Key columns**:
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+ | Column | Description |
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+ |--------|-------------|
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+ | `V.Mean.Sum` | Mean valence rating (1-9) |
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+ | `A.Mean.Sum` | Mean arousal rating (1-9) |
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+ | `D.Mean.Sum` | Mean dominance rating (1-9) |
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+
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+ **When to control**: Control valence and arousal when your manipulation is not emotional, to ensure emotional content does not confound the critical comparison.
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+
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+ ## 5. Orthographic Neighborhood Density
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+
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+ ### Definition
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+
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+ Orthographic neighborhood density (Coltheart's N) = the number of words that can be created by changing one letter of the target word while preserving word length (Coltheart et al., 1977).
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+
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+ ### Sources
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+
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+ | Tool | URL | Features |
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+ |------|-----|----------|
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+ | **N-Watch** | https://www.pc.rhul.ac.uk/staff/c.davis/Utilities/N-Watch/ | N, frequency-weighted N, bigram frequency |
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+ | **CLEARPOND** | http://clearpond.northwestern.edu/ | Cross-linguistic; N for English, Dutch, French, German, Spanish |
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+ | **English Lexicon Project** | https://elexicon.wustl.edu/ | N, OLD20, phonological N, and many other metrics |
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+
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+ ### Key Metrics
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+
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+ | Metric | Description | When to Control |
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+ |--------|-------------|-----------------|
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+ | **Coltheart's N** | Count of orthographic neighbors | Always, for single-word reading tasks |
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+ | **OLD20** | Mean Levenshtein distance to 20 nearest orthographic neighbors | More sensitive than N; recommended (Yarkoni et al., 2008) |
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+ | **Frequency-weighted N** | N weighted by neighbor frequency | When high-frequency neighbors might prime/inhibit the target |
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+
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+ ## 6. Multi-Variable Lookup Tools
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+
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+ ### English Lexicon Project (ELP)
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+
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+ **URL**: https://elexicon.wustl.edu/
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+ **Features**: One-stop lookup for frequency (HAL, SUBTLEX), length, N, OLD20, morphological information, plus behavioral data (lexical decision RT, naming RT) for ~40,000 words (Balota et al., 2007).
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+
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+ **Behavioral benchmarks from ELP** (Balota et al., 2007):
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+ - Average lexical decision RT: ~**620 ms** (correct responses)
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+ - High frequency words: ~**550-580 ms**
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+ - Low frequency words: ~**680-750 ms**
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+ - Very low frequency words: ~**800+ ms**
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+
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+ ### Other Multi-Variable Tools
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+
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+ | Tool | URL | Coverage |
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+ |------|-----|----------|
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+ | **WordSmith** | Various | Corpus analysis toolkit |
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+ | **ARC Nonword Database** | https://www.cogsci.mq.edu.au/research/resources/nwdb/ | Nonword generation with controlled properties |
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+ | **Wuggy** | http://crr.ugent.be/programs-data/wuggy | Pseudoword generation matching real-word properties |
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+
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+ ## 7. Practical Workflow for Lexical Matching
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+
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+ ### Step-by-Step Protocol
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+
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+ 1. **List all critical words** per condition
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+ 2. **Query SUBTLEX-US** for `Lg10WF` (frequency)
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+ 3. **Query Kuperman et al.** for AoA
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+ 4. **Query Brysbaert et al.** for concreteness
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+ 5. **Query ELP** for word length, N, OLD20
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+ 6. **Create a comparison table** with condition means and SDs for each variable
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+ 7. **Run independent-samples t-tests** (2 conditions) or one-way ANOVAs (3+ conditions) on each variable
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+ 8. **Criterion**: All p-values > 0.20 (conservative) or > 0.10 (minimum acceptable)
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+ 9. If any variable differs: replace problematic items or add as covariate
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+
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+ ### Example Comparison Table
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+
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+ | Variable | Condition A (M +/- SD) | Condition B (M +/- SD) | t | p |
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+ |----------|----------------------|----------------------|---|---|
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+ | SUBTLEX Lg10WF | 2.85 +/- 0.62 | 2.78 +/- 0.71 | 0.42 | 0.68 |
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+ | Length (chars) | 5.2 +/- 1.1 | 5.4 +/- 1.3 | -0.67 | 0.51 |
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+ | Concreteness | 3.82 +/- 0.94 | 3.71 +/- 0.88 | 0.48 | 0.63 |
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+ | AoA (years) | 6.3 +/- 2.1 | 6.8 +/- 2.4 | -0.89 | 0.38 |
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+ | Coltheart's N | 4.1 +/- 3.2 | 3.8 +/- 2.9 | 0.39 | 0.70 |
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+
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+ All p > 0.20: conditions are adequately matched.
