Ole solheim

David Bouget, Demah Alsinan, Valeria Gaitan et al.

For patients suffering from central nervous system tumors, prognosis estimation, treatment decisions, and postoperative assessments are made from the analysis of a set of magnetic resonance (MR) scans. Currently, the lack of open tools for standardized and automatic tumor segmentation and generation of clinical reports, incorporating relevant tumor characteristics, leads to potential risks from inherent decisions' subjectivity. To tackle this problem, the proposed Raidionics open-source software has been developed, offering both a user-friendly graphical user interface and stable processing backend. The software includes preoperative segmentation models for each of the most common tumor types (i.e., glioblastomas, lower grade gliomas, meningiomas, and metastases), together with one early postoperative glioblastoma segmentation model. Preoperative segmentation performances were quite homogeneous across the four different brain tumor types, with an average Dice around 85% and patient-wise recall and precision around 95%. Postoperatively, performances were lower with an average Dice of 41%. Overall, the generation of a standardized clinical report, including the tumor segmentation and features computation, requires about ten minutes on a regular laptop. The proposed Raidionics software is the first open solution enabling an easy use of state-of-the-art segmentation models for all major tumor types, including preoperative and postsurgical standardized reports.

Ragnhild Holden Helland, Alexandros Ferles, André Pedersen et al.

Extent of resection after surgery is one of the main prognostic factors for patients diagnosed with glioblastoma. To achieve this, accurate segmentation and classification of residual tumor from post-operative MR images is essential. The current standard method for estimating it is subject to high inter- and intra-rater variability, and an automated method for segmentation of residual tumor in early post-operative MRI could lead to a more accurate estimation of extent of resection. In this study, two state-of-the-art neural network architectures for pre-operative segmentation were trained for the task. The models were extensively validated on a multicenter dataset with nearly 1000 patients, from 12 hospitals in Europe and the United States. The best performance achieved was a 61\% Dice score, and the best classification performance was about 80\% balanced accuracy, with a demonstrated ability to generalize across hospitals. In addition, the segmentation performance of the best models was on par with human expert raters. The predicted segmentations can be used to accurately classify the patients into those with residual tumor, and those with gross total resection.

Mathilde Gajda Faanes, David Bouget, Asgeir S. Jakola et al.

T2-weighted fluid-attenuated inversion recovery (FLAIR) magnetic resonance imaging (MRI) scans are important for diagnosis, treatment planning and monitoring of brain tumors. Depending on the brain tumor type, the FLAIR hyperintensity volume is an important measure to asses the tumor volume or surrounding edema, and an automatic segmentation of this would be useful in the clinic. In this study, around 5000 FLAIR images of various tumors types and acquisition time points from different centers were used to train a unified FLAIR hyperintensity segmentation model using an Attention U-Net architecture. The performance was compared against dataset specific models, and was validated on different tumor types, acquisition time points and against BraTS. The unified model achieved an average Dice score of 88.65\% for pre-operative meningiomas, 80.08% for pre-operative metastasis, 90.92% for pre-operative and 84.60% for post-operative gliomas from BraTS, and 84.47% for pre-operative and 61.27\% for post-operative lower grade gliomas. In addition, the results showed that the unified model achieved comparable segmentation performance to the dataset specific models on their respective datasets, and enables generalization across tumor types and acquisition time points, which facilitates the deployment in a clinical setting. The model is integrated into Raidionics, an open-source software for CNS tumor analysis.

Bahareh Behboodi, Francois-Xavier Carton, Matthieu Chabanas et al.

Purpose: Registration and segmentation of magnetic resonance (MR) and ultrasound (US) images play an essential role in surgical planning and resection of brain tumors. However, validating these techniques is challenging due to the scarcity of publicly accessible sources with high-quality ground truth information. To this end, we propose a unique annotation dataset of tumor tissues and resection cavities from the previously published RESECT dataset (Xiao et al. 2017) to encourage a more rigorous assessments of image processing techniques. Acquisition and validation methods: The RESECT database consists of MR and intraoperative US (iUS) images of 23 patients who underwent resection surgeries. The proposed dataset contains tumor tissues and resection cavity annotations of the iUS images. The quality of annotations were validated by two highly experienced neurosurgeons through several assessment criteria. Data format and availability: Annotations of tumor tissues and resection cavities are provided in 3D NIFTI formats. Both sets of annotations are accessible online in the \url{https://osf.io/6y4db}. Discussion and potential applications: The proposed database includes tumor tissue and resection cavity annotations from real-world clinical ultrasound brain images to evaluate segmentation and registration methods. These labels could also be used to train deep learning approaches. Eventually, this dataset should further improve the quality of image guidance in neurosurgery.

Mathilde Faanes, Ragnhild Holden Helland, Ole Solheim et al.

Automatic segmentation of brain tumors in intra-operative ultrasound (iUS) images could facilitate localization of tumor tissue during resection surgery. The lack of large annotated datasets limits the current models performances. In this paper, we investigated the use of tumor annotations in magnetic resonance imaging (MRI) scans, which are more accessible than annotations in iUS images, for training of deep learning models for iUS brain tumor segmentation. We used 180 annotated MRI scans with corresponding unannotated iUS images, and 29 annotated iUS images. Image registration was performed to transfer the MRI annotations to the corresponding iUS images before training the nnU-Net model with different configurations of the data and label origins. The results showed no significant difference in Dice score for a model trained with only MRI annotated tumors compared to models trained with only iUS annotations and both, and to expert annotations, indicating that MRI tumor annotations can be used as a substitute for iUS tumor annotations to train a deep learning model for automatic brain tumor segmentation in iUS images. The best model obtained an average Dice score of $0.62\pm0.31$, compared to $0.67\pm0.25$ for an expert neurosurgeon, where the performance on larger tumors were similar, but lower for the models on smaller tumors. In addition, the results showed that removing smaller tumors from the training sets improved the results. The main models are available here: https://github.com/mathildefaanes/us_brain_tumor_segmentation/tree/main

David Bouget, Mathilde Gajda Faanes, Asgeir Store Jakola et al.

