TBI lesion segmentation in head CT: impact of preprocessing and data augmentation

Automatic segmentation of lesions in head CT provides keyinformation for patient management, prognosis and disease monitoring.Despite its clinical importance, method development has mostly focusedon multi-parametric MRI. Analysis of the brain in CT is challengingdue to limited soft tissue contrast and its mono-modal nature. We studythe under-explored problem of fine-grained CT segmentation of multiplelesion types (core, blood, oedema) in traumatic brain injury (TBI). Weobserve that preprocessing and data augmentation choices greatly impactthe segmentation accuracy of a neural network, yet these factors arerarely thoroughly assessed in prior work. We design an empirical studythat extensively evaluates the impact of different data preprocessing andaugmentation methods. We show that these choices can have an impactof up to 18% DSC. We conclude that resampling to isotropic resolutionyields improved performance, skull-stripping can be replaced by using theright intensity window, and affine-to-atlas registration is not necessaryif we use sufficient spatial augmentation. Since both skull-stripping andaffine-to-atlas registration are susceptible to failure, we recommend theiralternatives to be used in practice. We believe this is the first work toreport results for fine-grained multi-class segmentation of TBI in CT. Ourfindings may inform further research in this under-explored yet clinicallyimportant task of automatic head CT lesion segmentation