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+
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+ ## References
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+
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+ - Adelman, J. S., Brown, G. D. A., & Quesada, J. F. (2006). Contextual diversity, not word frequency, determines word-naming and lexical decision times. *Psychological Science*, 17, 814-823.
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+ - Balota, D. A., Yap, M. J., Cortese, M. J., et al. (2007). The English Lexicon Project. *Behavior Research Methods*, 39, 445-459.
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+ - Brysbaert, M., & New, B. (2009). Moving beyond Kucera and Francis: A critical evaluation of current word frequency norms. *Behavior Research Methods*, 41, 977-990.
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+ - Brysbaert, M., Warriner, A. B., & Kuperman, V. (2014). Concreteness ratings for 40 thousand generally known English word lemmas. *Behavior Research Methods*, 46, 904-911.
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+ - Coltheart, M., Davelaar, E., Jonasson, J. T., & Besner, D. (1977). Access to the internal lexicon. In S. Dornic (Ed.), *Attention and performance VI*. Erlbaum.
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+ - Kuperman, V., Stadthagen-Gonzalez, H., & Brysbaert, M. (2012). Age-of-acquisition ratings for 30,000 English words. *Behavior Research Methods*, 44, 978-990.
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+ - van Heuven, W. J. B., Mandera, P., Keuleers, E., & Brysbaert, M. (2014). SUBTLEX-UK: A new and improved word frequency database for British English. *Quarterly Journal of Experimental Psychology*, 67, 1176-1190.
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+ - Warriner, A. B., Kuperman, V., & Brysbaert, M. (2013). Norms of valence, arousal, and dominance for 13,915 English lemmas. *Behavior Research Methods*, 45, 1191-1207.
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+ - Yarkoni, T., Balota, D., & Yap, M. (2008). Moving beyond Coltheart's N: A new measure of orthographic similarity. *Psychonomic Bulletin & Review*, 15, 971-979.
@@ -0,0 +1,226 @@
1
+ ---
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+ name: "eeg-paradigm-designer"
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+ description: "Expert guidance for designing EEG paradigms optimized to isolate specific ERP components, with domain-validated timing, trial count, and control condition parameters"
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+ domain: "cognitive-neuroscience"
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+ version: "1.0.0"
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+ authors:
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+ - "AI-assisted (Claude)"
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+ papers:
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+ - "Luck, 2014"
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+ - "Kappenman & Luck, 2010"
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+ - "Kappenman et al., 2021"
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+ - "Boudewyn et al., 2018"
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+ - "Keil et al., 2014"
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+ - "Jensen & MacDonald, 2023"
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+ dependencies:
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+ required:
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+ - research-literacy
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+ recommended:
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+ - erp-analysis
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+ - cognitive-paradigm-design
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+ review_status: "ai-generated"
22
+ ---
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+
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+ # EEG Paradigm Designer
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+
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+ ## Purpose
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+
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+ This skill encodes expert knowledge for designing EEG experimental paradigms that reliably isolate specific event-related potential (ERP) components. Designing an EEG paradigm differs fundamentally from designing a behavioral experiment: timing constraints are stricter, stimulus properties must be controlled to avoid confounding sensory ERPs with cognitive ERPs, trial counts must be higher to achieve adequate signal-to-noise ratios, and the choice of control condition directly determines which neural process can be isolated via subtraction. A general-purpose programmer or experimental psychologist without EEG training would get many of these decisions wrong.
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+
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+ For ERP preprocessing and analysis after data collection, see the `erp-analysis` skill. For general experimental paradigm selection (behavioral focus), see the `cognitive-paradigm-design` skill.
