@brainpilot/skills 0.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.d.ts +6 -0
- package/dist/index.d.ts.map +1 -0
- package/dist/index.js +28 -0
- package/dist/index.js.map +1 -0
- package/package.json +35 -0
- package/skills/01_Meta-Skills/contribute-skill/SKILL.md +277 -0
- package/skills/01_Meta-Skills/contribute-skills-via-pr/SKILL.md +163 -0
- package/skills/01_Meta-Skills/paper-to-skill/SKILL.md +435 -0
- package/skills/01_Meta-Skills/paper-to-skill/references/extraction-guide.md +286 -0
- package/skills/01_Meta-Skills/paper-to-skill/references/skill-template.md +250 -0
- package/skills/01_Meta-Skills/repo-to-skill/SKILL.md +289 -0
- package/skills/01_Meta-Skills/share-case/SKILL.md +253 -0
- package/skills/01_Meta-Skills/share-usage/README.md +63 -0
- package/skills/01_Meta-Skills/share-usage/SKILL.md +395 -0
- package/skills/01_Meta-Skills/verify-skill/SKILL.md +331 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/SKILL.md +194 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/effect-sizes.md +352 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/sample-size-guide.md +407 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-statistics/SKILL.md +361 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-statistics/references/common-analyses.md +517 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-visualization/SKILL.md +292 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-visualization/references/plot-recipes.md +709 -0
- package/skills/02_Cross-Domain_Foundation/research-literacy/SKILL.md +286 -0
- package/skills/02_Cross-Domain_Foundation/research-literacy/references/common-assumptions.md +320 -0
- package/skills/02_Cross-Domain_Foundation/research-literacy/references/planning-template.md +143 -0
- package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/SKILL.md +197 -0
- package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/references/instruction-templates.md +60 -0
- package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/SKILL.md +246 -0
- package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/classic-paradigms.md +435 -0
- package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/design-principles.md +256 -0
- package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/SKILL.md +270 -0
- package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/references/lavaan-templates.md +172 -0
- package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/SKILL.md +238 -0
- package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/references/scoring-rubric.md +143 -0
- package/skills/03_Cognitive_Psychology/drift-diffusion-model/SKILL.md +203 -0
- package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/fitting-guide.md +571 -0
- package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/model-variants.md +427 -0
- package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/SKILL.md +310 -0
- package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/references/ez-diffusion-formulas.md +137 -0
- package/skills/03_Cognitive_Psychology/signal-detection-analysis/SKILL.md +300 -0
- package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/application-guide.md +278 -0
- package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/sdt-formulas.md +318 -0
- package/skills/03_Cognitive_Psychology/visual-search-array-generator/SKILL.md +283 -0
- package/skills/03_Cognitive_Psychology/visual-search-array-generator/references/array-generation-parameters.yaml +111 -0
- package/skills/04_Psycholinguistics/reading-time-analysis/SKILL.md +301 -0
- package/skills/04_Psycholinguistics/reading-time-analysis/references/measure-computation-guide.md +195 -0
- package/skills/04_Psycholinguistics/self-paced-reading-designer/SKILL.md +257 -0
- package/skills/04_Psycholinguistics/self-paced-reading-designer/references/analysis-guide.md +356 -0
- package/skills/04_Psycholinguistics/self-paced-reading-designer/references/region-segmentation.md +266 -0
- package/skills/04_Psycholinguistics/sentence-stimulus-norming/SKILL.md +346 -0
- package/skills/04_Psycholinguistics/sentence-stimulus-norming/references/lexical-databases-guide.md +184 -0
- package/skills/05_EEG_ERP/eeg-paradigm-designer/SKILL.md +226 -0
- package/skills/05_EEG_ERP/eeg-paradigm-designer/references/component-paradigm-map.md +276 -0
- package/skills/05_EEG_ERP/eeg-paradigm-designer/references/timing-parameters.md +244 -0
- package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/SKILL.md +367 -0
- package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/references/parameter-lookup-tables.md +138 -0
- package/skills/05_EEG_ERP/erp-analysis/SKILL.md +185 -0
- package/skills/05_EEG_ERP/erp-analysis/references/erp-components.md +447 -0
- package/skills/05_EEG_ERP/erp-analysis/references/preprocessing-pipeline.md +277 -0
- package/skills/05_EEG_ERP/erp-analysis/references/statistical-approaches.md +351 -0
- package/skills/05_EEG_ERP/mne-python-guide/SKILL.md +174 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/decoding.md +178 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/io_formats.md +160 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/preprocessing.md +259 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/simulation.md +173 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/source_localization.md +234 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/statistics.md +196 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/time_frequency.md +165 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/visualization.md +175 -0
- package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/SKILL.md +317 -0
- package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
- package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/SKILL.md +296 -0
- package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/design-matrix-guide.md +214 -0
- package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/statistical-inference.md +288 -0
- package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/SKILL.md +274 -0
- package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/quality-control.md +336 -0
- package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/step-by-step-pipeline.md +380 -0
- package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/SKILL.md +264 -0
- package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/references/design-optimization-examples.md +114 -0
- package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/SKILL.md +273 -0
- package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/decoding-methods.md +170 -0
- package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/rsa-guide.md +266 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/SKILL.md +123 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/database-subjects.md +179 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/dataset-types.md +208 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/freesurfer-fmriprep.md +162 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mapping-transforms.md +181 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mni-utils.md +207 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/surface-analysis.md +219 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/visualization.md +251 -0
- package/skills/07_Computational_Modeling/act-r-model-builder/SKILL.md +297 -0
- package/skills/07_Computational_Modeling/act-r-model-builder/references/model-patterns.md +197 -0
- package/skills/07_Computational_Modeling/act-r-model-builder/references/parameter-table.yaml +204 -0
- package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/SKILL.md +294 -0
- package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/diagnostics-checklist.md +351 -0
- package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/prior-selection-guide.md +241 -0
