Native space pipelines outperform template space in subcortical segmentation

Native space-based UNet pipelines outperform template space ones in subcortical segmentation, showing higher Dice scores and lower HD95 values for the Subthalamic Nucleus, Red Nucleus, and Substantia Nigra. Performance drops significantly when applied to 3T images, with synthetic 3T training data providing only modest gains, highlighting a persistent domain gap between 7T and 3T MRI.