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+
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+ ## When to Use This Skill
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+
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+ - Designing a new EEG experiment targeting a specific ERP component
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+ - Choosing between paradigm variants to optimize a particular ERP signal
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+ - Determining timing parameters (SOA, ISI, epoch length) for an EEG study
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+ - Calculating minimum trial counts per condition for a target component
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+ - Selecting electrode montage density for a given research question
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+ - Designing control conditions that enable clean difference waveforms
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+ - Reviewing an existing EEG paradigm design for methodological issues
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+
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+ ## Research Planning Protocol
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+
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+ Before executing the domain-specific steps below, you MUST:
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+
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+ 1. **State the research question** -- What specific cognitive process is this EEG paradigm targeting?
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+ 2. **Justify the method choice** -- Why EEG (not fMRI, behavior-only, MEG)? What alternatives were considered?
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+ 3. **Declare expected outcomes** -- Which ERP component(s) do you expect, with what polarity/latency/scalp distribution?
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+ 4. **Note assumptions and limitations** -- What does this paradigm assume? Where could it mislead?
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+ 5. **Present the plan to the user and WAIT for confirmation** before proceeding.
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+
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+ For detailed methodology guidance, see the `research-literacy` skill.
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+
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+
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+ ## ⚠️ Verification Notice
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+
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+ This skill was generated by AI from academic literature. All parameters, thresholds, and citations require independent verification before use in research. If you find errors, please [open an issue](https://github.com/HaoxuanLiTHUAI/awesome_cognitive_and_neuroscience_skills/issues).
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+
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+ ## Core Design Workflow
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+
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+ ### Step 1: Identify the Target ERP Component
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+
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+ Map the research question to a specific ERP component. The component determines everything else: paradigm type, timing, electrode montage, trial count, and analysis strategy.
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+
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+ Use the Component-Paradigm Quick Reference below or consult `references/component-paradigm-map.md` for full details.
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+
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+ #### Component-Paradigm Quick Reference
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+
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+ | Component | Canonical Paradigm | Key Manipulation | Latency (ms) | Max Site |
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+ |---|---|---|---|---|
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+ | **P1** | Spatial attention (Posner) | Attended vs. unattended location | 80--130 | O1/O2 |
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+ | **N1** | Spatial attention / discrimination | Attended vs. unattended stimulus | 150--200 | PO7/PO8 |
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+ | **N170** | Face perception | Faces vs. non-face objects | 140--200 | P7/P8 |
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+ | **MMN** | Passive oddball | Deviant vs. standard (no response) | 100--250 | Fz/FCz |
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+ | **N2pc** | Lateralized visual search | Contralateral vs. ipsilateral to target | 200--300 | PO7/PO8 |
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+ | **P3a** | Novelty oddball | Novel/unexpected stimuli | 250--350 | Fz/Cz |
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+ | **P3b** | Target oddball | Rare targets vs. frequent standards | 300--600 | Pz |
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+ | **N400** | Semantic violation / priming | Incongruent vs. congruent words | 300--500 | Cz/CPz |
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+ | **P600** | Syntactic violation | Ungrammatical vs. grammatical | 500--800 | Pz/CPz |
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+ | **ERN** | Speeded response (flanker, Go/NoGo) | Error vs. correct (response-locked) | 0--100 post-resp | FCz |
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+ | **LRP** | Choice-RT with lateralized responses | Contralateral vs. ipsilateral motor cortex | Sustained pre-resp | C3/C4 |
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+ | **CNV** | S1-S2 foreperiod | Warning signal before imperative stimulus | Sustained | Cz/FCz |
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+ | **SSVEP** | Frequency tagging / flicker | Periodic visual stimulation at fixed Hz | Steady-state | Oz |
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+
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+ ### Step 2: Select and Configure the Paradigm
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+
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+ Once the target component is identified, select the appropriate paradigm class and configure its parameters. See `references/component-paradigm-map.md` for detailed paradigm specifications per component, and `references/timing-parameters.md` for timing configurations.
