@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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1
+ # VLSM Pipeline: Step-by-Step Workflow
2
+
3
+ This reference document supplements `SKILL.md` with a detailed step-by-step workflow for voxel-based lesion-symptom mapping.
4
+
5
+ ## Pre-Analysis Checklist
6
+
7
+ Before starting VLSM, verify:
8
+
9
+ - [ ] N >= 50 patients (N >= 100 preferred; Sperber, 2020)
10
+ - [ ] All patients have T1 (and ideally FLAIR) images
11
+ - [ ] Behavioral data available for all patients (continuous preferred)
12
+ - [ ] Time post-onset is > 3 months for all (or most) patients
13
+ - [ ] Etiology is consistent (e.g., all ischemic stroke) or will be modeled
14
+
15
+ ## Step 1: Lesion Segmentation
16
+
17
+ ### Manual Tracing Protocol
18
+
19
+ 1. **Imaging modality**: Use T1 for chronic lesions (hypointense); FLAIR for acute/subacute lesions (hyperintense) or white matter lesions
20
+ 2. **Software**: MRIcron, ITK-SNAP, or 3D Slicer
21
+ 3. **Tracing procedure**:
22
+ - Trace on each axial slice (or coronal if preferred)
23
+ - Include all clearly damaged tissue
24
+ - Exclude peri-lesional edema if visible
25
+ - Include both cortical and subcortical damage
26
+ 4. **Inter-rater reliability**: If multiple raters, compute Dice coefficient; target >= 0.85 (Pustina et al., 2016)
27
+ 5. **Save as binary mask** (0 = healthy, 1 = lesioned) in the same space as the T1
28
+
29
+ ### Semi-Automated Segmentation
30
+
31
+ If using LINDA or lesion_gnb:
32
+ 1. Run the automated pipeline
33
+ 2. **CRITICAL**: Visually inspect EVERY patient's segmentation on all slices
34
+ 3. Manually correct errors (over-segmentation of ventricles, missed lesion regions)
35
+ 4. Document the correction process
36
+
37
+ ## Step 2: Spatial Normalization
38
+
39
+ ### Using ANTs (recommended)
40
+
41
+ ```bash
42
+ # Create lesion cost function mask (inverted lesion)
43
+ fslmaths lesion_mask.nii.gz -binv lesion_costmask.nii.gz
44
+
45
+ # Register T1 to MNI with cost function masking
46
+ antsRegistrationSyNQuick.sh \
47
+ -d 3 \
48
+ -f MNI152_T1_1mm.nii.gz \
49
+ -m patient_T1.nii.gz \
50
+ -x lesion_costmask.nii.gz \
51
+ -o patient_to_MNI_
52
+
53
+ # Apply warp to lesion mask
54
+ antsApplyTransforms \
55
+ -d 3 \
56
+ -i lesion_mask.nii.gz \
57
+ -r MNI152_T1_1mm.nii.gz \
58
+ -o lesion_mask_MNI.nii.gz \
59
+ -t patient_to_MNI_1Warp.nii.gz \
60
+ -t patient_to_MNI_0GenericAffine.mat \
61
+ -n NearestNeighbor
62
+ ```
63
+
64
+ ### Using FSL
65
+
66
+ ```bash
67
+ # Register with lesion masking
68
+ flirt -in patient_T1 -ref MNI152_T1_2mm -omat affine.mat \
69
+ -inweight lesion_costmask -cost mutualinfo
70
+
71
+ fnirt --in=patient_T1 --ref=MNI152_T1_2mm --aff=affine.mat \
72
+ --inmask=lesion_costmask --cout=warp_coeff
73
+
74
+ applywarp --in=lesion_mask --ref=MNI152_T1_2mm \
75
+ --warp=warp_coeff --out=lesion_mask_MNI --interp=nn
76
+ ```
77
+
78
+ ### Quality Control
79
+
80
+ For every patient:
81
+ 1. Overlay the warped T1 on the MNI template
82
+ 2. Check anatomical landmark alignment (ventricles, central sulcus, Sylvian fissure)
83
+ 3. Overlay the warped lesion mask on the template
84
+ 4. Verify the lesion location is anatomically plausible
85
+ 5. Flag and exclude patients with poor registration quality
86
+
87
+ ## Step 3: Create Lesion Overlap Map
88
+
89
+ 1. Sum all binarized lesion masks in MNI space
90
+ 2. Inspect the overlap map to understand lesion distribution
91
+ 3. Set minimum overlap threshold:
92
+ - Include voxels where >= **N_min patients** have lesions
93
+ - N_min = max(10, 10% of sample) (Kimberg et al., 2007)
94
+ - This creates the analysis mask
95
+
96
+ ## Step 4: Run VLSM Analysis
97
+
98
+ ### Using NiiStat (MATLAB)
99
+
100
+ ```matlab
101
+ % Load lesion masks and behavioral data
102
+ nii_stat(lesion_folder, behavior_file, ...