- package/skills/07_Computational_Modeling/parameter-recovery-checker/SKILL.md +269 -0
- package/skills/07_Computational_Modeling/parameter-recovery-checker/references/recovery-diagnostics.md +207 -0
- package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/SKILL.md +317 -0
- package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
- package/skills/08_Computational_Neuroscience/neural-decoding-analysis/SKILL.md +273 -0
- package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/decoding-methods.md +170 -0
- package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/rsa-guide.md +266 -0
- package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/SKILL.md +305 -0
- package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/data-requirements.md +60 -0
- package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/method-comparison.md +151 -0
- package/skills/08_Computational_Neuroscience/spiking-network-model-builder/SKILL.md +376 -0
- package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/hh-parameters.md +117 -0
- package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/network-regimes.md +130 -0
- package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/SKILL.md +258 -0
- package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/indicator-parameters.md +242 -0
- package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/pipeline-details.md +211 -0
- package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/SKILL.md +261 -0
- package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/opsin-catalog.md +124 -0
- package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/stimulation-parameters.md +304 -0
- package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/SKILL.md +367 -0
- package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/disconnection-guide.md +152 -0
- package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/vlsm-pipeline.md +182 -0
- package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/SKILL.md +250 -0
- package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/deficit-profiles.md +302 -0
- package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/test-catalog.md +304 -0
- package/skills/11_Developmental_Cognition/infant-looking-time-designer/SKILL.md +345 -0
- package/skills/11_Developmental_Cognition/infant-looking-time-designer/references/age-parameters.yaml +186 -0
- package/skills/12_Social_Cognition/tom-task-selector/SKILL.md +379 -0
- package/skills/12_Social_Cognition/tom-task-selector/references/task-database.md +317 -0
- package/skills/13_Visualization/nature-figure/README.md +442 -0
- package/skills/13_Visualization/nature-figure/SKILL.md +60 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-01-bar-charts.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-02-line-trends.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-03-heatmaps.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-04-scatter-bubble.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-05-radar-polar.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-06-distributions.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-07-forest-interval.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-08-area-stacked.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-09-image-plates.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-10-network-matrix.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_motivation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation_distillation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_contrastive.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_CEDAR.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_IEDB.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_schematic.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/RNAGenScape_schematic.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/ablation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/comparison.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_ablation.py +86 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_comparison.py +109 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/diffusion_swiss_roll.py +97 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/diffusion_swiss_roll.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.pdf +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_Trajectory.pdf +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_Trajectory.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/figX_comparison_Ablation.pdf +0 -0
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- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Ablation.py +64 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_GeneRegulatory.py +74 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Trajectory.py +74 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/figures/idea.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/figures/illustration.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/plot_idea.py +76 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/plot_illustration.py +404 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_FPGM/figures/freq_prior.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_FPGM/plot_freq_prior.py +146 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_ablation_Cancer.png +0 -0
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- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/plot_bars.py +216 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/raw_data.py +125 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/figures/manifold.png +0 -0
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- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_comparison.py +228 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_hole_manifold.py +82 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_manifold.py +61 -0
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- package/skills/13_Visualization/nature-figure/assets/gallery/fig4-single-cell-systems-rich.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/gallery/fig5-validation-perturbation-rich.png +0 -0
- package/skills/13_Visualization/nature-figure/evals/evals.json +37 -0
- package/skills/13_Visualization/nature-figure/manifest.yaml +57 -0
- package/skills/13_Visualization/nature-figure/references/api.md +428 -0
- package/skills/13_Visualization/nature-figure/references/backend-selection.md +100 -0
- package/skills/13_Visualization/nature-figure/references/chart-types.md +281 -0
- package/skills/13_Visualization/nature-figure/references/common-patterns.md +350 -0
- package/skills/13_Visualization/nature-figure/references/demos.md +65 -0
- package/skills/13_Visualization/nature-figure/references/design-theory.md +436 -0
- package/skills/13_Visualization/nature-figure/references/figure-contract.md +93 -0
- package/skills/13_Visualization/nature-figure/references/nature-2026-observations.md +112 -0
- package/skills/13_Visualization/nature-figure/references/qa-contract.md +119 -0
- package/skills/13_Visualization/nature-figure/references/r-template-index.md +66 -0
- package/skills/13_Visualization/nature-figure/references/r-workflow.md +161 -0
- package/skills/13_Visualization/nature-figure/references/tutorials.md +251 -0
- package/skills/13_Visualization/nature-figure/static/core/contract.md +29 -0
- package/skills/13_Visualization/nature-figure/static/core/stance.md +37 -0
- package/skills/13_Visualization/nature-figure/static/fragments/backend/python.md +37 -0
- package/skills/13_Visualization/nature-figure/static/fragments/backend/r.md +44 -0
- package/skills/14_Writing/markdown-report-writing/SKILL.md +306 -0
- package/skills/14_Writing/markdown-report-writing/references/compatibility-matrix.md +72 -0
