Sulci 3D mapping from human cranial endocasts: A powerful tool to study hominin brain evolution.

Key questions in paleoneurology concern the timing and emergence of derived cerebral features within the human lineage. Endocasts are replicas of the internal table of the bony braincase that are widely used in paleoneurology as a proxy for reconstructing a timeline for hominin brain evolution in the fossil record. The accurate identification of cerebral sulci imprints in endocasts is critical for assessing the topographic extension and structural organisation of cortical regions in fossil hominins. High-resolution imaging techniques combined with established methods based on population-specific brain atlases offer new opportunities for tracking detailed endocranial characteristics. This study provides the first documentation of sulcal pattern imprints from the superolateral surface of the cerebrum using a population-based atlas technique on extant human endocasts. Human crania from the Pretoria Bone Collection (South Africa) were scanned using micro-CT. Endocasts were virtually extracted, and sulci were automatically detected and manually labelled. A density map method was applied to project all the labels onto an averaged endocast to visualise the mean distribution of each identified sulcal imprint. This method allowed for the visualisation of inter-individual variation of sulcal imprints, for example, frontal lobe sulci, correlating with previous brain-MRI studies and for the first time the extensive overlapping of imprints in historically debated areas of the endocast (e.g. occipital lobe). In providing an innovative, non-invasive, observer-independent method to investigate human endocranial structural organisation, our analytical protocol introduces a promising perspective for future research in paleoneurology and for discussing critical hypotheses on the evolution of cognitive abilities among hominins.

Mechanistic Illustration: How Newly-Formed Blood Vessels Stopped by the Mineral Blocks of Bone Substitutes Can Be Avoided by Using Innovative Combined Therapeutics.

One major limitation for the vascularization of bone substitutes used for filling is the presence of mineral blocks. The newly-formed blood vessels are stopped or have to circumvent the mineral blocks, resulting in inefficient delivery of oxygen and nutrients to the implant. This leads to necrosis within the implant and to poor engraftment of the bone substitute. The aim of the present study is to provide a bone substitute currently used in the clinic with suitably guided vascularization properties. This therapeutic hybrid bone filling, containing a mineral and a polymeric component, is fortified with pro-angiogenic smart nano-therapeutics that allow the release of angiogenic molecules. Our data showed that the improved vasculature within the implant promoted new bone formation and that the newly-formed bone swapped the mineral blocks of the bone substitutes much more efficiently than in non-functionalized bone substitutes. Therefore, we demonstrated that our therapeutic bone substitute is an advanced therapeutical medicinal product, with great potential to recuperate and guide vascularization that is stopped by mineral blocks, and can improve the regeneration of critical-sized bone defects. We have also elucidated the mechanism to understand how the newly-formed vessels can no longer encounter mineral blocks and pursue their course of vasculature, giving our advanced therapeutical bone filling great potential to be used in many applications, by combining filling and nano-regenerative medicine that currently fall short because of problems related to the lack of oxygen and nutrients.

Semi-automatic segmentation of whole-body images in longitudinal studies.

We propose a semi-automatic segmentation pipeline designed for longitudinal studies considering structures with large anatomical variability, where expert interactions are required for relevant segmentations. Our pipeline builds on the regularized Fast Marching (rFM) segmentation approach by Risseret al(2018). It consists in transporting baseline multi-label FM seeds on follow-up images, selecting the relevant ones and finally performing the rFM approach. It showed increased, robust and faster results compared to clinical manual segmentation. Our method was evaluated on 3D synthetic images and patients' whole-body MRI. It allowed a robust and flexible handling of organs longitudinal deformations while considerably reducing manual interventions.

Sulcal pattern variation in extant human endocasts.

Our knowledge of human brain evolution primarily relies on the interpretation of palaeoneurological evidence. In this context, an endocast or replica of the inside of the bony braincase can be used to reconstruct a timeline of cerebral changes that occurred during human evolution, including changes in topographic extension and structural organisation of cortical areas. These changes can be tracked by identifying cerebral imprints, particularly cortical sulci. The description of these crucial landmarks in fossil endocasts is, however, challenging. High-resolution imaging techniques in palaeoneurology offer new opportunities for tracking detailed endocranial neural characteristics. In this study, we use high-resolution imaging techniques to document the variation in extant human endocranial sulcal patterns for subsequent use as a platform for comparison with the fossil record. We selected 20 extant human crania from the Pretoria Bone Collection (University of Pretoria, South Africa), which were detailed using X-ray microtomography at a spatial resolution ranging from 94 to 123 µm (isometric). We used Endex to extract, and Matlab to analyse the cortical imprints on the endocasts. We consistently identified superior, middle and inferior sulci on the frontal lobe; and superior and inferior sulci on the temporal lobe. We were able to label sulci bordering critical functional areas such as Broca's cap. Mapping the sulcal patterns on extant endocasts is a prerequisite for constructing an atlas which can be used for automatic sulci recognition.

