Co-Planar Stereotaxic Atlas of the Human Brain—3-Dimensional Proportional System: An Approach to Cerebral Imaging, J. Talairach, P. Tournoux. Georg Thieme Verlag, New York (1988), 122 pp., 130 figs. DM 268

Information processing in the cerebral cortex involves interactions among distributed areas. Anatomical connectivity suggests that certain areas form local hierarchical relations such as within the visual system. Other connectivity patterns, particularly among association areas, suggest the presence of large-scale circuits without clear hierarchical relations. In this study the organization of networks in the human cerebrum was explored using resting-state functional connectivity MRI. Data from 1,000 subjects were registered using surface-based alignment. A clustering approach was employed to identify and replicate networks of functionally coupled regions across the cerebral cortex. The results revealed local networks confined to sensory and motor cortices as well as distributed networks of association regions. Within the sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas. In association cortex, the connectivity patterns often showed abrupt transitions between network boundaries. Focused analyses were performed to better understand properties of network connectivity. A canonical sensory-motor pathway involving primary visual area, putative middle temporal area complex (MT+), lateral intraparietal area, and frontal eye field was analyzed to explore how interactions might arise within and between networks. Results showed that adjacent regions of the MT+ complex demonstrate differential connectivity consistent with a hierarchical pathway that spans networks. The functional connectivity of parietal and prefrontal association cortices was next explored. Distinct connectivity profiles of neighboring regions suggest they participate in distributed networks that, while showing evidence for interactions, are embedded within largely parallel, interdigitated circuits. We conclude by discussing the organization of these large-scale cerebral networks in relation to monkey anatomy and their potential evolutionary expansion in humans to support cognition.

The organization of the human cerebral cortex estimated by intrinsic functional connectivity

Deep convolutional neural networks have performed remarkably well on many Computer Vision tasks. However, these networks are heavily reliant on big data to avoid overfitting. Overfitting refers to the phenomenon when a network learns a function with very high variance such as to perfectly model the training data. Unfortunately, many application domains do not have access to big data, such as medical image analysis. This survey focuses on Data Augmentation, a data-space solution to the problem of limited data. Data Augmentation encompasses a suite of techniques that enhance the size and quality of training datasets such that better Deep Learning models can be built using them. The image augmentation algorithms discussed in this survey include geometric transformations, color space augmentations, kernel filters, mixing images, random erasing, feature space augmentation, adversarial training, generative adversarial networks, neural style transfer, and meta-learning. The application of augmentation methods based on GANs are heavily covered in this survey. In addition to augmentation techniques, this paper will briefly discuss other characteristics of Data Augmentation such as test-time augmentation, resolution impact, final dataset size, and curriculum learning. This survey will present existing methods for Data Augmentation, promising developments, and meta-level decisions for implementing Data Augmentation. Readers will understand how Data Augmentation can improve the performance of their models and expand limited datasets to take advantage of the capabilities of big data.

/pdf/a-survey-on-image-data-augmentation-for-deep-learning-4ru1bj2hbb.pdf

A survey on Image Data Augmentation for Deep Learning

CA : A Cancer Journal for Clinicians

The minimal preprocessing pipelines for the Human Connectome Project.

Brain tissue segmentation from multimodal MRI is a key building block of many neuroscience analysis pipelines. It could also play an important role in many clinical imaging scenarios. Established tissue segmentation approaches have however not been developed to cope with large anatomical changes resulting from pathology. The effect of the presence of brain lesions, for example, on their performance is thus currently uncontrolled and practically unpredictable. Contrastingly, with the advent of deep neural networks (DNNs), segmentation of brain lesions has matured significantly and is achieving performance levels making it of interest for clinical use. However, few existing approaches allow for jointly segmenting normal tissue and brain lesions. Developing a DNN for such joint task is currently hampered by the fact that annotated datasets typically address only one specific task and rely on a task-specific hetero-modal imaging protocol. In this work, we propose a novel approach to build a joint tissue and lesion segmentation model from task-specific hetero-modal and partially annotated datasets. Starting from a variational formulation of the joint problem, we show how the expected risk can be decomposed and optimised empirically. We exploit an upper-bound of the risk to deal with missing imaging modalities. For each task, our approach reaches comparable performance than task-specific and fully-supervised models.