- package/skills/14_Writing/markdown-report-writing/references/templates.md +299 -0
- package/skills/15_Others/neuroimaging-power-guide/SKILL.md +324 -0
- package/skills/15_Others/neuroimaging-power-guide/references/effect-size-lookup-tables.md +102 -0
- package/skills/15_Others/neuroimaging-sample-size-calculator/SKILL.md +330 -0
- package/skills/15_Others/neuroimaging-sample-size-calculator/references/worked-examples.md +220 -0
package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/vlsm-pipeline.md
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# VLSM Pipeline: Step-by-Step Workflow
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This reference document supplements `SKILL.md` with a detailed step-by-step workflow for voxel-based lesion-symptom mapping.
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## Pre-Analysis Checklist
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Before starting VLSM, verify:
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- [ ] N >= 50 patients (N >= 100 preferred; Sperber, 2020)
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- [ ] All patients have T1 (and ideally FLAIR) images
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- [ ] Behavioral data available for all patients (continuous preferred)
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- [ ] Time post-onset is > 3 months for all (or most) patients
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- [ ] Etiology is consistent (e.g., all ischemic stroke) or will be modeled
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## Step 1: Lesion Segmentation
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### Manual Tracing Protocol
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1. **Imaging modality**: Use T1 for chronic lesions (hypointense); FLAIR for acute/subacute lesions (hyperintense) or white matter lesions
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2. **Software**: MRIcron, ITK-SNAP, or 3D Slicer
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3. **Tracing procedure**:
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- Trace on each axial slice (or coronal if preferred)
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- Include all clearly damaged tissue
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- Exclude peri-lesional edema if visible
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- Include both cortical and subcortical damage
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4. **Inter-rater reliability**: If multiple raters, compute Dice coefficient; target >= 0.85 (Pustina et al., 2016)
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5. **Save as binary mask** (0 = healthy, 1 = lesioned) in the same space as the T1
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### Semi-Automated Segmentation
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If using LINDA or lesion_gnb:
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1. Run the automated pipeline
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2. **CRITICAL**: Visually inspect EVERY patient's segmentation on all slices
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3. Manually correct errors (over-segmentation of ventricles, missed lesion regions)
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4. Document the correction process
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## Step 2: Spatial Normalization
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### Using ANTs (recommended)
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```bash
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# Create lesion cost function mask (inverted lesion)
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fslmaths lesion_mask.nii.gz -binv lesion_costmask.nii.gz
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# Register T1 to MNI with cost function masking
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antsRegistrationSyNQuick.sh \
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-d 3 \
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-f MNI152_T1_1mm.nii.gz \
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-m patient_T1.nii.gz \
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-x lesion_costmask.nii.gz \
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-o patient_to_MNI_
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# Apply warp to lesion mask
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antsApplyTransforms \
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-d 3 \
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-i lesion_mask.nii.gz \
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-r MNI152_T1_1mm.nii.gz \
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-o lesion_mask_MNI.nii.gz \
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-t patient_to_MNI_1Warp.nii.gz \
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-t patient_to_MNI_0GenericAffine.mat \
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-n NearestNeighbor
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```
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### Using FSL
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```bash
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# Register with lesion masking
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flirt -in patient_T1 -ref MNI152_T1_2mm -omat affine.mat \
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-inweight lesion_costmask -cost mutualinfo
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fnirt --in=patient_T1 --ref=MNI152_T1_2mm --aff=affine.mat \
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--inmask=lesion_costmask --cout=warp_coeff
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applywarp --in=lesion_mask --ref=MNI152_T1_2mm \
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--warp=warp_coeff --out=lesion_mask_MNI --interp=nn
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```
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### Quality Control
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For every patient:
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1. Overlay the warped T1 on the MNI template
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2. Check anatomical landmark alignment (ventricles, central sulcus, Sylvian fissure)
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3. Overlay the warped lesion mask on the template
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4. Verify the lesion location is anatomically plausible
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5. Flag and exclude patients with poor registration quality
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## Step 3: Create Lesion Overlap Map
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1. Sum all binarized lesion masks in MNI space
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2. Inspect the overlap map to understand lesion distribution
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3. Set minimum overlap threshold:
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- Include voxels where >= **N_min patients** have lesions
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- N_min = max(10, 10% of sample) (Kimberg et al., 2007)
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- This creates the analysis mask
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## Step 4: Run VLSM Analysis
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### Using NiiStat (MATLAB)
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```matlab
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% Load lesion masks and behavioral data
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nii_stat(lesion_folder, behavior_file, ...