In vivo localization of cortical areas using a 3D computerized atlas of the marmoset brain.

We created a volumetric template of the marmoset (Callithrix jacchus) brain, which enables localization of the cortical areas defined in the Paxinos et al. (The marmoset brain in stereotaxic coordinates. Elsevier Academic Press, Cambridge, 2012) marmoset brain atlas, as well as seven broader cortical regions (occipital, temporal, parietal, prefrontal, motor, limbic, insular), different brain compartments (white matter, gray matter, cerebro-spinal fluid including ventricular spaces), and various other structures (brain stem, cerebellum, olfactory bulb, hippocampus). The template was designed from T1-weighted MR images acquired using a 3 T MRI scanner. It was based on a single fully segmented marmoset brain image, which was transported onto the mean of 13 adult marmoset brain images using a diffeomorphic strategy that fully preserves the brain topology. In addition, we offer an automatic segmentation pipeline which fully exploits the proposed template. The segmentation pipeline was quantitatively assessed by comparing the results of manual and automated segmentations. An associated program, written in Python, can be used from a command-line interface, or used interactively as a module of the 3DSlicer software. This program can be applied to the analysis of multimodal images, to map specific cortical areas in lesions or to define the seeds for further tractography analyses.

ICP: From Correlation to Causation.

Intracranial pressure (ICP) is a complex modality in the sense that it largely interconnects various systemic and intra-cranial variables such as cerebral blood flow and volume, cerebrospinal fluid flow and absoption, craniospinal container. In this context, although empirical correlation is an interesting tool for establishing relations between pairs of observed variables, it may be limited to establishing causation relations. For instance, if variables X and Y are mainly influenced by variable Z, their correlation is strong, but does not mean that X has a causation relation with Y or vice versa. In this work, we explore the use of the statistical concept of partial correlation to ICP and other derived measures to apprehend the interplay between correlation and causation.

A DCE-MRI Driven 3-D Reaction-Diffusion Model of Solid Tumor Growth.

Predicting tumor growth and its response to therapy remains a major challenge in cancer research and strongly relies on tumor growth models. In this paper, we introduce, calibrate, and verify a novel image-driven reaction-diffusion model of avascular tumor growth. The model allows for proliferation, death and spread of tumor cells, and accounts for nutrient distribution and hypoxia. It is constrained by longitudinal time series of dynamic contrast-enhancement-MRI images. Tumor specific parameters are estimated from two early time points and used to predict the spatio-temporal evolution of the tumor volume and cell densities at later time points. We first test our parameter estimation approach on synthetic data from 15 generated tumors. Our in silico study resulted in small volume errors (<5%) and high Dice overlaps (>97%), showing that model parameters can be successfully recovered and used to accurately predict the tumor growth. Encouraged by these results, we apply our model to seven pre-clinical cases of breast carcinoma. We are able to show promising preliminary results, especially for the estimation for early time points. Processes like angiogenesis and apoptosis should be included to further improve predictions for later time points.

Spatially-varying metric learning for diffeomorphic image registration: a variational framework.

This paper introduces a variational strategy to learn spatially-varying metrics on large groups of images, in the Large Deformation Diffeomorphic Metric Mapping (LDDMM) framework. Spatially-varying metrics we learn not only favor local deformations but also correlated deformations in different image regions and in different directions. In addition, metric parameters can be efficiently estimated using a gradient descent method. We first describe the general strategy and then show how to use it on 3D medical images with reasonable computational ressources. Our method is assessed on the 3D brain images of the LPBA40 dataset. Results are compared with ANTS-SyN and LDDMM with spatially-homogeneous metrics.

An implicit sliding-motion preserving regularisation via bilateral filtering for deformable image registration.