/pdf/learning-joint-lesion-and-tissue-segmentation-from-task-77ujvyz4qq.pdf

Learning joint lesion and tissue segmentation from task-specific hetero-modal datasets

Anatomically plausible image registration often requires volumetric preservation. Previous approaches to incompressible image registration have exploited relaxed constraints, ad hoc optimisation methods or practically intractable computational schemes. Divergence-free velocity fields have been used to achieve incompressibility in the continuous domain, although, after discretisation, no guarantees have been provided. In this paper, we introduce stationary velocity fields (SVFs) parameterised by divergence-conforming B-splines in the context of image registration. We demonstrate that sparse linear constraints on the parameters of such divergence-conforming B-Splines SVFs lead to being exactly divergence-free at any point of the continuous spatial domain. In contrast to previous approaches, our framework can easily take advantage of modern solvers for constrained optimisation, symmetric registration approaches, arbitrary image similarity and additional regularisation terms. We study the numerical incompressibility error for the transformation in the case of an Euler integration, which gives theoretical insights on the improved accuracy error over previous methods. We evaluate the proposed framework using synthetically deformed multimodal brain images, and the STACOM’11 myocardial tracking challenge. Accuracy measurements demonstrate that our method compares favourably with state-of-the-art methods whilst achieving volume preservation.

Incompressible Image Registration Using Divergence-Conforming B-Splines

Classical pairwise image registration methods search for a spatial transformation that optimises a numerical measure that indicates how well a pair of moving and fixed images are aligned. Current learning-based registration methods have adopted the same paradigm and typically predict, for any new input image pair, dense correspondences in the form of a dense displacement field or parameters of a spatial transformation model. However, in many applications of registration, the spatial transformation itself is only required to propagate points or regions of interest (ROIs). In such cases, detailed pixel- or voxel-level correspondence within or outside of these ROIs often have little clinical value. In this paper, we propose an alternative paradigm in which the location of corresponding image-specific ROIs, defined in one image, within another image is learnt. This results in replacing image registration by a conditional segmentation algorithm, which can build on typical image segmentation networks and their widely-adopted training strategies. Using the registration of 3D MRI and ultrasound images of the prostate as an example to demonstrate this new approach, we report a median target registration error (TRE) of 2.1 mm between the ground-truth ROIs defined on intraoperative ultrasound images and those propagated from the preoperative MR images. Significantly lower (>34%) TREs were obtained using the proposed conditional segmentation compared with those obtained from a previously-proposed spatial-transformation-predicting registration network trained with the same multiple ROI labels for individual image pairs. We conclude this work by using a quantitative bias-variance analysis to provide one explanation of the observed improvement in registration accuracy.

Conditional Segmentation in Lieu of Image Registration

Randomized phase 2 trial of adaptive dose painting vs. standard IMRT for head and neck cancer

Super-resolution (SR) methods have seen significant advances thanks to the development of convolutional neural networks (CNNs). CNNs have been successfully employed to improve the quality of endomicroscopy imaging. Yet, the inherent limitation of research on SR in endomicroscopy remains the lack of ground truth high-resolution (HR) images, commonly used for both supervised training and reference-based image quality assessment (IQA). Therefore, alternative methods, such as unsupervised SR are being explored. To address the need for non-reference image quality improvement, we designed a novel zero-shot super-resolution (ZSSR) approach that relies only on the endomicroscopy data to be processed in a self-supervised manner without the need for ground-truth HR images. We tailored the proposed pipeline to the idiosyncrasies of endomicroscopy by introducing both: a physically-motivated Voronoi downscaling kernel accounting for the endomicroscope's irregular fibre-based sampling pattern, and realistic noise patterns. We also took advantage of video sequences to exploit a sequence of images for self-supervised zero-shot image quality improvement. We run ablation studies to assess our contribution in regards to the downscaling kernel and noise simulation. We validate our methodology on both synthetic and original data. Synthetic experiments were assessed with reference-based IQA, while our results for original images were evaluated in a user study conducted with both expert and non-expert observers. The results demonstrated superior performance in image quality of ZSSR reconstructions in comparison to the baseline method. The ZSSR is also competitive when compared to supervised single-image SR, especially being the preferred reconstruction technique by experts.

/pdf/zero-shot-super-resolution-with-a-physically-motivated-11u22njrgy.pdf

Tom Vercauteren

Papers

Learning joint lesion and tissue segmentation from task-specific hetero-modal datasets

Incompressible Image Registration Using Divergence-Conforming B-Splines

Conditional Segmentation in Lieu of Image Registration

Randomized phase 2 trial of adaptive dose painting vs. standard IMRT for head and neck cancer

Zero-shot super-resolution with a physically-motivated downsampling kernel for endomicroscopy