Spherical coordinates transformation pre-processing in Deep Convolution Neural Networks for brain tumor segmentation in MRI

Magnetic Resonance Imaging (MRI) is used in everyday clinical practice to assess brain tumors. Deep Convolutional Neural Networks (DCNN) have recently shown very promising results in brain tumor segmentation tasks; however, DCNN models fail the task when applied to volumes that are different from the training dataset. One of the reasons is due to the lack of data standardization to adjust for different models and MR machines. In this work, a 3D spherical coordinates transform during the pre-processing phase has been hypothesized to improve DCNN models' accuracy and to allow more generalizable results even when the model is trained on small and heterogeneous datasets and translated into different domains. Indeed, the spherical coordinate system avoids several standardization issues since it works independently of resolution and imaging settings. The model trained on spherical transform pre-processed inputs resulted in superior performance over the Cartesian-input trained model on predicting gliomas' segmentation on Tumor Core and Enhancing Tumor classes, achieving a further improvement in accuracy by merging the two models together. The proposed model is not resolution-dependent, thus improving segmentation accuracy and theoretically solving some transfer learning problems related to the domain shifting, at least in terms of image resolution in the datasets.

Automated summary

MRI is used for brain tumor assessment, and DCNN has potential in brain tumor segmentation tasks but may fail on different dataset volumes. Utilizing a 3D spherical coordinates transform during preprocessing can improve model accuracy and generalizability.