Several biomedical applications require accurate image registration that can cope effectively with complex organ deformations. This paper addresses this problem by introducing a generic deformable registration algorithm with a new regularization scheme, which is performed through bilateral filtering of the deformation field. The proposed approach is primarily designed to handle smooth deformations both between and within body structures, and also more challenging deformation discontinuities exhibited by sliding organs. The conventional Gaussian smoothing of deformation fields is replaced by a bilateral filtering procedure, which compromises between the spatial smoothness and local intensity similarity kernels, and is further supported by a deformation field similarity kernel. Moreover, the presented framework does not require any explicit prior knowledge about the organ motion properties (e.g. segmentation) and therefore forms a fully automated registration technique. Validation was performed using synthetic phantom data and publicly available clinical 4D CT lung data sets. In both cases, the quantitative analysis shows improved accuracy when compared to conventional Gaussian smoothing. In addition, we provide experimental evidence that masking the lungs in order to avoid the problem of sliding motion during registration performs similarly in terms of the target registration error when compared to the proposed approach, however it requires accurate lung segmentation. Finally, quantification of the level and location of detected sliding motion yields visually plausible results by demonstrating noticeable sliding at the pleural cavity boundaries.

Longitudinal deformation models, spatial regularizations and learning strategies to quantify Alzheimer's disease progression.

In the context of Alzheimer's disease, two challenging issues are (1) the characterization of local hippocampal shape changes specific to disease progression and (2) the identification of mild-cognitive impairment patients likely to convert. In the literature, (1) is usually solved first to detect areas potentially related to the disease. These areas are then considered as an input to solve (2). As an alternative to this sequential strategy, we investigate the use of a classification model using logistic regression to address both issues (1) and (2) simultaneously. The classification of the patients therefore does not require any a priori definition of the most representative hippocampal areas potentially related to the disease, as they are automatically detected. We first quantify deformations of patients' hippocampi between two time points using the large deformations by diffeomorphisms framework and transport these deformations to a common template. Since the deformations are expected to be spatially structured, we perform classification combining logistic loss and spatial regularization techniques, which have not been explored so far in this context, as far as we know. The main contribution of this paper is the comparison of regularization techniques enforcing the coefficient maps to be spatially smooth (Sobolev), piecewise constant (total variation) or sparse (fused LASSO) with standard regularization techniques which do not take into account the spatial structure (LASSO, ridge and ElasticNet). On a dataset of 103 patients out of ADNI, the techniques using spatial regularizations lead to the best classification rates. They also find coherent areas related to the disease progression.

Flexible multivariate hemodynamics fMRI data analyses and simulations with PyHRF.

As part of fMRI data analysis, the pyhrf package provides a set of tools for addressing the two main issues involved in intra-subject fMRI data analysis: (1) the localization of cerebral regions that elicit evoked activity and (2) the estimation of activation dynamics also known as Hemodynamic Response Function (HRF) recovery. To tackle these two problems, pyhrf implements the Joint Detection-Estimation framework (JDE) which recovers parcel-level HRFs and embeds an adaptive spatio-temporal regularization scheme of activation maps. With respect to the sole detection issue (1), the classical voxelwise GLM procedure is also available through nipy, whereas Finite Impulse Response (FIR) and temporally regularized FIR models are concerned with HRF estimation (2) and are specifically implemented in pyhrf. Several parcellation tools are also integrated such as spatial and functional clustering. Parcellations may be used for spatial averaging prior to FIR/RFIR analysis or to specify the spatial support of the HRF estimates in the JDE approach. These analysis procedures can be applied either to volume-based data sets or to data projected onto the cortical surface. For validation purpose, this package is shipped with artificial and real fMRI data sets, which are used in this paper to compare the outcome of the different available approaches. The artificial fMRI data generator is also described to illustrate how to simulate different activation configurations, HRF shapes or nuisance components. To cope with the high computational needs for inference, pyhrf handles distributing computing by exploiting cluster units as well as multi-core machines. Finally, a dedicated viewer is presented, which handles n-dimensional images and provides suitable features to explore whole brain hemodynamics (time series, maps, ROI mask overlay).

Diffeomorphic registration with self-adaptive spatial regularization for the segmentation of non-human primate brains.

Cerebral aging has been linked to structural and functional changes in the brain throughout life. Here, we study the marmoset, a small non-human primate, in order to get insights into the mechanisms of brain aging in normal and pathological conditions. Imaging the brain of small animals with techniques such as MRI, quickly becomes a challenging task when compared with human brain imaging. Very often, a simple pre-processing step such as brain extraction cannot be achieved with classical tools. In this paper, we propose a diffeomorphic registration algorithm, which makes use of learned constraints to propagate the manual segmentation of a marmoset brain template to other MR images of marmoset brains. The main methological contribution of our paper is to explore a new strategy to automatically tune the spatial regularization of the deformations. Results show that we obtain a robust segmentation of the brain, even for images with a low contrast.