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+
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+ #### EEG-Specific Timing Constraints
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+
91
+ EEG paradigms have stricter timing requirements than behavioral experiments for three reasons a non-specialist would not anticipate:
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+
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+ 1. **ERP overlap**: When stimuli arrive too quickly, the ERP to one stimulus overlaps with the ERP to the next, making components unresolvable. The minimum ISI must be long enough for the slowest ERP component of interest to resolve -- typically **>= 1000 ms** for fast components (P1, N1) and **>= 1500--2000 ms** for slow components (N400, P300, P600) (Luck, 2014, Ch. 6).
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+
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+ 2. **Alpha-band contamination**: Rhythmic stimulation near **10 Hz** (ISI ~ 100 ms) entrains alpha oscillations, producing steady-state responses that obscure transient ERPs. Avoid ISIs that create stimulus rates in the **8--13 Hz** range unless studying SSVEPs (Luck, 2014, Ch. 6).
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+
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+ 3. **Habituation and refractoriness**: Sensory ERPs (P1, N1) are attenuated by repetition. Short ISIs (< 500 ms) produce refractory-period suppression of early components, reducing sensitivity to experimental manipulations. For paradigms targeting P1/N1, use ISIs of **>= 1000 ms** or jitter ISIs widely (Luck, 2005; Coles & Rugg, 1995).
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+
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+ #### Jittering
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+
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+ Always jitter the ISI to prevent anticipatory CNV buildup from contaminating the pre-stimulus baseline and to support regression-based overlap correction (e.g., LIMO, unfold). Recommended jitter: **+/- 200--500 ms** uniform or exponential distribution around the mean ISI (Luck, 2014, Ch. 6; Woldorff, 1993).
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+
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+ ### Step 3: Determine Trial Counts
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+
105
+ Trial counts for EEG must be substantially higher than for behavioral studies because the ERP signal is extracted from noisy single-trial EEG by averaging, and the signal-to-noise ratio improves with the square root of the number of trials.
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+
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+ **There is no universal minimum trial count.** The required number depends on the interaction of effect magnitude, number of participants, and component-specific noise levels (Boudewyn et al., 2018; Jensen & MacDonald, 2023). The table below provides component-specific starting recommendations for typical effect sizes in well-designed paradigms:
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+
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+ | Component | Minimum Trials/Condition | Recommended Trials/Condition | Rationale |
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+ |---|---|---|---|
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+ | P3b (oddball) | 30 | 50--80 | Large effect; SNR good at Pz (Luck, 2014, Ch. 9; Kappenman et al., 2021) |
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+ | N400 (semantic) | 30 | 40--60 | Large effect for strong violations; more for graded manipulations (Boudewyn et al., 2018) |
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+ | N170 (faces) | 40 | 60--80 | Moderate effect; requires adequate face and control exemplars (Rossion & Jacques, 2008) |
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+ | N2pc (search) | 100 | 150--200 | Small lateralized difference; many trials needed (Luck, 2014, Ch. 3; Kappenman et al., 2021) |
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+ | MMN (oddball) | 150 (deviants) | 200--300 (deviants) | Small amplitude; passive paradigm adds noise (Naatanen et al., 2007; Duncan et al., 2009) |
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+ | ERN (errors) | 6 | 10--15 | Large amplitude but depends on error rate (Olvet & Hajcak, 2009; Boudewyn et al., 2018) |
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+ | LRP (lateralized) | 40 | 80--100 | Small lateralized difference; high trial-to-trial variability (Boudewyn et al., 2018) |
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+ | P600 (syntactic) | 30 | 40--60 | Large effect for clear violations (Osterhout & Holcomb, 1992) |
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+ | CNV (foreperiod) | 30 | 40--60 | Moderate amplitude; slow wave requires low-frequency filtering (Brunia et al., 2012) |
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+ | SSVEP (flicker) | 10--20 blocks | 30+ blocks of 10--20 s | Frequency-domain; SNR depends on block duration (Norcia et al., 2015) |
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+
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+ > **Critical note**: These are *minimum retained trials after artifact rejection*. Plan for **20--30% attrition** from artifacts. If you need 40 clean trials, design for at least **50--55 trials per condition** (Luck, 2014, Ch. 6).
