My Fetal BET

A customized version of inference script of fetal-BET with enhanced functionality and code improvements.

Key Differences

• Support for 4D data
• Improved code structure and organization
• File-based input (no longer requires only folder input)
• Customizable output file suffix

Requirements

To install the necessary dependencies, run:

pip install -r requirements.txt

Weights Download

Download the singularity file:

singularity pull fetal-bet.sif docker://faghihpirayesh/fetal-bet

Copy the weights to local host:

singularity exec /path/to/fetal-bet.sif cp /app/src/saved_models/AttUNet.pth .

Usage

python inference.py --input_path /path/to/input \
                    --output_path /path/to/output_folder \
                    --saved_model_path /path/to/weights \
                    --suffix mask

Example 1 (file inference)

python inference.py --input_path /data/sub-001/T2.nii.gz \
                    --output_path /data/sub-001/ \
                    --saved_model_path /code/fetal-bet/AttUNet.pth \
                    --suffix fetalbet_mask

The output will be:

 data/
   └──sub-001/
        ├── T2.nii.gz 
        └── T2_fetalbet_mask.nii.gz 

Example 2 (folder inference)

python inference.py --input_path /data/sub-001 \
                    --output_path /data/sub-001_mask/ \
                    --saved_model_path /code/fetal-bet/AttUNet.pth \
                    --suffix fetalbet_mask

The output will be:

 data/
   ├──sub-001/
   |    ├── T2_run_1.nii.gz 
   |    └── T2_run_2.nii.gz 
   |
   └──sub-001_mask/    
        ├── T2_run_1_fetalbet_mask.nii.gz 
        └── T2_run_2_fetalbet_mask.nii.gz