Hybrid feature-based diffeomorphic registration for tumor tracking in 2-D liver ultrasound images.

Real-time ultrasound image acquisition is a pivotal resource in the medical community, in spite of its limited image quality. This poses challenges to image registration methods, particularly to those driven by intensity values. We address these difficulties in a novel diffeomorphic registration technique for tumor tracking in series of 2-D liver ultrasound. Our method has two main characteristics: 1) each voxel is described by three image features: intensity, local phase, and phase congruency; 2) we compute a set of forces from either local information (Demons-type of forces), or spatial correspondences supplied by a block-matching scheme, from each image feature. A family of update deformation fields which are defined by these forces, and inform upon the local or regional contribution of each image feature are then composed to form the final transformation. The method is diffeomorphic, which ensures the invertibility of deformations. The qualitative and quantitative results yielded by both synthetic and real clinical data show the suitability of our method for the application at hand.

Toward physiologically motivated registration of diagnostic CT and PET/CT of lung volumes.

PURPOSE: Current clinical practice for lung cancer diagnosis and staging requires the acquisition of a diagnostic computed tomography (CT) as well as positron emission tomography (PET)/CT volumes from a hybrid scanner, where the CT is used for attenuation correction (AC-CT). The PET and AC-CT images are implicitly aligned, however, image registration between the diagnostic CT and PET volumes is needed to relate the anatomical correspondences. This is an important but difficult task due to the absence of a direct or functional relationship between the intensities. Alternatively, here we propose the diagnostic CT can be aligned with the PET image through an indirect registration process that uses the AC-CT. The resultant deformation field can then be used to align the PET image to the diagnostic CT. The registration of the diagnostic CT to AC-CT registration still presents two major challenges: (a) it is a multimodal registration problem since the diagnostic CT is acquired after the injection of a contrast agent, and (b) the type and amplitude of the deformations require a registration process that includes physically motivated properties to achieve an accurate and physiologically plausible alignment. METHODS: The authors propose a new framework based on fluid registration including three physiologically motivated properties: (i) sliding motion of the lungs against the pleura; (ii) preservation of rigid structures; (iii) preservation of topology. The sliding motion is modeled using direction dependent regularization that decouples the tangential and the normal components of the external force term. The rigid shape of the bones is preserved using a spatially varying filter for the deformations. Finally, the topology is maintained using the concept of log-unbiased deformations. To solve the multimodal problem, the authors use local cross correlation (LCC) as the similarity measure. RESULTS: The proposed framework is first evaluated on CT lung image pairs representing several phases of the respiratory cycle. The authors show that their proposed framework has a superior performance compared to the classic fluid registration, both in quantitative and qualitative terms. The authors then evaluate the framework using ten real patient scans, where the authors also demonstrate how their physiologically motivated registration framework can be successfully applied to the task of fusing diagnostic CT with the PET/CT image volumes. CONCLUSIONS: The proposed registration framework has better results for the fusion of diagnostic CT with PET images in comparison to the classic fluid registration framework.

Left-invariant metrics for diffeomorphic image registration with spatially-varying regularisation.

We present a new framework for diffeomorphic image registration which supports natural interpretations of spatially-varying metrics. This framework is based on left-invariant diffeomorphic metrics (LIDM) and is closely related to the now standard large deformation diffeomorphic metric mapping (LDDMM). We discuss the relationship between LIDM and LDDMM and introduce a computationally convenient class of spatially-varying metrics appropriate for both frameworks. Finally, we demonstrate the effectiveness of our method on a 2D toy example and on the 40 3D brain images of the LPBA40 dataset.

Complex lung motion estimation via adaptive bilateral filtering of the deformation field.

Estimation of physiologically plausible deformations is critical for several medical applications. For example, lung cancer diagnosis and treatment requires accurate image registration which preserves sliding motion in the pleural cavity, and the rigidity of chest bones. This paper addresses these challenges by introducing a novel approach for regularisation of non-linear transformations derived from a bilateral filter. For this purpose, the classic Gaussian kernel is replaced by a new kernel that smoothes the estimated deformation field with respect to the spatial position, intensity and deformation dissimilarity. The proposed regularisation is a spatially adaptive filter that is able to preserve discontinuity between the lungs and the pleura and reduces any rigid structures deformations in volumes. Moreover, the presented framework is fully automatic and no prior knowledge of the underlying anatomy is required. The performance of our novel regularisation technique is demonstrated on phantom data for a proof of concept as well as 3D inhale and exhale pairs of clinical CT lung volumes. The results of the quantitative evaluation exhibit a significant improvement when compared to the corresponding state-of-the-art method using classic Gaussian smoothing.

