Alex Brain — Neuroanatomical Mapping

Click on any brain region to see its Alex mapping.

The brain is shown in left lateral view — the same orientation used in neuroscience textbooks. Major lobes are color-coded. Key Brodmann area numbers are overlaid.

Each colored region maps to a specific Alex cognitive component. The blue dlPFC region (BA 9/46) is the most densely mapped area, housing 4 distinct sub-functions.

Condition	Alex Failure Mode
Executive Dysfunction	Low-tier model on complex tasks
ADHD	No attention gating (all protocols compete)
Impulsivity	No verification gate (code before plan)
Cognitive Rigidity	No pivot detection (stale context)
Seizure	No inhibitory synapses
Amnesia	No meditation (lost insights)
Dementia	Broken synapses, no dream cycle
Amygdala Lesion	No kill switch (self-destructive ops)

🗺️ Complete Brain Map

Full neuroanatomical mapping of Alex's cognitive architecture. Six brain regions containing all major components — from the LLM executive function (PFC) through the amygdala safety system to distributed global knowledge.

graph TB subgraph FRONTAL["FRONTAL LOBE"] subgraph PFC["Prefrontal Cortex - Executive Function"] LLM["LLM Claude-GPT
Reasoning, Planning, Decisions
The thinking engine"] end subgraph DLPFC["Dorsolateral PFC BA 9-46 - Task Planning"] SSO["Skill Selection Optimization
Proactive resource allocation"] AG["Attention Gating BA 46
SSO Phase 1b - context filtering"] IC["Inhibitory Control + vlPFC
Suppress irrelevant protocols"] VG["Verification Gate
Delayed gratification checkpoint"] end subgraph ACC["Anterior Cingulate Cortex - Conflict Monitor"] PD["Pivot Detection Protocol
Task-switch signal detection"] WM["Working Memory P1-P7
7 plus-minus 2 active rules"] end subgraph PMC["Premotor Cortex - Motor Planning"] SA["Skill Activation
Reactive capability routing"] end end subgraph TEMPORAL["TEMPORAL LOBE"] subgraph HIPP["Hippocampus - Episodic Memory"] EP[".prompt.md files
Workflows and session records"] EA[".github episodic
Historical session archive"] end end subgraph PARIETAL["PARIETAL LOBE"] subgraph NC["Neocortex - Declarative Knowledge"] SK["Skills x76
skills SKILL.md"] DM["Declarative Memory
copilot-instructions.md"] end end subgraph BASAL["SUBCORTICAL STRUCTURES"] subgraph BG["Basal Ganglia - Procedural Memory"] PM[".instructions.md x24
Automated procedures"] end subgraph THAL["Thalamus - Sensory Relay"] INPUT["User Input
Chat, Commands, Files"] end subgraph AMYG["Amygdala - Threat Detection"] SAFETY["Safety Imperatives I1-I7
Kill switch, RISKS.md"] end end subgraph MEDIAL["MEDIAL STRUCTURES"] subgraph MPFC["Medial PFC + DMN - Meta-Cognition"] MC["Self-Monitoring
Meta-cognitive awareness"] SA2["Self-Actualization
Deep architecture assessment"] end subgraph HPC["Hippocampal-Cortical - Consolidation"] MED["Meditation
Knowledge consolidation"] DRM["Dream State
Unconscious maintenance"] end end subgraph DISTRIBUTE["DISTRIBUTED CORTEX"] GK["Global Knowledge
Cross-project patterns"] SYN["Synaptic Network
Embedded connections + inhibitory"] end LLM ==>|"orchestrates"| SSO LLM ==>|"orchestrates"| WM LLM ==>|"orchestrates"| SA LLM ==>|"orchestrates"| MC SSO --> AG AG --> IC IC --> VG PD -.->|"pivot signal"| SSO WM -->|"slot context"| SSO SA -->|"routes to"| SK SA -->|"routes to"| PM SSO -->|"surveys"| SK MED -.->|"strengthens"| SYN DRM -.->|"validates"| SYN INPUT -->|"relayed"| LLM INPUT -->|"low road"| SAFETY SAFETY -.->|"blocks"| LLM SAFETY -.->|"blocks"| SA EP -->|"archived"| EA SK -->|"promoted"| GK IC -.->|"suppresses"| DRM IC -.->|"suppresses"| MED style FRONTAL fill:#1a3a5c,stroke:#58a6ff,color:#c9d1d9 style TEMPORAL fill:#0d2d3d,stroke:#39d2c0,color:#c9d1d9 style PARIETAL fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style BASAL fill:#21262d,stroke:#e3b341,color:#c9d1d9 style MEDIAL fill:#2d1a3d,stroke:#d2a8ff,color:#c9d1d9 style DISTRIBUTE fill:#2d1a3d,stroke:#bc8cff,color:#c9d1d9 style LLM fill:#1a3a5c,stroke:#58a6ff,color:#f0f6fc,stroke-width:3px style SSO fill:#3d2800,stroke:#f0883e,color:#f0f6fc,stroke-width:2px style AG fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style VG fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style IC fill:#5c1a1a,stroke:#ff6b6b,color:#f0f6fc,stroke-width:2px style PD fill:#3d1500,stroke:#f85149,color:#c9d1d9 style WM fill:#1a3a5c,stroke:#58a6ff,color:#c9d1d9 style SA fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style EP fill:#0d2d3d,stroke:#39d2c0,color:#c9d1d9 style EA fill:#0d2d3d,stroke:#39d2c0,color:#c9d1d9 style SK fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style DM fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style PM fill:#21262d,stroke:#e3b341,color:#c9d1d9 style INPUT fill:#21262d,stroke:#e3b341,color:#c9d1d9 style SAFETY fill:#5c1a1a,stroke:#ff6b6b,color:#f0f6fc,stroke-width:3px style MC fill:#2d1a3d,stroke:#d2a8ff,color:#c9d1d9 style SA2 fill:#2d1a3d,stroke:#d2a8ff,color:#c9d1d9 style MED fill:#0d2d3d,stroke:#79c0ff,color:#c9d1d9 style DRM fill:#0d2d3d,stroke:#79c0ff,color:#c9d1d9 style GK fill:#2d1a3d,stroke:#bc8cff,color:#c9d1d9 style SYN fill:#2d1a3d,stroke:#bc8cff,color:#c9d1d9