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+
124
+ ### Step 4: Design the Difference Waveform
125
+
126
+ ERP components are best isolated using difference waveforms that subtract overlapping activity common to two conditions, leaving only the neural process of interest (Luck, 2014, Ch. 2; Kappenman et al., 2021).
127
+
128
+ **Design principle**: For every target component, explicitly define the subtraction that will isolate it.
129
+
130
+ | Component | Subtraction | What It Removes |
131
+ |---|---|---|
132
+ | N400 | Incongruent minus Congruent | Sensory ERP, P1/N1, baseline activity |
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+ | P3b | Target minus Standard | Sensory response to frequent stimuli |
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+ | MMN | Deviant minus Standard | Obligatory auditory response |
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+ | N2pc | Contralateral minus Ipsilateral | Bilateral sensory activity, P1/N1 |
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+ | ERN | Error minus Correct (response-locked) | Motor preparation, baseline activity |
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+ | LRP | (C3-C4 left hand) averaged with (C4-C3 right hand) | Non-lateralized activity |
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+ | N170 | Faces minus Control objects | Low-level visual ERPs |
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+
140
+ > **Warning**: The subtraction is only valid if the two conditions are matched on all low-level stimulus properties (luminance, spatial frequency, size, contrast, position) and differ only on the cognitive dimension of interest. Failure to match stimuli is the most common source of confounded ERP results (Luck, 2014, Ch. 2; Kappenman & Luck, 2010).
141
+
142
+ ### Step 5: Choose Electrode Montage
143
+
144
+ The required electrode density depends on the spatial precision needed:
145
+
146
+ | Montage | Channels | Best For | Not Sufficient For |
147
+ |---|---|---|---|
148
+ | Low-density | 32 | P3b, N400, ERN, MMN (midline components) | N2pc, LRP, source localization |
149
+ | Medium-density | 64 | N2pc, LRP, N170, most ERP research | High-resolution source localization |
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+ | High-density | 128--256 | Source localization, CSD analysis, spatial mapping | Overkill for standard ERP analysis on midline components |
151
+
152
+ **Decision rules** (Luck, 2014, Ch. 4; Keil et al., 2014):
153
+
154
+ - If studying lateralized components (N2pc, LRP, N170 laterality), use **>= 64 channels** to ensure adequate lateral coverage
155
+ - If using average reference, use **>= 64 channels** to approximate a neutral reference (Luck, 2014, Ch. 5)
156
+ - If studying midline-maximal components only (P3b, N400, ERN), **32 channels** is adequate with linked-mastoid reference
157
+ - If source localization is planned, use **>= 128 channels** (Keil et al., 2014)
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+
159
+ ### Step 6: Verify Against Common Pitfalls
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+
161
+ Before finalizing the paradigm, check for these non-obvious EEG-specific design flaws:
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+
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+ 1. **Overlapping ERPs from adjacent events**: If ISI < the duration of the slowest component, ERPs overlap. For P3b (300--600 ms), this means ISIs under **~1200 ms** create overlap. For P600 (500--800+ ms), ISIs under **~1500 ms** are problematic. Use the ADJAR procedure or linear modeling (e.g., unfold toolbox) if fast ISIs are required (Woldorff, 1993; Ehinger & Dimigen, 2019).
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+ 2. **Stimulus confounds masquerading as cognitive ERPs**: Differences in luminance, contrast, spatial frequency, size, or retinal position between conditions produce P1/N1 differences that are sensory, not cognitive. Always equate low-level stimulus properties or use difference waveforms that cancel them (Luck, 2014, Ch. 2).
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+ 3. **Inadequate baselines**: If pre-stimulus activity differs between conditions (e.g., from a preceding cue or from CNV buildup during fixed foreperiods), standard baseline correction (-200 to 0 ms) will distort post-stimulus ERP measurements. Use jittered ISIs and verify baseline equivalence (Luck, 2014, Ch. 6; Alday, 2019).
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+ 4. **Motor confounds with cognitive ERPs**: If conditions differ in response requirements (e.g., one condition has button press, the other does not), motor-related ERPs (LRP, readiness potential) contaminate the cognitive ERP. Use conditions with identical motor responses or analyze only stimulus-locked, pre-response windows (Luck, 2014, Ch. 6).