103
+ 'design', 'continuous', ... % or 'binomial'
104
+ 'stat', 'brunner-munzel', ... % or 'ttest'
105
+ 'perm', 5000, ... % permutation count
106
+ 'minOverlap', 10); % minimum lesion overlap
107
+ ```
108
+
109
+ ### Using LESYMAP (R)
110
+
111
+ ```r
112
+ library(LESYMAP)
113
+ lsm = lesymap(
114
+ lesions.list = lesion_files,
115
+ behavior = behavior_scores,
116
+ method = "BM", # Brunner-Munzel
117
+ multipleComparison = "FWE",
118
+ nperm = 5000,
119
+ minSubjectPerVoxel = 10
120
+ )
121
+ ```
122
+
123
+ ### Controlling for Lesion Volume
124
+
125
+ **Method 1: Direct covariate (recommended)**
126
+ ```r
127
+ lsm = lesymap(
128
+ lesions.list = lesion_files,
129
+ behavior = behavior_scores,
130
+ method = "regress", # Regression-based
131
+ covariates = data.frame(lesion_vol = volumes),
132
+ multipleComparison = "FWE",
133
+ nperm = 5000
134
+ )
135
+ ```
136
+
137
+ **Method 2: Residualization**
138
+ ```r
139
+ residuals = resid(lm(behavior ~ lesion_volume))
140
+ # Use residuals as behavior in standard VLSM
141
+ ```
142
+
143
+ ## Step 5: Interpret Results
144
+
145
+ ### What the Map Shows
146
+
147
+ - Each supra-threshold voxel indicates a statistical association between damage at that voxel and worse behavioral performance
148
+ - The map does NOT directly prove causation; it shows association (confounded by vascular territory collinearity)
149
+ - Report peak coordinates, cluster extent, and statistical values
150
+
151
+ ### What the Map Does NOT Show
152
+
153
+ - It does not identify "the region responsible for X" (collinearity caveat)
154
+ - It does not account for white matter disconnection effects
155
+ - It does not reveal whether the deficit is due to damage at the voxel or at a distant connected region
156
+
157
+ ### Supplementary Analyses
158
+
159
+ After VLSM, consider:
160
+ 1. **Disconnection analysis**: Run BCBToolkit to identify which tracts are disrupted
161
+ 2. **ROI validation**: Extract lesion load in a priori ROIs and test association with behavior
162
+ 3. **Lesion network mapping**: Identify the functional network disrupted by the lesion locations
163
+
164
+ ## Common Quality Control Issues
165
+
166
+ | Issue | Detection | Solution |
167
+ |---|---|---|
168
+ | Poor registration | Visual inspection of overlay | Re-run with different parameters or enantiomorphic approach |
169
+ | Lesion extends beyond brain boundary | Visual inspection | Mask lesion with brain mask |
170
+ | Ventricle labeled as lesion | Compare to template ventricles | Manually correct segmentation |
171
+ | Behavioral outliers | Box plots, Cook's distance | Investigate; consider robust statistics (Brunner-Munzel) |
172
+ | Insufficient lesion overlap | Overlap map shows sparse coverage | Lower voxel threshold or use ROI approach |
173
+
174
+ ## References
175
+
176
+ - Avants, B. B., et al. (2011). A reproducible evaluation of ANTs similarity metric performance in brain image registration. *NeuroImage*, 54(3), 2033--2044.
177
+ - Bates, E., et al. (2003). Voxel-based lesion-symptom mapping. *Nature Neuroscience*, 6(5), 448--450.
178
+ - Brett, M., et al. (2001). Spatial normalization of brain images with focal lesions using cost function masking. *NeuroImage*, 14(2), 486--500.
179
+ - Kimberg, D. Y., et al. (2007). Power in voxel-based lesion-symptom mapping. *Journal of Cognitive Neuroscience*, 19(7), 1067--1080.
180
+ - Pustina, D., et al. (2016). Automated segmentation of chronic stroke lesions using LINDA. *Human Brain Mapping*, 37(4), 1405--1421.
181
+ - Pustina, D., et al. (2018). Improved accuracy of lesion to symptom mapping with multivariate sparse canonical correlations. *Neuropsychologia*, 115, 154--166.
182
+ - Sperber, C. (2020). Rethinking causality and data complexity in brain lesion-behaviour inference. *Cortex*, 126, 49--62.
