Despite great advances in brain tumor segmentation and clear clinical need, translation of state-of-the-art computational methods into clinical routine and scientific practice remains a major challenge. Several factors impede successful implementations, including data standardization and preprocessing. However, these steps are pivotal for the deployment of state-of-the-art image segmentation algorithms. To overcome these issues, we present BraTS Toolkit. BraTS Toolkit is a holistic approach to brain tumor segmentation and consists of three components: First, the BraTS Preprocessor facilitates data standardization and preprocessing for researchers and clinicians alike. It covers the entire image analysis workflow prior to tumor segmentation, from image conversion and registration to brain extraction. Second, BraTS Segmentor enables orchestration of BraTS brain tumor segmentation algorithms for generation of fully-automated segmentations. Finally, Brats Fusionator can combine the resulting candidate segmentations into consensus segmentations using fusion methods such as majority voting and iterative SIMPLE fusion. The capabilities of our tools are illustrated with a practical example to enable easy translation to clinical and scientific practice.

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Registration of longitudinal brain Magnetic Resonance Imaging (MRI) scans containing pathologies is challenging due to tissue appearance changes, and still an unsolved problem. This paper describes the first Brain Tumor Sequence Registration (BraTS-Reg) challenge, focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a brain diffuse glioma. The BraTS-Reg challenge intends to establish a public benchmark environment for deformable registration algorithms. The associated dataset comprises de-identified multi-institutional multi-parametric MRI (mpMRI) data, curated for each scan's size and resolution, according to a common anatomical template. Clinical experts have generated extensive annotations of landmarks points within the scans, descriptive of distinct anatomical locations across the temporal domain. The training data along with these ground truth annotations will be released to participants to design and develop their registration algorithms, whereas the annotations for the validation and the testing data will be withheld by the organizers and used to evaluate the containerized algorithms of the participants. Each submitted algorithm will be quantitatively evaluated using several metrics, such as the Median Absolute Error (MAE), Robustness, and the Jacobian determinant.

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Re-identifying locations of interest in pre-and post-operative images is a hard identification problem, as the anatomical landscape changes dramatically due to tumor resection and tissue displacement. Classical image registration techniques oftentimes fail in vicinity of the tumor, where the enclosing structures are massively altered from one scan to another. Still, locations nearby the tumor or the resection cavity are the most relevant for evaluating tumor progression patterns and for comparing pre-and post-operative radiomic signatures. We address this issue by exploring a Reinforcement Learning (RL) approach. An artificial agent is self-taught to find the optimal path towards a target driven by a feedback signal from the environment. Incorporating anatomical guidance, we restrict the agent's search space to surgery-unaffected structures only. By defining landmarks for each patient individually, we aim to obtain a patient-specific representation of its differential radiomic features across different time points for enhancing image alignment. Estimated landmarks reach a remarkable mean distance error around 3 mm. In addition, they show a high agreement with expert annotations on a challenging dataset of MR scans from the brain before and after tumor resection.