# 📥 APIS Dataset - Download Instructions

**This directory is ready for your APIS dataset files.**

---

## ✅ 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)
```

---

## 📋 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/)

---

## 🔍 Verify Download

After extracting files, verify the structure:

```powershell
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

---

## 🚀 Next Step

Once verification passes, run the complete workflow:

```powershell
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! 🚀**