CEREBRUM: a fast and fully-volumetric Convolutional Encoder-decodeR for weakly-supervised sEgmentation of BRain strUctures from out-of-the-scanner MRI

Many functional and structural neuroimaging studies call for accurate morphometric segmentation of different brain structures starting from image intensity values of MRI scans. Current automatic (multi-) atlas-based segmentation strategies often lack accuracy on difficult-to-segment brain structures and, since these methods rely on atlas-to-scan alignment, they may take long processing times. Alternatively, recent methods deploying solutions based on Convolutional Neural Networks (CNNs) are enabling the direct analysis of out-of-the-scanner data. However, current CNN-based solutions partition the test volume into 2D or 3D patches, which are processed independently. This process entails a loss of global contextual information, thereby negatively impacting the segmentation accuracy. In this work, we design and test an optimised end-to-end CNN architecture that makes the exploitation of global spatial information computationally tractable, allowing to process a whole MRI volume at once. We adopt a weakly supervised learning strategy by exploiting a large dataset composed of 947 out-of-the-scanner (3 Tesla T1-weighted 1mm isotropic MP-RAGE 3D sequences) MR Images. The resulting model is able to produce accurate multi-structure segmentation results in only a few seconds. Different quantitative measures demonstrate an improved accuracy of our solution when compared to state-of-the-art techniques. Moreover, through a randomised survey involving expert neuroscientists, we show that subjective judgements favour our solution with respect to widely adopted atlas-based software

Segmentation uncertainty estimation as a sanity check for image biomarker studies

SIMPLE SUMMARY: Radiomics is referred to as quantitative image biomarker analysis. Due to the uncertainty in image acquisition, processing, and segmentation (delineation) protocols, the radiomic biomarkers lack reproducibility. In this manuscript, we show how this protocol-induced uncertainty can drastically reduce prognostic model performance and propose some insights on how to use it for developing better prognostic models. ABSTRACT: Problem. Image biomarker analysis, also known as radiomics, is a tool for tissue characterization and treatment prognosis that relies on routinely acquired clinical images and delineations. Due to the uncertainty in image acquisition, processing, and segmentation (delineation) protocols, radiomics often lack reproducibility. Radiomics harmonization techniques have been proposed as a solution to reduce these sources of uncertainty and/or their influence on the prognostic model performance. A relevant question is how to estimate the protocol-induced uncertainty of a specific image biomarker, what the effect is on the model performance, and how to optimize the model given the uncertainty. Methods. Two non-small cell lung cancer (NSCLC) cohorts, composed of 421 and 240 patients, respectively, were used for training and testing. Per patient, a Monte Carlo algorithm was used to generate three hundred synthetic contours with a surface dice tolerance measure of less than 1.18 mm with respect to the original GTV. These contours were subsequently used to derive 104 radiomic features, which were ranked on their relative sensitivity to contour perturbation, expressed in the parameter η. The top four (low η) and the bottom four (high η) features were selected for two models based on the Cox proportional hazards model. To investigate the influence of segmentation uncertainty on the prognostic model, we trained and tested the setup in 5000 augmented realizations (using a Monte Carlo sampling method); the log-rank test was used to assess the stratification performance and stability of segmentation uncertainty. Results. Although both low and high η setup showed significant testing set log-rank p-values (p = 0.01) in the original GTV delineations (without segmentation uncertainty introduced), in the model with high uncertainty, to effect ratio, only around 30% of the augmented realizations resulted in model performance with p < 0.05 in the test set. In contrast, the low η setup performed with a log-rank p < 0.05 in 90% of the augmented realizations. Moreover, the high η setup classification was uncertain in its predictions for 50% of the subjects in the testing set (for 80% agreement rate), whereas the low η setup was uncertain only in 10% of the cases. Discussion. Estimating image biomarker model performance based only on the original GTV segmentation, without considering segmentation, uncertainty may be deceiving. The model might result in a significant stratification performance, but can be unstable for delineation variations, which are inherent to manual segmentation. Simulating segmentation uncertainty using the method described allows for more stable image biomarker estimation, selection, and model development. The segmentation uncertainty estimation method described here is universal and can be extended to estimate other protocol uncertainties (such as image acquisition and pre-processing)