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'design', 'continuous', ... % or 'binomial'
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'stat', 'brunner-munzel', ... % or 'ttest'
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'perm', 5000, ... % permutation count
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'minOverlap', 10); % minimum lesion overlap
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```
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### Using LESYMAP (R)
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```r
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library(LESYMAP)
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lsm = lesymap(
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lesions.list = lesion_files,
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behavior = behavior_scores,
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method = "BM", # Brunner-Munzel
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multipleComparison = "FWE",
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nperm = 5000,
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minSubjectPerVoxel = 10
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)
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```
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### Controlling for Lesion Volume
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**Method 1: Direct covariate (recommended)**
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```r
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lsm = lesymap(
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lesions.list = lesion_files,
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behavior = behavior_scores,
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method = "regress", # Regression-based
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covariates = data.frame(lesion_vol = volumes),
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multipleComparison = "FWE",
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nperm = 5000
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)
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```
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**Method 2: Residualization**
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```r
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residuals = resid(lm(behavior ~ lesion_volume))
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# Use residuals as behavior in standard VLSM
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```
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## Step 5: Interpret Results
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### What the Map Shows
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- Each supra-threshold voxel indicates a statistical association between damage at that voxel and worse behavioral performance
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- The map does NOT directly prove causation; it shows association (confounded by vascular territory collinearity)
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- Report peak coordinates, cluster extent, and statistical values
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### What the Map Does NOT Show
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- It does not identify "the region responsible for X" (collinearity caveat)
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- It does not account for white matter disconnection effects
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- It does not reveal whether the deficit is due to damage at the voxel or at a distant connected region
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### Supplementary Analyses
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After VLSM, consider:
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1. **Disconnection analysis**: Run BCBToolkit to identify which tracts are disrupted
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2. **ROI validation**: Extract lesion load in a priori ROIs and test association with behavior
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3. **Lesion network mapping**: Identify the functional network disrupted by the lesion locations
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## Common Quality Control Issues
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| Issue | Detection | Solution |
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|---|---|---|
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| Poor registration | Visual inspection of overlay | Re-run with different parameters or enantiomorphic approach |
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| Lesion extends beyond brain boundary | Visual inspection | Mask lesion with brain mask |
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| Ventricle labeled as lesion | Compare to template ventricles | Manually correct segmentation |
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| Behavioral outliers | Box plots, Cook's distance | Investigate; consider robust statistics (Brunner-Munzel) |
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| Insufficient lesion overlap | Overlap map shows sparse coverage | Lower voxel threshold or use ROI approach |
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## References
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- Avants, B. B., et al. (2011). A reproducible evaluation of ANTs similarity metric performance in brain image registration. *NeuroImage*, 54(3), 2033--2044.
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- Bates, E., et al. (2003). Voxel-based lesion-symptom mapping. *Nature Neuroscience*, 6(5), 448--450.
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- Brett, M., et al. (2001). Spatial normalization of brain images with focal lesions using cost function masking. *NeuroImage*, 14(2), 486--500.
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- Kimberg, D. Y., et al. (2007). Power in voxel-based lesion-symptom mapping. *Journal of Cognitive Neuroscience*, 19(7), 1067--1080.
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- Pustina, D., et al. (2016). Automated segmentation of chronic stroke lesions using LINDA. *Human Brain Mapping*, 37(4), 1405--1421.
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- Pustina, D., et al. (2018). Improved accuracy of lesion to symptom mapping with multivariate sparse canonical correlations. *Neuropsychologia*, 115, 154--166.
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- Sperber, C. (2020). Rethinking causality and data complexity in brain lesion-behaviour inference. *Cortex*, 126, 49--62.
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---
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name: "neuropsych-battery-selector"
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description: "Domain-validated decision logic for selecting neuropsychological test batteries matched to suspected cognitive deficit profiles"
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domain: "clinical-neuroscience"
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authors:
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- "Claude Code Agent"
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version: "1.0.0"
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papers:
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- "Lezak et al., 2012"
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- "Strauss et al., 2006"
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- "Mitrushina et al., 2005"
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- "Heilbronner et al., 2010"
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dependencies:
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required:
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- research-literacy
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review_status: "ai-generated"
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---
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# Neuropsychological Battery Selector
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## Purpose
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Selecting a neuropsychological test battery is a clinical judgment task, not a checklist exercise. A competent programmer without clinical neuropsychology training will get this wrong because:
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- **Not all "memory tests" test the same construct.** The CVLT-II/III assesses list learning with encoding strategies; Logical Memory tests narrative recall; the BVMT-R tests visual-spatial memory. Each is sensitive to different lesion profiles (Lezak et al., 2012, Ch. 11).