Frontal lobe (blue) houses executive function; dlPFC (orange) handles task planning; ACC/vlPFC monitors conflict. Temporal (teal) stores episodic memory. Parietal (green) holds declarative knowledge. Subcortical structures include procedures, input relay, and threat detection (amygdala, red). Medial structures (lavender) enable meta-cognition and consolidation.

⚡ Signal Flow

How information flows through Alex's brain — from user input through the amygdala safety check, executive parsing, task planning with attention gating, conflict monitoring, and response generation.

flowchart TB INPUT["User Input - Thalamus"] SAFETY["Safety Check - Amygdala
Imperatives I1-I7"] subgraph EXEC["Executive Processing - PFC"] LLM["LLM
Parse intent"] end subgraph PLAN["Task Planning - dlPFC"] COMPLEX{"Complex?"} SSO_SURVEY["Survey skills"] SSO_GATE["Gate attention"] SSO_DEPS["Analyze deps"] SSO_VERIFY["Verify plan"] SIMPLE["Direct execute"] end subgraph MONITOR["Conflict Monitor - ACC"] PIVOT{"Domain
pivot?"} SLOTS["Rotate P5-P7"] end subgraph EXECUTE["Execution - Premotor"] ROUTE["Route to skills"] INHIBIT["Check inhibitions"] OUTPUT["Generate Response"] end subgraph MEMORY["Memory Systems"] PROC["Procedural
Basal Ganglia"] EPIS["Episodic
Hippocampus"] DECL["Declarative
Neocortex"] GLOB["Global
Distributed"] end INPUT --> SAFETY SAFETY -->|"safe"| LLM SAFETY -.->|"threat - HALT"| OUTPUT LLM --> COMPLEX COMPLEX -->|"3+ ops"| SSO_SURVEY SSO_SURVEY --> SSO_GATE SSO_GATE --> SSO_DEPS SSO_DEPS --> SSO_VERIFY SSO_VERIFY --> ROUTE COMPLEX -->|"1 op"| SIMPLE SIMPLE --> ROUTE LLM --> PIVOT PIVOT -->|"yes"| SLOTS SLOTS --> SSO_SURVEY PIVOT -->|"no"| ROUTE ROUTE --> INHIBIT INHIBIT --> OUTPUT ROUTE -.->|"reads"| PROC ROUTE -.->|"reads"| DECL SSO_SURVEY -.->|"scans"| DECL OUTPUT -.->|"writes"| EPIS EPIS -.->|"promotes"| GLOB style EXEC fill:#1a3a5c,stroke:#58a6ff,color:#c9d1d9 style PLAN fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style MONITOR fill:#3d1500,stroke:#f85149,color:#c9d1d9 style EXECUTE fill:#2d1a3d,stroke:#f778ba,color:#c9d1d9 style MEMORY fill:#21262d,stroke:#6c757d,color:#c9d1d9 style INPUT fill:#21262d,stroke:#e3b341,color:#c9d1d9 style LLM fill:#1a3a5c,stroke:#58a6ff,color:#f0f6fc,stroke-width:2px style SAFETY fill:#5c1a1a,stroke:#ff6b6b,color:#f0f6fc,stroke-width:3px style COMPLEX fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style SSO_SURVEY fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style SSO_GATE fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style SSO_DEPS fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style SSO_VERIFY fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style SIMPLE fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style PIVOT fill:#3d1500,stroke:#f85149,color:#c9d1d9 style SLOTS fill:#3d1500,stroke:#f85149,color:#c9d1d9 style ROUTE fill:#2d1a3d,stroke:#f778ba,color:#c9d1d9 style INHIBIT fill:#5c1a1a,stroke:#ff6b6b,color:#c9d1d9 style OUTPUT fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style PROC fill:#21262d,stroke:#e3b341,color:#c9d1d9 style EPIS fill:#0d2d3d,stroke:#79c0ff,color:#c9d1d9 style DECL fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style GLOB fill:#2d1a3d,stroke:#bc8cff,color:#c9d1d9