Piecewise-diffeomorphic image registration: application to the motion estimation between 3D CT lung images with sliding conditions.

In this paper, we propose a new strategy for modelling sliding conditions when registering 3D images in a piecewise-diffeomorphic framework. More specifically, our main contribution is the development of a mathematical formalism to perform Large Deformation Diffeomorphic Metric Mapping registration with sliding conditions. We also show how to adapt this formalism to the LogDemons diffeomorphic registration framework. We finally show how to apply this strategy to estimate the respiratory motion between 3D CT pulmonary images. Quantitative tests are performed on 2D and 3D synthetic images, as well as on real 3D lung images from the MICCAI EMPIRE10 challenge. Results show that our strategy estimates accurate mappings of entire 3D thoracic image volumes that exhibit a sliding motion, as opposed to conventional registration methods which are not capable of capturing discontinuous deformations at the thoracic cage boundary. They also show that although the deformations are not smooth across the location of sliding conditions, they are almost always invertible in the whole image domain. This would be helpful for radiotherapy planning and delivery.

Coupling and robustness of intra-cortical vascular territories.

Vascular domains have been described as being coupled to neuronal functional units enabling dynamic blood supply to the cerebral cyto-architecture. Recent experiments have shown that penetrating arterioles of the grey matter are the building blocks for such units. Nevertheless, vascular territories are still poorly known, as the collection and analysis of large three-dimensional micro-vascular networks are difficult. By using an exhaustive reconstruction of the micro-vascular network in an 18 mm(3) volume of marmoset cerebral cortex, we numerically computed the blood flow in each blood vessel. We thus defined arterial and venular territories and examined their overlap. A large part of the intracortical vascular network was found to be supplied by several arteries and drained by several venules. We quantified this multiple potential to compensate for deficiencies by introducing a new robustness parameter. Robustness proved to be positively correlated with cortical depth and a systematic investigation of coupling maps indicated local patterns of overlap between neighbouring arteries and neighbouring venules. However, arterio-venular coupling did not have a spatial pattern of overlap but showed locally preferential functional coupling, especially of one artery with two venules, supporting the notion of vascular units. We concluded that intra-cortical perfusion in the primate was characterised by both very narrow functional beds and a large capacity for compensatory redistribution, far beyond the nearest neighbour collaterals.

Motion correction and parameter estimation in dceMRI sequences: application to colorectal cancer.

We present a novel Bayesian framework for non-rigid motion correction and pharmacokinetic parameter estimation in dceMRI sequences which incorporates a physiological image formation model into the similarity measure used for motion correction. The similarity measure is based on the maximization of the joint posterior probability of the transformations which need to be applied to each image in the dataset to bring all images into alignment, and the physiological parameters which best explain the data. The deformation framework used to deform each image is based on the diffeomorphic logDemons algorithm. We then use this method to co-register images from simulated and real dceMRI datasets and show that the method leads to an improvement in the estimation of physiological parameters as well as improved alignment of the images.

Simultaneous multi-scale registration using large deformation diffeomorphic metric mapping.

In the framework of large deformation diffeomorphic metric mapping (LDDMM), we present a practical methodology to integrate prior knowledge about the registered shapes in the regularizing metric. Our goal is to perform rich anatomical shape comparisons from volumetric images with the mathematical properties offered by the LDDMM framework. We first present the notion of characteristic scale at which image features are deformed. We then propose a methodology to compare anatomical shape variations in a multi-scale fashion, i.e., at several characteristic scales simultaneously. In this context, we propose a strategy to quantitatively measure the feature differences observed at each characteristic scale separately. After describing our methodology, we illustrate the performance of the method on phantom data. We then compare the ability of our method to segregate a group of subjects having Alzheimer's disease and a group of controls with a classical coarse to fine approach, on standard 3D MR longitudinal brain images. We finally apply the approach to quantify the anatomical development of the human brain from 3D MR longitudinal images of pre-term babies. Results show that our method registers accurately volumetric images containing feature differences at several scales simultaneously with smooth deformations.