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- **Test selection must match the referral question.** A dementia screen requires different instruments than a TBI return-to-work evaluation or a pre-surgical epilepsy workup.
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- **Normative data are not interchangeable.** Age, education, cultural background, and premorbid ability all determine which norms to apply and whether a given score is actually impaired (Mitrushina et al., 2005).
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- **Redundant tests waste time and fatigue patients.** Over-testing degrades performance and inflates apparent impairment, particularly in older adults and those with attentional deficits (Strauss et al., 2006).
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## When to Use This Skill
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Use this skill when you need to:
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- Select neuropsychological tests matched to a suspected cognitive deficit profile
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- Assemble a battery for a specific referral question (dementia differential, TBI, pre-surgical, forensic)
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- Advise on which cognitive domains to assess given a neurological condition
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- Evaluate whether a proposed battery has adequate domain coverage or problematic redundancy
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- Choose between brief screening vs. comprehensive evaluation
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Do NOT use this skill for:
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- Interpreting test scores (that requires a different skill)
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- Diagnosing neurological conditions from test results alone
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- Administering tests (this requires licensed clinical training)
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## Research Planning Protocol
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Before executing the domain-specific steps below, you MUST:
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1. **State the research question** -- What cognitive domain(s) are being assessed and why?
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2. **Justify the method choice** -- Why neuropsychological testing (not neuroimaging, behavioral paradigm)? What alternatives were considered?
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3. **Declare expected outcomes** -- What deficit pattern would support the clinical/research hypothesis?
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4. **Note assumptions and limitations** -- What does this battery assume about the patient? 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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For detailed methodology guidance, see the `research-literacy` skill.
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---
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## ⚠️ Verification Notice
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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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## Step 1: Clarify the Referral Question
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The referral question determines everything. Map it to one of these categories:
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| Referral Type | Primary Goal | Typical Battery Length |
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|---|---|---|
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| Dementia differential diagnosis | Distinguish AD vs. FTD vs. VaD vs. DLB | 3--4 hours |
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| Mild cognitive impairment screening | Detect early decline, track progression | 1.5--2 hours |
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| TBI evaluation (acute/subacute) | Document deficits, guide rehabilitation | 2--3 hours |
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| TBI evaluation (chronic/forensic) | Quantify residual deficits, effort testing | 4--6 hours |
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| Pre-surgical epilepsy workup | Lateralize/localize function, predict risk | 3--5 hours |
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| Psychiatric differential | Distinguish cognitive vs. psychiatric etiology | 2--3 hours |
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| Return-to-work/fitness-for-duty | Functional capacity in specific domains | 2--4 hours |
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(Lezak et al., 2012, Ch. 5; Sweet et al., 2011 -- 78% of neuropsychologists use a flexible battery approach)
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---
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## Step 2: Identify Target Cognitive Domains
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Based on the referral question and suspected condition, select domains to assess. Every battery MUST cover at least attention/processing speed, memory, and executive function. Add domains based on the clinical picture.
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### Cognitive Domain Framework
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**Attention / Processing Speed**
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- WAIS-IV Processing Speed Index (Coding, Symbol Search): **~15 min** (Wechsler, 2008)
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- Trail Making Test Part A: **~3 min** (Reitan, 1958; deficient if >78 sec, ages 25--54)
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- Continuous Performance Test (CPT-3): **~14 min** (Conners, 2014)
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- WAIS-IV Digit Span (Forward): **~5 min** (Wechsler, 2008)
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**Executive Function**
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- Wisconsin Card Sorting Test (WCST-64): **~15 min** (Heaton et al., 1993)
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- Trail Making Test Part B: **~5 min** (Reitan, 1958; deficient if >273 sec, ages 25--54)
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- Stroop Color-Word Test: **~5 min** (Golden, 1978)
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- Tower of London/D-KEFS Tower: **~15 min** (Shallice, 1982; Delis et al., 2001)
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- Verbal Fluency -- FAS: **~5 min** (Benton et al., 1994; mean ~36--44 words total for ages 25--54, education 12+ years)
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- Verbal Fluency -- Animals: **~2 min** (Strauss et al., 2006; mean ~20--24 animals for ages 25--54)