Magnetic resonance (MR) imaging is essential for evaluating central nervous system (CNS) tumors, guiding surgical planning, treatment decisions, and assessing postoperative outcomes and complication risks. While recent work has advanced automated tumor segmentation and report generation, most efforts have focused on preoperative data, with limited attention to postoperative imaging analysis. This study introduces a comprehensive pipeline for standardized postsurtical reporting in CNS tumors. Using the Attention U-Net architecture, segmentation models were trained for the preoperative (non-enhancing) tumor core, postoperative contrast-enhancing residual tumor, and resection cavity. Additionally, MR sequence classification and tumor type identification for contrast-enhancing lesions were explored using the DenseNet architecture. The models were integrated into a reporting pipeline, following the RANO 2.0 guidelines. Training was conducted on multicentric datasets comprising 2000 to 7000 patients, using a 5-fold cross-validation. Evaluation included patient-, voxel-, and object-wise metrics, with benchmarking against the latest BraTS challenge results. The segmentation models achieved average voxel-wise Dice scores of 87%, 66%, 70%, and 77% for the tumor core, non-enhancing tumor core, contrast-enhancing residual tumor, and resection cavity, respectively. Classification models reached 99.5% balanced accuracy in MR sequence classification and 80% in tumor type classification. The pipeline presented in this study enables robust, automated segmentation, MR sequence classification, and standardized report generation aligned with RANO 2.0 guidelines, enhancing postoperative evaluation and clinical decision-making. The proposed models and methods were integrated into Raidionics, open-source software platform for CNS tumor analysis, now including a dedicated module for postsurgical analysis.

Santiago Cepeda, Roberto Romero, Daniel Garcia-Perez et al.

Accurately assessing tumor removal is paramount in the management of glioblastoma. We developed a pipeline using MRI scans and neural networks to segment tumor subregions and the surgical cavity in postoperative images. Our model excels in accurately classifying the extent of resection, offering a valuable tool for clinicians in assessing treatment effectiveness.

David Bouget, André Pedersen, Sayied Abdol Mohieb Hosainey et al.

Meningiomas are the most common type of primary brain tumor, accounting for approximately 30% of all brain tumors. A substantial number of these tumors are never surgically removed but rather monitored over time. Automatic and precise meningioma segmentation is therefore beneficial to enable reliable growth estimation and patient-specific treatment planning. In this study, we propose the inclusion of attention mechanisms over a U-Net architecture: (i) Attention-gated U-Net (AGUNet) and (ii) Dual Attention U-Net (DAUNet), using a 3D MRI volume as input. Attention has the potential to leverage the global context and identify features' relationships across the entire volume. To limit spatial resolution degradation and loss of detail inherent to encoder-decoder architectures, we studied the impact of multi-scale input and deep supervision components. The proposed architectures are trainable end-to-end and each concept can be seamlessly disabled for ablation studies. The validation studies were performed using a 5-fold cross validation over 600 T1-weighted MRI volumes from St. Olavs University Hospital, Trondheim, Norway. For the best performing architecture, an average Dice score of 81.6% was reached for an F1-score of 95.6%. With an almost perfect precision of 98%, meningiomas smaller than 3ml were occasionally missed hence reaching an overall recall of 93%. Leveraging global context from a 3D MRI volume provided the best performances, even if the native volume resolution could not be processed directly. Overall, near-perfect detection was achieved for meningiomas larger than 3ml which is relevant for clinical use. In the future, the use of multi-scale designs and refinement networks should be further investigated to improve the performance. A larger number of cases with meningiomas below 3ml might also be needed to improve the performance for the smallest tumors.

David Bouget, André Pedersen, Sayied Abdol Mohieb Hosainey et al.

Automatic and consistent meningioma segmentation in T1-weighted MRI volumes and corresponding volumetric assessment is of use for diagnosis, treatment planning, and tumor growth evaluation. In this paper, we optimized the segmentation and processing speed performances using a large number of both surgically treated meningiomas and untreated meningiomas followed at the outpatient clinic. We studied two different 3D neural network architectures: (i) a simple encoder-decoder similar to a 3D U-Net, and (ii) a lightweight multi-scale architecture (PLS-Net). In addition, we studied the impact of different training schemes. For the validation studies, we used 698 T1-weighted MR volumes from St. Olav University Hospital, Trondheim, Norway. The models were evaluated in terms of detection accuracy, segmentation accuracy and training/inference speed. While both architectures reached a similar Dice score of 70% on average, the PLS-Net was more accurate with an F1-score of up to 88%. The highest accuracy was achieved for the largest meningiomas. Speed-wise, the PLS-Net architecture tended to converge in about 50 hours while 130 hours were necessary for U-Net. Inference with PLS-Net takes less than a second on GPU and about 15 seconds on CPU. Overall, with the use of mixed precision training, it was possible to train competitive segmentation models in a relatively short amount of time using the lightweight PLS-Net architecture. In the future, the focus should be brought toward the segmentation of small meningiomas (less than 2ml) to improve clinical relevance for automatic and early diagnosis as well as speed of growth estimates.