A nnU-Net-based Automatic Segmentation of FCD Type II Lesions in 3D Flair MRI Images

Shubham Joshi^1*Millie Pant^1*Arnav Malhotra²Kusum Deep¹VACLAV SNASEL³

• ¹Indian Institute of Technology Roorkee, Roorkee, India
• ²Lassonde School of Engineering, York University, Toronto, Ontario, Canada
• ³VSB-Technical University of Ostrava, Ostrava, Moravian-Silesian Region, Czechia

Focal Cortical Dysplasia (FCD) Type II is a common cause of epilepsy and is challenging to detect due to its similarities with other brain conditions. Finding these lesions accurately is essential for successful surgery and seizure control. Manual detection is slow and challenging because the MRI features are subtle. Deep learning, especially convolutional neural networks, has shown great potential in automating image classification and segmentation by learning and extracting features. The nnU-Net framework is known for its ability to adapt its settings, including preprocessing, network design, training, and post-processing, to any new medical imaging task. This study employs an automated slice selection approach that ranks axial FLAIR slices by their peak voxel intensity and retains the five highest-ranked slices per scan, thereby focusing the network on lesion-rich slices and uses nnU-Net to automate the segmentation of FCD Type II lesions on 3D FLAIR MRI images. The study was conducted on 85 FCD Type II subjects and results are evaluated through five-fold cross-validation. Using nnU-Net's flexible and robust design, this study aims to improve the accuracy and speed of lesion detection, helping with better presurgical evaluations and outcomes for epilepsy patients.