raw/README_DOWNLOAD_HERE.md

📥 APIS Dataset - Download Instructions

This directory is ready for your APIS dataset files.

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✅ Expected Directory Structure

Place your downloaded APIS dataset files in this structure:

raw/
├── ct/                    # ← CT volumes go here
│   ├── case_001/
│   │   └── ct.nii.gz
│   ├── case_002/
│   │   └── ct.nii.gz
│   └── ... (60 cases)
│
├── adc/                   # ← ADC/MRI volumes go here
│   ├── case_001/
│   │   └── adc.nii.gz
│   ├── case_002/
│   │   └── adc.nii.gz
│   └── ... (60 cases)
│
└── lesion_masks/          # ← Lesion annotations go here
    ├── case_001.nii.gz
    ├── case_002.nii.gz
    └── ... (60 files)

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📋 Download Steps

1. Register: Go to https://bivl2ab.uis.edu.co/challenges/apis
2. Accept: Accept the Data Usage Agreement
3. Download: Download CT, ADC/MRI, and lesion mask archives
4. Extract: Extract files into the directories above (ct/, adc/, lesion_masks/)

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🔍 Verify Download

After extracting files, verify the structure:

wsl bash -c "cd /mnt/c/Users/User/Documents/ClinFuseDiff && bash workflow/02_verify_setup.sh"

This will check:

• ✅ Number of CT volumes found
• ✅ Number of ADC/MRI volumes found
• ✅ Number of lesion masks found
• ✅ File naming consistency

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🚀 Next Step

Once verification passes, run the complete workflow:

wsl bash -c "cd /mnt/c/Users/User/Documents/ClinFuseDiff && source ~/miniconda3/etc/profile.d/conda.sh && conda activate clinfusediff && bash workflow/complete_workflow_with_logging.sh apis run_$(date +%Y%m%d_%H%M%S)"

This will automatically:

1. Preprocess all cases (ANTs registration + TotalSegmentator masks)
2. Create train/val/test splits
3. Train the model
4. Evaluate with comprehensive metrics
5. Save all outputs (logs, visualizations, checkpoints, results)

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Ready to download? Visit the APIS challenge portal! 🚀