Manuscript Workspace Structure

Created: 2024-12-22 Project: SwiFT_v2 - Self-Supervised 4D Swin Transformer for fMRI Analysis

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📁 Complete Directory Tree

manuscript/
│
├── 📄 OVERVIEW.md                    # 📌 MASTER DOCUMENT - Start here!
├── 📄 QUICK_START.md                 # Quick reference guide
├── 📄 STRUCTURE_SUMMARY.md           # This file
│
├── 📚 papers/                         # Reference papers (PDFs)
│   ├── README.md                     # Paper organization guide
│   ├── transformers/                 # Vision transformer papers
│   ├── fmri_analysis/                # Brain imaging DL papers
│   └── pretraining/                  # Self-supervised learning papers
│
├── ✍️  drafts/                        # Writing workspace
│   └── current_draft.md              # Active working draft (template included)
│
├── 📊 figures/                        # All visualizations
│   ├── architecture/                 # Model diagrams (Figure 1)
│   ├── results/                      # Performance plots (Figures 3-4)
│   └── ablation/                     # Ablation studies (Figure 5)
│
├── 📈 data/                           # Supporting data
│   ├── tables/                       # Result tables (CSV format)
│   └── statistics/                   # Statistical test results
│
├── 🔧 scripts/                        # Helper scripts
│   └── README.md                     # Script documentation
│
├── 📎 supplements/                    # Supplementary materials
│
└── 📝 reviews/                        # Submission tracking
    └── submission_history.md         # Review rounds & responses

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🎯 Key Files

Core Documents

File	Purpose	Update Frequency
OVERVIEW.md	Master tracking, planning, status	Daily/Weekly
QUICK_START.md	Quick reference guide	Rarely (reference only)
drafts/current_draft.md	Active manuscript writing	Daily

Organization Files

File	Purpose
papers/README.md	Reference paper organization
scripts/README.md	Script documentation
reviews/submission_history.md	Review tracking

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📋 What's in Each Directory

/papers/ - Reference Management

Purpose: Store and organize reference PDFs for AI agent access

Subdirectories:

• transformers/ - ViT, Swin, Video Transformers
• fmri_analysis/ - BrainNetCNN, fMRI-specific DL
• pretraining/ - SimCLR, MAE, SimMIM, BEiT

Usage:

1. Upload PDFs with naming: FirstAuthor_YYYY_Title.pdf
2. AI can read via: mcp__pdf-reader-mcp__read_pdf
3. Track in OVERVIEW.md "Reference Papers" section

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/drafts/ - Writing Workspace

Purpose: Version-controlled manuscript drafts

Key File: current_draft.md - Full paper template with:

• Abstract, Introduction, Methods, Experiments, Results, Discussion
• Section-by-section guidance
• Placeholder text for structure

Versioning:

• Save milestones: v1_20241222_initial.md
• Track progress in OVERVIEW.md "Drafting Progress" table

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/figures/ - Visualizations

Purpose: Organized figure storage by type

Subdirectories:

• architecture/ - Model diagrams, 4D Swin Transformer architecture
• results/ - Main performance plots, comparisons
• ablation/ - Ablation study visualizations

Workflow:

1. Create generation script in scripts/
2. Save outputs to appropriate subdir
3. Update OVERVIEW.md figure status
4. Reference in current_draft.md

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/data/ - Supporting Data

Purpose: Store experimental results and analyses

Subdirectories:

• tables/ - CSV files with results (main_results.csv, ablation_results.csv)
• statistics/ - Statistical test outputs, significance tests

Usage:

• Source data for figures and tables
• Input to scripts/ for processing
• Referenced in paper for reproducibility

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/scripts/ - Automation

Purpose: Reproducible figure/table generation

Planned Scripts (see scripts/README.md):

• generate_figures.py - Master figure generator
• compile_results.py - Aggregate results to tables
• statistical_tests.py - Significance testing

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/supplements/ - Supplementary Materials

Purpose: Additional materials beyond main paper

Typical Contents:

• Extended results
• Additional ablation studies
• Detailed architecture specifications
• Hyperparameter sensitivity analysis

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/reviews/ - Submission Tracking

Purpose: Track submission process and reviews

Key File: submission_history.md - Template for:

• Submission timeline
• Reviewer comments
• Response strategy
• Revision plans

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🔄 Recommended Workflow

Phase 1: Setup (✅ Complete)

• Create directory structure
• Set up OVERVIEW.md
• Create templates and guides

Phase 2: Planning (Current)

• Upload reference papers to papers/
• Update OVERVIEW.md narrative
• Define figure/table plan
• Set submission target

Phase 3: Execution

• Generate all figures
• Compile result tables
• Draft sections
• Internal review

Phase 4: Submission

• Final polish
• Format for venue
• Submit!

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💡 Pro Tips

Keep OVERVIEW.md Updated

✅ Update section status after each writing session ✅ Check off action items as completed ✅ Add new ideas to "Notes & Ideas" ✅ Track weekly progress

Use AI Agents Effectively

✅ "Read papers/transformers/Liu_2021_SwinTransformer.pdf and summarize..." ✅ Reference papers by full path for AI to access PDFs ✅ Ask for comparisons across multiple papers

Organize as You Go

✅ Name files consistently ✅ Update README files when adding new categories ✅ Version drafts before major changes ✅ Save intermediate analysis results

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📊 Current Status

Workspace: ✅ Fully set up and ready Next Steps:

1. Upload reference papers
2. Review OVERVIEW.md and customize
3. Start literature review
4. Generate first figures

Quick Actions:

# View structure
ls -la manuscript/

# Open master document
open manuscript/OVERVIEW.md

# Start writing
open manuscript/drafts/current_draft.md

# Upload a paper
cp /path/to/paper.pdf manuscript/papers/transformers/FirstAuthor_YYYY_Title.pdf

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🆘 Need Help?

1. Start here: Read OVERVIEW.md (comprehensive guide)
2. Quick reference: Check QUICK_START.md
3. Paper organization: See papers/README.md
4. Scripts: Check scripts/README.md

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Your manuscript workspace is ready! 🚀

Begin by customizing OVERVIEW.md to match your specific paper goals and timeline.