Enrichment of the NLST and NSCLC-Radiomics computed tomography collections with AI-derived annotations

Public imaging datasets are critical for the development and evaluation of automated tools in cancer imaging. Unfortunately, many do not include annotations or image-derived features, complicating their downstream analysis. Artificial intelligence-based annotation tools have been shown to achieve acceptable performance and thus can be used to automatically annotate large datasets. As part of the effort to enrich public data available within NCI Imaging Data Commons (IDC), here we introduce AI-generated annotations for two collections of computed tomography images of the chest, NSCLC-Radiomics, and the National Lung Screening Trial. Using publicly available AI algorithms we derived volumetric annotations of thoracic organs at risk, their corresponding radiomics features, and slice-level annotations of anatomical landmarks and regions. The resulting annotations are publicly available within IDC, where the DICOM format is used to harmonize the data and achieve FAIR principles. The annotations are accompanied by cloud-enabled notebooks demonstrating their use. This study reinforces the need for large, publicly accessible curated datasets and demonstrates how AI can be used to aid in cancer imaging

CEREBRUM-7T: Fast and Fully-volumetric Brain Segmentation of 7 Tesla MR Volumes

Ultra-high-field magnetic resonance imaging (MRI) enables sub-millimetre resolution imaging of the human brain, allowing the study of functional circuits of cortical layers at the meso-scale. An essential step in many functional and structural neuroimaging studies is segmentation, the operation of partitioning the MR images in anatomical structures. Despite recent efforts in brain imaging analysis, the literature lacks in accurate and fast methods for segmenting 7-tesla (7T) brain MRI. We here present CEREBRUM-7T, an optimised end-to-end convolutional neural network, which allows fully automatic segmentation of a whole 7T T1w MRI brain volume at once, without partitioning the volume, pre-processing, nor aligning it to an atlas. The trained model is able to produce accurate multi-structure segmentation masks on six different classes plus background in only a few seconds. The experimental part, a combination of objective numerical evaluations and subjective analysis, confirms that the proposed solution outperforms the training labels it was trained on and is suitable for neuroimaging studies, such as layer functional MRI studies. Taking advantage of a fine-tuning operation on a reduced set of volumes, we also show how it is possible to effectively apply CEREBRUM-7T to different sites data. Furthermore, we release the code, 7T data, and other materials, including the training labels and the Turing test

CEREBRUM-7T: fast and fully volumetric brain segmentation of 7 Tesla MR volumes

Ultra-high-field magnetic resonance imaging (MRI) enables sub-millimetre resolution imaging of the human brain, allowing the study of functional circuits of cortical layers at the meso-scale. An essential step in many functional and structural neuroimaging studies is segmentation, the operation of partitioning the MR images in anatomical structures. Despite recent efforts in brain imaging analysis, the literature lacks in accurate and fast methods for segmenting 7-tesla (7T) brain MRI. We here present CEREBRUM-7T, an optimised end-to-end convolutional neural network, which allows fully automatic segmentation of a whole 7T T1w MRI brain volume at once, without partitioning the volume, pre-processing, nor aligning it to an atlas. The trained model is able to produce accurate multi-structure segmentation masks on six different classes plus background in only a few seconds. The experimental part, a combination of objective numerical evaluations and subjective analysis, confirms that the proposed solution outperforms the training labels it was trained on and is suitable for neuroimaging studies, such as layer functional MRI studies. Taking advantage of a fine-tuning operation on a reduced set of volumes, we also show how it is possible to effectively apply CEREBRUM-7T to different sites data. Furthermore, we release the code, 7T data, and other materials, including the training labels and the Turing test