@@ -0,0 +1,250 @@
1
+ ---
2
+ name: "neuropsych-battery-selector"
3
+ description: "Domain-validated decision logic for selecting neuropsychological test batteries matched to suspected cognitive deficit profiles"
4
+ domain: "clinical-neuroscience"
5
+ authors:
6
+ - "Claude Code Agent"
7
+ version: "1.0.0"
8
+ papers:
9
+ - "Lezak et al., 2012"
10
+ - "Strauss et al., 2006"
11
+ - "Mitrushina et al., 2005"
12
+ - "Heilbronner et al., 2010"
13
+ dependencies:
14
+ required:
15
+ - research-literacy
16
+ review_status: "ai-generated"
17
+ ---
18
+
19
+ # Neuropsychological Battery Selector
20
+
21
+ ## Purpose
22
+
23
+ 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:
24
+
25
+ - **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).
26
+ - **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.
27
+ - **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).
28
+ - **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).
29
+
30
+ ## When to Use This Skill
31
+
32
+ Use this skill when you need to:
33
+
34
+ - Select neuropsychological tests matched to a suspected cognitive deficit profile
35
+ - Assemble a battery for a specific referral question (dementia differential, TBI, pre-surgical, forensic)
36
+ - Advise on which cognitive domains to assess given a neurological condition
37
+ - Evaluate whether a proposed battery has adequate domain coverage or problematic redundancy
38
+ - Choose between brief screening vs. comprehensive evaluation
39
+
40
+ Do NOT use this skill for:
41
+
42
+ - Interpreting test scores (that requires a different skill)
43
+ - Diagnosing neurological conditions from test results alone
44
+ - Administering tests (this requires licensed clinical training)
45
+
46
+ ## Research Planning Protocol
47
+
48
+ Before executing the domain-specific steps below, you MUST:
49
+
50
+ 1. **State the research question** -- What cognitive domain(s) are being assessed and why?
51
+ 2. **Justify the method choice** -- Why neuropsychological testing (not neuroimaging, behavioral paradigm)? What alternatives were considered?
52
+ 3. **Declare expected outcomes** -- What deficit pattern would support the clinical/research hypothesis?
53
+ 4. **Note assumptions and limitations** -- What does this battery assume about the patient? Where could it mislead?
54
+ 5. **Present the plan to the user and WAIT for confirmation** before proceeding.
55
+
56
+ For detailed methodology guidance, see the `research-literacy` skill.
57
+
58
+ ---
59
+
60
+
61
+ ## ⚠️ Verification Notice
62
+
63
+ 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).
64
+
65
+ ## Step 1: Clarify the Referral Question
66
+
67
+ The referral question determines everything. Map it to one of these categories:
68
+
69
+ | Referral Type | Primary Goal | Typical Battery Length |
70
+ |---|---|---|
71
+ | Dementia differential diagnosis | Distinguish AD vs. FTD vs. VaD vs. DLB | 3--4 hours |
72
+ | Mild cognitive impairment screening | Detect early decline, track progression | 1.5--2 hours |
73
+ | TBI evaluation (acute/subacute) | Document deficits, guide rehabilitation | 2--3 hours |
74
+ | TBI evaluation (chronic/forensic) | Quantify residual deficits, effort testing | 4--6 hours |
75
+ | Pre-surgical epilepsy workup | Lateralize/localize function, predict risk | 3--5 hours |
76
+ | Psychiatric differential | Distinguish cognitive vs. psychiatric etiology | 2--3 hours |
77
+ | Return-to-work/fitness-for-duty | Functional capacity in specific domains | 2--4 hours |
78
+
79
+ (Lezak et al., 2012, Ch. 5; Sweet et al., 2011 -- 78% of neuropsychologists use a flexible battery approach)
80
+
81
+ ---
82
+
83
+ ## Step 2: Identify Target Cognitive Domains
84
+
85
+ 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.
