To accurately analyze changes of anatomical structures in longitudinal imaging studies, consistent segmentation across multiple time-points is required. Existing solutions often involve independent registration and segmentation components. Registration between time-points is used either as a prior for segmentation in a subsequent time point or to perform segmentation in a common space. In this work, we propose a novel hybrid convolutional neural network (CNN) that integrates segmentation and registration into a single procedure. We hypothesize that the joint optimization leads to increased performance on both tasks. The hybrid CNN is trained by minimizing an integrated loss function composed of four different terms, measuring segmentation accuracy, similarity between registered images, deformation field smoothness, and segmentation consistency. We applied this method to the segmentation of white matter tracts, describing functionally grouped axonal fibers, using N = 8045 longitudinal brain MRI data of 3249 individuals. The proposed method was compared with two multistage pipelines using two existing segmentation methods combined with a conventional deformable registration algorithm. In addition, we assessed the added value of the joint optimization for segmentation and registration separately. The hybrid CNN yielded significantly higher accuracy, consistency and reproducibility of segmentation than the multistage pipelines, and was orders of magnitude faster. Therefore, we expect it can serve as a novel tool to support clinical and epidemiological analyses on understanding microstructural brain changes over time.@en

Deep learning techniques are often criticized to heavily depend on a large quantity of labeled data. This problem is even more challenging in medical image analysis where the annotator expertise is often scarce. We propose a novel data-augmentation method to regularize neural network regressors that learn from a single global label per image. The principle of the method is to create new samples by recombining existing ones. We demonstrate the performance of our algorithm on two tasks: estimation of the number of enlarged perivascular spaces in the basal ganglia, and estimation of white matter hyperintensities volume. We show that the proposed method improves the performance over more basic data augmentation. The proposed method reached an intraclass correlation coefficient between ground truth and network predictions of 0.73 on the first task and 0.84 on the second task, only using between 25 and 30 scans with a single global label per scan for training. With the same number of training scans, more conventional data augmentation methods could only reach intraclass correlation coefficients of 0.68 on the first task, and 0.79 on the second task.

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