File size: 2,141 Bytes
e2ee1e3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | # 📥 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! 🚀** |