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+ 5. **Probability confounds in oddball paradigms**: In P3b oddball designs, the rare target differs from the frequent standard in both probability and task relevance. To disentangle these, include a rare non-target condition (three-stimulus oddball) or use an equiprobable control (Luck, 2014, Ch. 3; Polich, 2007).
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+ 6. **Physical-deviance confound in MMN**: The standard and deviant stimuli differ in physical features, which can produce differential N1 responses independent of memory-trace mismatch. Use a "many-standards" or "flip-flop" control design where the same physical stimulus serves as both standard and deviant across blocks (Naatanen et al., 2007; Jacobsen & Schroger, 2001).
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+ 7. **Lateralized eye movements confounding N2pc**: Saccades toward the target produce HEOG artifacts that mimic the contralateral negativity of the N2pc. Enforce fixation, reject trials with HEOG deviations > **+/- 16 uV** (corresponding to ~1 degree eye movement), or use residual HEOG correction (Luck, 2014, Ch. 3; Woodman & Luck, 2003).
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+ 8. **Insufficient error trials for ERN**: Error rate depends on task difficulty. If the task is too easy (< 5% errors), you will not accumulate enough error trials. Titrate difficulty to achieve **10--25% error rate** using adaptive procedures or speed-emphasis instructions (Gehring et al., 1993; Olvet & Hajcak, 2009).
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+ 9. **Confounding component overlap in language ERPs**: In sentence paradigms, an apparent N400 reduction may be driven by an overlapping P600 in the same condition, and vice versa. Report and interpret both components; consider component-overlap modeling (Luck, 2014, Ch. 2; Brouwer et al., 2017).
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+ 10. **High-pass filter artifacts for slow components**: If you plan to study CNV, P3b, N400, or P600, ensure the recording system and preprocessing pipeline allow high-pass cutoffs of **<= 0.1 Hz**. Cutoffs at **0.5 Hz or above** create artificial distortions of broad components (Tanner et al., 2015; see `erp-analysis` skill).
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+ ## EEG-Specific Additions to Standard Paradigm Design
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+ When adapting a behavioral paradigm for EEG, apply these modifications:
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+ | Feature | Behavioral Design | EEG Adaptation | Reason |
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+ |---|---|---|---|
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+ | ISI | 500--1500 ms | 1200--2500 ms | Avoid ERP overlap (Luck, 2014, Ch. 6) |
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+ | ISI variability | Fixed or blocked | Jittered +/- 200--500 ms | Prevent CNV, enable overlap correction |
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+ | Trial count | 40--80/condition | 50--200+/condition (component-dependent) | SNR from averaging |
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+ | Response hand | Any | Counterbalanced across blocks | LRP contamination |
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+ | Rest breaks | Every 50--100 trials | Every 30--60 trials (1--2 min breaks) | Reduce muscle artifact, blink accumulation |
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+ | Block length | 5--10 min | 3--5 min | Alpha drift, impedance changes |
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+ | Stimulus duration | Until response | Fixed 100--300 ms (for transient ERPs) | Standardize sensory input |
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+ | Practice | 10--20 trials | 20--40 trials with artifact feedback | Reduce blinks, movements in early blocks |
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+
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+ ## References
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+
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+ - Alday, P. M. (2019). How much baseline correction do we need in ERP research? *Brain Topography*, 32, 167--174.
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+ - Boudewyn, M. A., Luck, S. J., Farrens, J. L., & Kappenman, E. S. (2018). How many trials does it take to get a significant ERP effect? *Psychophysiology*, 55(6), e13049.
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+ - Brouwer, H., Crocker, M. W., Venhuizen, N. J., & Hoeks, J. C. J. (2017). A neurocomputational model of the N400 and the P600 in language processing. *Cognitive Science*, 41, 1318--1352.
203
+ - Brunia, C. H. M., van Boxtel, G. J. M., & Bocker, K. B. E. (2012). Negative slow waves as indices of anticipation. In S. J. Luck & E. S. Kappenman (Eds.), *The Oxford Handbook of ERP Components*. Oxford University Press.