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**Memory**
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104
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- WMS-IV (Logical Memory I & II, Verbal Paired Associates I & II): **~30--45 min** including delay (Wechsler, 2009)
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105
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- CVLT-II/CVLT-3 (California Verbal Learning Test): **~30 min** (Delis et al., 2000/2017)
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- RAVLT (Rey Auditory Verbal Learning Test): **~15 min** (Rey, 1964; Schmidt, 1996)
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- BVMT-R (Brief Visuospatial Memory Test--Revised): **~25 min** including delay (Benedict, 1997)
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108
|
+
- Logical Memory (WMS-IV): immediate and delayed recall; **sensitivity 90--95% for MCI when combined with CVLT** (Rabin et al., 2009)
|
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109
|
+
|
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110
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+
**Language**
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111
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+
- Boston Naming Test (BNT-60): **~15--20 min** (Kaplan et al., 1983)
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112
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+
- Token Test (short form): **~10 min** (De Renzi & Vignolo, 1962)
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113
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+
- Controlled Oral Word Association (COWA/FAS): **~5 min** (listed above under executive; also indexes language)
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114
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+
- Western Aphasia Battery--Revised (WAB-R): **~30--60 min** (Kertesz, 2007; use for suspected aphasia)
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115
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+
|
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116
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+
**Visuospatial / Visuoconstructional**
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117
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+
- Rey Complex Figure Test -- Copy: **~5--10 min** (Osterrieth, 1944; Meyers & Meyers, 1995)
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118
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+
- WAIS-IV Block Design: **~10 min** (Wechsler, 2008)
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119
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+
- Judgment of Line Orientation (JLO): **~15 min** (Benton et al., 1994)
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120
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+
- Hooper Visual Organization Test (VOT): **~15 min** (Hooper, 1983)
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121
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+
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122
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+
**Motor Function**
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- Grooved Pegboard: **~5 min per hand** (Klove, 1963; Ruff & Parker, 1993)
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124
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+
- Finger Tapping Test: **~10 min** (Halstead, 1947; Reitan & Wolfson, 1993)
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125
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+
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126
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+
---
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+
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## Step 3: Assemble the Battery
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+
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### Core Battery (~2--3 hours)
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+
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Every evaluation should include these unless contraindicated:
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| Domain | Recommended Core Test(s) | Time |
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+
|---|---|---|
|
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136
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+
| Premorbid estimate | TOPF or WTAR | ~10 min |
|
|
137
|
+
| Attention / Processing Speed | TMT-A + WAIS-IV Coding + Digit Span | ~20 min |
|
|
138
|
+
| Executive Function | TMT-B + Verbal Fluency (FAS + Animals) + Stroop | ~15 min |
|
|
139
|
+
| Verbal Memory | CVLT-II/III or RAVLT | ~30 min |
|
|
140
|
+
| Visual Memory | BVMT-R or RCFT recall | ~25 min |
|
|
141
|
+
| Language | BNT (30- or 60-item) | ~15 min |
|
|
142
|
+
| Visuospatial | RCFT Copy or Block Design | ~10 min |
|
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143
|
+
| Motor | Grooved Pegboard (bilateral) | ~10 min |
|
|
144
|
+
| Effort/Validity | TOMM Trial 1 or embedded measures | ~10 min |
|
|
145
|
+
| **Total** | | **~145 min** |
|
|
146
|
+
|
|
147
|
+
### Extended Battery (~4--6 hours)
|
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148
|
+
|
|
149
|
+
Add these for complex referrals (forensic, dementia differential, pre-surgical):
|
|
150
|
+
|
|
151
|
+
| Domain | Additional Tests | Time |
|
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152
|
+
|---|---|---|
|
|
153
|
+
| Intelligence estimate | WAIS-IV (4 index scores) | ~70 min |
|
|
154
|
+
| Memory (expanded) | WMS-IV (full battery) | ~75 min |
|
|
155
|
+
| Executive (expanded) | WCST-64 + Tower | ~30 min |
|
|
156
|
+
| Language (expanded) | Token Test + WAB-R | ~40 min |
|
|
157
|
+
| Visuospatial (expanded) | JLO + Hooper VOT | ~30 min |
|
|
158
|
+
| Effort/Validity (expanded) | TOMM (full) + WMT or MSVT | ~30 min |
|
|
159
|
+
| **Added time** | | **~275 min** |
|
|
160
|
+
|
|
161
|
+
### Assembly Rules
|
|
162
|
+
|
|
163
|
+
1. **One verbal learning test**: Choose CVLT-II/III OR RAVLT, not both. They measure overlapping constructs (Strauss et al., 2006--778).
|
|
164
|
+
2. **One copy figure**: RCFT copy OR Block Design for visuoconstruction screening. Use both only if visuospatial function is the primary question.
|
|
165
|
+
3. **Delay intervals**: Schedule verbal memory delay recall (~20--30 min after learning) during non-memory tasks. Same for visual memory delay.
|
|
166
|
+
4. **Fatigue management**: Place demanding tests (WCST, CVLT) early. Place motor tests as breaks. Offer rest periods every 60--90 min (Lezak et al., 2012, Ch. 6).
|
|
167
|
+
5. **At least one validity measure**: Mandatory. Use TOMM Trial 1 (sensitivity 83%, specificity 93% at cutoff <=40; Denning, 2012) as a minimum. For forensic cases, use two or more PVTs from different modalities (Sweet et al., 2011).