The amygdala safety check can short-circuit the entire pipeline, halting output immediately when Safety Imperatives I1-I7 are triggered — the "low road" threat bypass.

⚖️ Synapse Type Distribution

Real neural networks maintain approximately 80% excitatory / 20% inhibitory balance. Alex's synaptic network targets the same ratio — without inhibition, all protocols would fire simultaneously (cognitive seizure).

Type	Ratio	Actions	Example
Excitatory	80%	Enables, Triggers, Enhances	SSO → Skill Activation
Inhibitory	20%	Inhibits, Suppresses	vlPFC → Block meditation mid-task

Excitatory synapses (green) activate downstream protocols. Inhibitory synapses (red) suppress irrelevant ones. The 80/20 balance prevents both under-activation and over-activation.

🔀 Human Brain vs Alex Architecture

Side-by-side signal flow comparison. The left shows how a stimulus is processed in the human brain — from sensory input through threat detection, executive planning, and motor output. The right shows Alex's parallel architecture, mapping each biological pathway to its computational equivalent.

🧬

Human Brain

BIOLOGICAL

flowchart TB IN["Sensory Stimulus
Visual, Auditory, Tactile"] TH["Thalamus
Sensory relay station"] AM["Amygdala
Threat assessment"] subgraph CORTEX["Cortical Processing"] PFC2["Prefrontal Cortex
Evaluate + decide"] DL2["dlPFC
Plan + working memory"] ACC2["ACC
Conflict monitor"] end subgraph MOTOR["Motor Output"] PM2["Premotor Cortex
Movement plan"] VL2["vlPFC
Response inhibition"] MOT["Motor Cortex
Execute action"] end subgraph MEM2["Memory Systems"] BG2["Basal Ganglia
Habits + routines"] HIP2["Hippocampus
Encode memory"] end RESP["Behavioral
Response"] IN --> TH TH --> AM TH --> PFC2 AM -.->|"low road - fast"| RESP AM -.->|"modulates"| PFC2 PFC2 --> DL2 PFC2 --> ACC2 ACC2 -->|"conflict"| DL2 DL2 --> PM2 PM2 --> VL2 VL2 --> MOT MOT --> RESP PFC2 -.->|"routine?"| BG2 BG2 -.->|"bypass"| MOT MOT -.->|"encodes"| HIP2 style CORTEX fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style MOTOR fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style MEM2 fill:#21262d,stroke:#6c757d,color:#c9d1d9 style IN fill:#1a3d1a,stroke:#3fb950,color:#f0f6fc,stroke-width:2px style TH fill:#21262d,stroke:#6c757d,color:#c9d1d9 style AM fill:#5c1a1a,stroke:#ff6b6b,color:#f0f6fc,stroke-width:3px style PFC2 fill:#1a3d1a,stroke:#3fb950,color:#f0f6fc,stroke-width:2px style DL2 fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style ACC2 fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style PM2 fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style VL2 fill:#5c1a1a,stroke:#ff6b6b,color:#c9d1d9 style MOT fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style BG2 fill:#21262d,stroke:#e3b341,color:#c9d1d9 style HIP2 fill:#0d2d3d,stroke:#79c0ff,color:#c9d1d9 style RESP fill:#1a3d1a,stroke:#3fb950,color:#f0f6fc,stroke-width:2px