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+ - Coles, M. G. H., & Rugg, M. D. (1995). Event-related brain potentials: An introduction. In M. D. Rugg & M. G. H. Coles (Eds.), *Electrophysiology of Mind*. Oxford University Press.
205
+ - Coles, M. G. H., Gratton, G., & Donchin, E. (1988). Detecting early communication: Using measures of movement-related potentials to illuminate human information processing. *Biological Psychology*, 26, 69--89.
206
+ - Duncan, C. C., et al. (2009). Event-related potentials in clinical research: Guidelines for eliciting, recording, and quantifying mismatch negativity, P300, and N400. *Clinical Neurophysiology*, 120(11), 1883--1908.
207
+ - Ehinger, B. V., & Dimigen, O. (2019). Unfold: An integrated toolbox for overlap correction, non-linear modeling, and regression-based EEG analysis. *PeerJ*, 7, e7838.
208
+ - Gehring, W. J., Goss, B., Coles, M. G. H., Meyer, D. E., & Donchin, E. (1993). A neural system for error detection and compensation. *Psychological Science*, 4(6), 385--390.
209
+ - Jacobsen, T., & Schroger, E. (2001). Is there pre-attentive memory-based comparison of pitch? *Psychophysiology*, 38(4), 723--727.
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+ - Jensen, K. M., & MacDonald, J. A. (2023). Towards thoughtful planning of ERP studies: How participants, trials, and effect magnitude interact to influence statistical power across seven ERP components. *Psychophysiology*, 60(7), e14245.
211
+ - Kappenman, E. S., & Luck, S. J. (2010). The effects of electrode impedance on data quality and statistical significance in ERP recordings. *Psychophysiology*, 47(5), 888--904.
212
+ - Kappenman, E. S., Farrens, J. L., Zhang, W., Stewart, A. X., & Luck, S. J. (2021). ERP CORE: An open resource for human event-related potential research. *NeuroImage*, 225, 117465.
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+ - Keil, A., et al. (2014). Committee report: Publication guidelines and recommendations for studies using EEG and MEG. *Psychophysiology*, 51(1), 1--21.
214
+ - Luck, S. J. (2005). Ten simple rules for designing ERP experiments. In T. C. Handy (Ed.), *Event-Related Potentials: A Methods Handbook*. MIT Press.
215
+ - Luck, S. J. (2014). *An Introduction to the Event-Related Potential Technique* (2nd ed.). MIT Press.
216
+ - Naatanen, R., Paavilainen, P., Rinne, T., & Alho, K. (2007). The mismatch negativity (MMN) in basic research of central auditory processing. *Clinical Neurophysiology*, 118(12), 2544--2590.
217
+ - Norcia, A. M., Appelbaum, L. G., Ales, J. M., Cottereau, B. R., & Rossion, B. (2015). The steady-state visual evoked potential in vision research: A review. *Journal of Vision*, 15(6), 4.
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+ - Olvet, D. M., & Hajcak, G. (2009). The stability of error-related brain activity with increasing number of trials. *Psychophysiology*, 46(5), 957--961.
219
+ - Osterhout, L., & Holcomb, P. J. (1992). Event-related brain potentials elicited by syntactic anomaly. *Journal of Memory and Language*, 31(6), 785--806.
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+ - Polich, J. (2007). Updating P300: An integrative theory of P3a and P3b. *Clinical Neurophysiology*, 118(10), 2128--2148.
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+ - Rossion, B., & Jacques, C. (2008). Does physical interstimulus variance account for early electrophysiological face sensitive responses? *NeuroImage*, 39(4), 1959--1966.
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+ - Tanner, D., Morgan-Short, K., & Luck, S. J. (2015). How inappropriate high-pass filters can produce artifactual effects. *Psychophysiology*, 52(8), 997--1009.
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+ - Woldorff, M. G. (1993). Distortion of ERP averages due to overlap from temporally adjacent ERPs: Analysis and correction. *Psychophysiology*, 30(1), 98--119.
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+ - Woodman, G. F., & Luck, S. J. (2003). Serial deployment of attention during visual search. *Journal of Experimental Psychology: Human Perception and Performance*, 29(1), 121--138.
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+ See `references/` for detailed component-paradigm mapping and timing parameter tables.