|
|
168
|
+
|
|
169
|
+
---
|
|
170
|
+
|
|
171
|
+
## Step 4: Select Appropriate Norms
|
|
172
|
+
|
|
173
|
+
### Normative Data Decision Tree
|
|
174
|
+
|
|
175
|
+
1. **Age**: Always match. Most tests provide age-stratified norms.
|
|
176
|
+
2. **Education**: Use education-corrected norms when available (e.g., Heaton et al., 2004 norms for TMT, WCST, verbal fluency).
|
|
177
|
+
3. **Premorbid IQ**: For patients with estimated IQ far from average, IQ-adjusted norms improve accuracy over education alone. MOANS norms found BNT, Token Test, and JLO correlate more strongly with IQ (r = .47--.61) than with education (r = .24--.31) (Steinberg et al., 2005).
|
|
178
|
+
4. **Cultural/linguistic background**: US-normed tests may overestimate impairment in non-English speakers or culturally diverse populations (Lucas et al., 2005; Pena-Casanova et al., 2009). Use population-specific norms when available (e.g., NP-NUMBRS for Spanish speakers).
|
|
179
|
+
5. **Sex**: Match when norms are available. Grooved Pegboard shows significant sex differences: women faster than men (Ruff & Parker, 1993). Finger Tapping: men faster, especially in older groups.
|
|
180
|
+
|
|
181
|
+
### Premorbid Estimation
|
|
182
|
+
|
|
183
|
+
- **TOPF** (Test of Premorbid Functioning): 70 irregular words, co-normed with WAIS-IV/WMS-IV, IQ range 53--141 (Pearson, 2009). Preferred for current use.
|
|
184
|
+
- **WTAR** (Wechsler Test of Adult Reading): predecessor to TOPF, co-normed with WAIS-III/WMS-III (Wechsler, 2001). Acceptable if TOPF unavailable.
|
|
185
|
+
- **Caution**: Both underestimate premorbid IQ in high-functioning individuals and overestimate in low-functioning individuals (Bright & van der Linde, 2020). Supplement with demographic-based estimates.
|
|
186
|
+
|
|
187
|
+
---
|
|
188
|
+
|
|
189
|
+
## Step 5: Address Common Pitfalls
|
|
190
|
+
|
|
191
|
+
### Practice Effects in Serial Assessment
|
|
192
|
+
|
|
193
|
+
- Practice effects average **d = 0.24--0.28** on composite scores at 6--12 month retest intervals (Calamia et al., 2012).
|
|
194
|
+
- No consensus on minimum retest interval; effects persist for **2+ years** on some measures (Heilbronner et al., 2010).
|
|
195
|
+
- Tests most susceptible: PASAT, Stroop interference, verbal fluency, TMT-B (Beglinger et al., 2005).
|
|
196
|
+
- Tests least susceptible: Digit Span, Letter-Number Sequencing (Beglinger et al., 2005).
|
|
197
|
+
- **Mitigation**: Use alternate forms (CVLT-II has alternate form; RAVLT has multiple lists). Apply reliable change indices (RCIs) or standardized regression-based norms to interpret change (Chelune et al., 1993).
|
|
198
|
+
|
|
199
|
+
### Ceiling and Floor Effects
|
|
200
|
+
|
|
201
|
+
- **Ceiling effects**: TMT-A and simple attention tests may miss mild deficits in high-functioning individuals. Add more demanding measures (e.g., PASAT, D-KEFS verbal fluency switching) (Strauss et al., 2006).
|
|
202
|
+
- **Floor effects**: WCST and complex tests may be too difficult for moderate-to-severe dementia. Substitute with simpler tasks (e.g., clock drawing, category fluency) (Lezak et al., 2012, Ch. 18).
|
|
203
|
+
|
|
204
|
+
### Ecological Validity
|
|
205
|
+
|
|
206
|
+
- Neuropsychological tests have modest correlations (**r = .3--.5**) with real-world functioning (Chaytor & Schmitter-Edgecombe, 2003).
|
|
207
|
+
- Supplement with functional measures (e.g., Independent Living Scales, IADL checklists) when the referral question concerns everyday competence.
|
|
208
|
+
- Executive function tests have particularly limited ecological validity; consider adding the Behavioral Assessment of the Dysexecutive Syndrome (BADS) or real-world task simulations (Wilson et al., 1996).
|
|
209
|
+
|
|
210
|
+
### Symptom Validity Testing
|
|
211
|
+
|
|
212
|
+
- **TOMM** standard cutoff (<45 Trial 2): specificity .96--1.00 but sensitivity only .15--.50 (Tombaugh, 1996). Use Trial 1 cutoff <=40 for better sensitivity (.83) at .93 specificity (Denning, 2012).
|
|
213
|
+
- **WMT** (Word Memory Test): more sensitive than TOMM but higher false-positive rate in genuine MCI/dementia -- 67% of MCI patients classified as "poor effort" at standard cutoffs (Green, 2003). Use hard-easy comparison scores instead (sensitivity/specificity ~95%).