86
+
87
+ ### Cognitive Domain Framework
88
+
89
+ **Attention / Processing Speed**
90
+ - WAIS-IV Processing Speed Index (Coding, Symbol Search): **~15 min** (Wechsler, 2008)
91
+ - Trail Making Test Part A: **~3 min** (Reitan, 1958; deficient if >78 sec, ages 25--54)
92
+ - Continuous Performance Test (CPT-3): **~14 min** (Conners, 2014)
93
+ - WAIS-IV Digit Span (Forward): **~5 min** (Wechsler, 2008)
94
+
95
+ **Executive Function**
96
+ - Wisconsin Card Sorting Test (WCST-64): **~15 min** (Heaton et al., 1993)
97
+ - Trail Making Test Part B: **~5 min** (Reitan, 1958; deficient if >273 sec, ages 25--54)
98
+ - Stroop Color-Word Test: **~5 min** (Golden, 1978)
99
+ - Tower of London/D-KEFS Tower: **~15 min** (Shallice, 1982; Delis et al., 2001)
100
+ - Verbal Fluency -- FAS: **~5 min** (Benton et al., 1994; mean ~36--44 words total for ages 25--54, education 12+ years)
101
+ - Verbal Fluency -- Animals: **~2 min** (Strauss et al., 2006; mean ~20--24 animals for ages 25--54)
102
+
103
+ **Memory**
104
+ - WMS-IV (Logical Memory I & II, Verbal Paired Associates I & II): **~30--45 min** including delay (Wechsler, 2009)
105
+ - CVLT-II/CVLT-3 (California Verbal Learning Test): **~30 min** (Delis et al., 2000/2017)
106
+ - RAVLT (Rey Auditory Verbal Learning Test): **~15 min** (Rey, 1964; Schmidt, 1996)
107
+ - BVMT-R (Brief Visuospatial Memory Test--Revised): **~25 min** including delay (Benedict, 1997)
108
+ - Logical Memory (WMS-IV): immediate and delayed recall; **sensitivity 90--95% for MCI when combined with CVLT** (Rabin et al., 2009)
109
+
110
+ **Language**
111
+ - Boston Naming Test (BNT-60): **~15--20 min** (Kaplan et al., 1983)
112
+ - Token Test (short form): **~10 min** (De Renzi & Vignolo, 1962)
113
+ - Controlled Oral Word Association (COWA/FAS): **~5 min** (listed above under executive; also indexes language)
114
+ - Western Aphasia Battery--Revised (WAB-R): **~30--60 min** (Kertesz, 2007; use for suspected aphasia)
115
+
116
+ **Visuospatial / Visuoconstructional**
117
+ - Rey Complex Figure Test -- Copy: **~5--10 min** (Osterrieth, 1944; Meyers & Meyers, 1995)
118
+ - WAIS-IV Block Design: **~10 min** (Wechsler, 2008)
119
+ - Judgment of Line Orientation (JLO): **~15 min** (Benton et al., 1994)
120
+ - Hooper Visual Organization Test (VOT): **~15 min** (Hooper, 1983)
121
+
122
+ **Motor Function**
123
+ - Grooved Pegboard: **~5 min per hand** (Klove, 1963; Ruff & Parker, 1993)
124
+ - Finger Tapping Test: **~10 min** (Halstead, 1947; Reitan & Wolfson, 1993)
125
+
126
+ ---
127
+
128
+ ## Step 3: Assemble the Battery
129
+
130
+ ### Core Battery (~2--3 hours)
131
+
132
+ Every evaluation should include these unless contraindicated:
133
+
134
+ | Domain | Recommended Core Test(s) | Time |
135
+ |---|---|---|
136
+ | 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 |
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)
148
+
149
+ Add these for complex referrals (forensic, dementia differential, pre-surgical):
150
+
151
+ | Domain | Additional Tests | Time |
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.
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+ - **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
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+
221
+ For expected deficit profiles by condition, see `references/deficit-profiles.md`. Below are summary battery modifications:
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+
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+ | Condition | Add to Core | Remove/De-emphasize | Key Rationale |
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+ |---|---|---|---|
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+ | 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) |
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+ | FTD (behavioral variant) | WCST, D-KEFS, social cognition measures, personality inventory | De-emphasize visuospatial | Executive/behavioral profile dominates (Rascovsky et al., 2011) |
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+ | 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) |
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+ | TBI (moderate-severe) | CPT-3, PASAT, verbal fluency, motor tests bilateral | None -- broad battery needed | Diffuse deficits: attention, speed, memory, executive (Rabinowitz & Levin, 2014) |
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+ | 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) |
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+ | Parkinson's disease | Verbal fluency (semantic + phonemic), JLO, clock drawing, Grooved Pegboard | None | Dual-syndrome: frontostriatal vs. posterior cortical (Kehagia et al., 2013) |
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+ | 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 |
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+
233
+ ---
234
+
235
+ ## Quick Reference: Test-to-Domain Mapping
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+
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+ For a comprehensive catalog of tests with administration times, normative samples, and sensitivity data, see `references/test-catalog.md`.
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+
239
+ ---
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+
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.
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+ - Delis, D. C., Kaplan, E., & Kramer, J. H. (2001). *Delis-Kaplan Executive Function System*. Pearson.
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+ - 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.
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+ - 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.
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+ - Strauss, E., Sherman, E. M. S., & Spreen, O. (2006). *A Compendium of Neuropsychological Tests* (3rd ed.). Oxford University Press.
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+ - Sweet, J. J., Nelson, N. W., & Moberg, P. J. (2011). The TCN/AACN 2010 "salary survey." *The Clinical Neuropsychologist*, 25, 218--245.