Automated, fast, robust brain extraction on contrast-enhanced T1-weighted MRI in presence of brain tumors: an optimized model based on multi-center datasets

Objectives Existing brain extraction models should be further optimized to provide more information for oncological analysis. We aimed to develop an nnU-Net–based deep learning model for automated brain extraction on contrast-enhanced T1-weighted (T1CE) images in presence of brain tumors. Methods This is a multi-center, retrospective study involving 920 patients. A total of 720 cases with four types of intracranial tumors from private institutions were collected and set as the training group and the internal test group. Mann–Whitney U test ( U test) was used to investigate if the model performance was associated with pathological types and tumor characteristics. Then, the generalization of model was independently tested on public datasets consisting of 100 glioma and 100 vestibular schwannoma cases. Results In the internal test, the model achieved promising performance with median Dice similarity coefficient (DSC) of 0.989 (interquartile range (IQR), 0.988–0.991), and Hausdorff distance (HD) of 6.403 mm (IQR, 5.099–8.426 mm). U test suggested a slightly descending performance in meningioma and vestibular schwannoma group. The results of U test also suggested that there was a significant difference in peritumoral edema group, with median DSC of 0.990 (IQR, 0.989–0.991, p = 0.002), and median HD of 5.916 mm (IQR, 5.000–8.000 mm, p = 0.049). In the external test, our model also showed to be robust performance, with median DSC of 0.991 (IQR, 0.983–0.998) and HD of 8.972 mm (IQR, 6.164–13.710 mm). Conclusions For automated processing of MRI neuroimaging data presence of brain tumors, the proposed model can perform brain extraction including important superficial structures for oncological analysis. Clinical relevance statement The proposed model serves as a radiological tool for image preprocessing in tumor cases, focusing on superficial brain structures, which could streamline the workflow and enhance the efficiency of subsequent radiological assessments. Key Points • The nnU-Net–based model is capable of segmenting significant superficial structures in brain extraction. • The proposed model showed feasible performance, regardless of pathological types or tumor characteristics. • The model showed generalization in the public datasets.