|
|
214
|
+
- **Embedded PVTs**: Reliable Digit Span (RDS >= 7 as cutoff; Greiffenstein et al., 1994), CVLT-II Forced Choice <=15 (Delis et al., 2000). Use multiple embedded measures to supplement standalone PVTs.
|
|
215
|
+
- **Rule**: In forensic and disability evaluations, include at least **two standalone PVTs and two embedded PVTs** (Larrabee, 2012).
|
|
216
|
+
|
|
217
|
+
---
|
|
218
|
+
|
|
219
|
+
## Step 6: Condition-Specific Battery Recommendations
|
|
220
|
+
|
|
221
|
+
For expected deficit profiles by condition, see `references/deficit-profiles.md`. Below are summary battery modifications:
|
|
222
|
+
|
|
223
|
+
| Condition | Add to Core | Remove/De-emphasize | Key Rationale |
|
|
224
|
+
|---|---|---|---|
|
|
225
|
+
| Alzheimer's (suspected) | WMS-IV full, CVLT-3 intrusion analysis, BNT-60 | May shorten executive battery | Memory encoding/storage is primary deficit (Weintraub et al., 2012) |
|
|
226
|
+
| FTD (behavioral variant) | WCST, D-KEFS, social cognition measures, personality inventory | De-emphasize visuospatial | Executive/behavioral profile dominates (Rascovsky et al., 2011) |
|
|
227
|
+
| Vascular dementia | Processing speed emphasis (Coding, Symbol Search), TMT-A/B, verbal fluency | May abbreviate language | Processing speed and executive function most affected (Sachdev et al., 2014) |
|
|
228
|
+
| TBI (moderate-severe) | CPT-3, PASAT, verbal fluency, motor tests bilateral | None -- broad battery needed | Diffuse deficits: attention, speed, memory, executive (Rabinowitz & Levin, 2014) |
|
|
229
|
+
| Temporal lobe epilepsy | Verbal/visual memory (laterality-specific), BNT, verbal fluency | May abbreviate motor | Memory lateralization critical for surgical planning (Jones-Gotman et al., 2010) |
|
|
230
|
+
| Parkinson's disease | Verbal fluency (semantic + phonemic), JLO, clock drawing, Grooved Pegboard | None | Dual-syndrome: frontostriatal vs. posterior cortical (Kehagia et al., 2013) |
|
|
231
|
+
| Multiple sclerosis | SDMT, PASAT, CVLT-II/III, BVMT-R | May abbreviate language | BICAMS recommended minimum battery (Langdon et al., 2012): SDMT + CVLT-II + BVMT-R |
|
|
232
|
+
|
|
233
|
+
---
|
|
234
|
+
|
|
235
|
+
## Quick Reference: Test-to-Domain Mapping
|
|
236
|
+
|
|
237
|
+
For a comprehensive catalog of tests with administration times, normative samples, and sensitivity data, see `references/test-catalog.md`.
|
|
238
|
+
|
|
239
|
+
---
|
|
240
|
+
|
|
241
|
+
## Key References
|
|
242
|
+
|
|
243
|
+
- Benton, A. L., Sivan, A. B., Hamsher, K., Varney, N. R., & Spreen, O. (1994). *Contributions to Neuropsychological Assessment* (2nd ed.). Oxford University Press.
|
|
244
|
+
- Delis, D. C., Kaplan, E., & Kramer, J. H. (2001). *Delis-Kaplan Executive Function System*. Pearson.
|
|
245
|
+
- Heaton, R. K., Miller, S. W., Taylor, M. J., & Grant, I. (2004). *Revised Comprehensive Norms for an Expanded Halstead-Reitan Battery*. PAR.
|
|
246
|
+
- Heilbronner, R. L., Sweet, J. J., Attix, D. K., Krull, K. R., Henry, G. K., & Hart, R. P. (2010). Official position of the AACN on serial neuropsychological assessments. *The Clinical Neuropsychologist*, 24, 1267--1278.
|
|
247
|
+
- Lezak, M. D., Howieson, D. B., Bigler, E. D., & Tranel, D. (2012). *Neuropsychological Assessment* (5th ed.). Oxford University Press.
|
|
248
|
+
- Mitrushina, M., Boone, K. B., Razani, J., & D'Elia, L. F. (2005). *Handbook of Normative Data for Neuropsychological Assessment* (2nd ed.). Oxford University Press.
|
|
249
|
+
- Strauss, E., Sherman, E. M. S., & Spreen, O. (2006). *A Compendium of Neuropsychological Tests* (3rd ed.). Oxford University Press.
|
|
250
|
+
- Sweet, J. J., Nelson, N. W., & Moberg, P. J. (2011). The TCN/AACN 2010 "salary survey." *The Clinical Neuropsychologist*, 25, 218--245.
|