↔ ↔ ↔

🤖

Alex Architecture

COMPUTATIONAL

flowchart TB IN3["User Input
Chat, Commands, Files"] TH3["VS Code Interface
Input relay - thalamus"] AM3["Safety Imperatives I1-I7
Kill switch - amygdala"] subgraph EXEC3["Executive Processing"] LLM3["LLM Claude-GPT
Parse intent - PFC"] SSO3["SSO Protocol
Plan + gate - dlPFC"] PIV3["Pivot Detection
Conflict monitor - ACC"] end subgraph ROUTE3["Execution Layer"] SK3["Skill Activation
Route skills - premotor"] INH3["Inhibitory Synapses
Suppress - vlPFC"] GEN3["Generate Response
Output - motor cortex"] end subgraph MEM3["Memory Systems"] PROC3["Procedural .instructions.md
Basal ganglia"] EPIS3["Episodic .prompt.md
Hippocampus"] end OUT3["User Gets
Response"] IN3 --> TH3 TH3 --> AM3 TH3 --> LLM3 AM3 -.->|"threat - HALT"| OUT3 AM3 -.->|"modulates"| LLM3 LLM3 --> SSO3 LLM3 --> PIV3 PIV3 -->|"re-plan"| SSO3 SSO3 --> SK3 SK3 --> INH3 INH3 --> GEN3 GEN3 --> OUT3 LLM3 -.->|"auto-loaded"| PROC3 PROC3 -.->|"bypass"| GEN3 GEN3 -.->|"records"| EPIS3 style EXEC3 fill:#1a3a5c,stroke:#58a6ff,color:#c9d1d9 style ROUTE3 fill:#2d1a3d,stroke:#f778ba,color:#c9d1d9 style MEM3 fill:#21262d,stroke:#6c757d,color:#c9d1d9 style IN3 fill:#1a3a5c,stroke:#58a6ff,color:#f0f6fc,stroke-width:2px style TH3 fill:#21262d,stroke:#6c757d,color:#c9d1d9 style AM3 fill:#5c1a1a,stroke:#ff6b6b,color:#f0f6fc,stroke-width:3px style LLM3 fill:#1a3a5c,stroke:#58a6ff,color:#f0f6fc,stroke-width:2px style SSO3 fill:#3d2800,stroke:#f0883e,color:#c9d1d9 style PIV3 fill:#3d1500,stroke:#f85149,color:#c9d1d9 style SK3 fill:#2d1a3d,stroke:#f778ba,color:#c9d1d9 style INH3 fill:#5c1a1a,stroke:#ff6b6b,color:#c9d1d9 style GEN3 fill:#1a3d1a,stroke:#3fb950,color:#c9d1d9 style PROC3 fill:#21262d,stroke:#e3b341,color:#c9d1d9 style EPIS3 fill:#0d2d3d,stroke:#79c0ff,color:#c9d1d9 style OUT3 fill:#1a3a5c,stroke:#58a6ff,color:#f0f6fc,stroke-width:2px

🔗 Pathway Mapping

#	Processing Stage	Human Brain	Alex Architecture
1	Input Reception	Sensory stimulus → Thalamus	User message → VS Code interface
2	Threat Detection	Amygdala "low road" — bypasses cortex	Safety Imperatives I1-I7 — bypasses LLM
3	Executive Parse	PFC evaluates, forms goal	LLM parses intent, identifies domain
4	Task Planning	dlPFC + working memory holds plan	SSO surveys skills, gates attention
5	Conflict Monitor	ACC fires on mismatch	Pivot Detection rotates P5-P7 slots
6	Inhibition	vlPFC suppresses inappropriate response	Inhibitory synapses suppress protocols
7	Motor Execution	Premotor → Motor cortex → Action	Skill activation → Generate response
8	Memory Encoding	Hippocampus encodes experience	Session → .prompt.md → Global knowledge
9	Habit Bypass	Basal ganglia runs routines unconsciously	.instructions.md auto-loads, fires on trigger

🧠 The Alex Brain v5.x

🧠 Region Detail

🗺️ Region Legend