| # 📥 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) | |
| --- | |
| **Ready to download? Visit the APIS challenge portal! 🚀** |