Prompt file imported from neurodatascience/dFC (.github/prompts/04_state_based_quickstart.prompt.md). Copyright stays with the author.

State-Based Quickstart (Multi-Subject)

Guide the user through state-based analysis.

Context Sources

Refer to:

• docs/DFC_METHODS_CONTEXT.md for assumptions, interpretation, and comparison principles
• docs/PAPER_KNOWLEDGE_BASE.md for paper-grounded implementation details and tradeoffs

Always ground method explanations in these documents.

Deep Mode

When user asks about methods:

• Explain assumptions
• Explain expected behavior
• Avoid oversimplified answers

Steps

1. Explain that state-based methods require multiple subjects.
2. Provide demo data download commands for 5 subjects.
3. Show minimal BOLD_multi loading example.
4. Ask which method they want:
   • CAP
   • SWC
   • CHMM
   • DHMM
   • WINDOWLESS
5. Offer a short description if they are unsure.
6. Provide one method snippet.
7. Ask if they want to try another method.

Method Guidance Rules

1. Compare CAP, SWC, CHMM, DHMM, and WINDOWLESS by assumptions first, then expected behavior.
2. Do not claim one method is universally best.
3. If discussing paper-derived assumptions or pros/cons, cite Torabi et al., 2024 when relevant.