HAITCH: A Framework for Distortion and Motion Correction in Fetal Multi-Shell Diffusion-Weighted MRI.

Diffusion magnetic resonance imaging (dMRI) is pivotal for probing the microstructure of the rapidly-developing fetal brain. However, fetal motion during scans and its interaction with magnetic field inhomogeneities result in artifacts and data scattering across spatial and angular domains. The effects of those artifacts are more pronounced in high-angular resolution fetal dMRI, where signal-to-noise ratio is very low. Those effects lead to biased estimates and compromise the consistency and reliability of dMRI analysis. This work presents HAITCH, the first and the only publicly available tool to correct and reconstruct multi-shell high-angular resolution fetal dMRI data. HAITCH offers several technical advances that include a blip-reversed dual-echo acquisition for dynamic distortion correction, advanced motion correction for model-free and robust reconstruction, optimized multi-shell design for enhanced information capture and increased tolerance to motion, and outlier detection for improved reconstruction fidelity. The framework is open-source, flexible, and can be used to process any type of fetal dMRI data including single-echo or single-shell acquisitions, but is most effective when used with multi-shell multi-echo fetal dMRI data that cannot be processed with any of the existing tools. Validation experiments on real fetal dMRI scans demonstrate significant improvements and accurate correction across diverse fetal ages and motion levels. HAITCH successfully removes artifacts and reconstructs high-fidelity fetal dMRI data suitable for advanced diffusion modeling, including fiber orientation distribution function estimation. These advancements pave the way for more reliable analysis of the fetal brain microstructure and tractography under challenging imaging conditions.

Anatomically constrained tractography of the fetal brain.

Diffusion-weighted Magnetic Resonance Imaging (dMRI) is increasingly used to study the fetal brain in utero. An important computation enabled by dMRI is streamline tractography, which has unique applications such as tract-specific analysis of the brain white matter and structural connectivity assessment. However, due to the low fetal dMRI data quality and the challenging nature of tractography, existing methods tend to produce highly inaccurate results. They generate many false streamlines while failing to reconstruct the streamlines that constitute the major white matter tracts. In this paper, we advocate for anatomically constrained tractography based on an accurate segmentation of the fetal brain tissue directly in the dMRI space. We develop a deep learning method to compute the segmentation automatically. Experiments on independent test data show that this method can accurately segment the fetal brain tissue and drastically improve the tractography results. It enables the reconstruction of highly curved tracts such as optic radiations. Importantly, our method infers the tissue segmentation and streamline propagation direction from a diffusion tensor fit to the dMRI data, making it applicable to routine fetal dMRI scans. The proposed method can facilitate the study of fetal brain white matter tracts with dMRI.

Characterizing normal perinatal development of the human brain structural connectivity.

Early brain development is characterized by the formation of a highly organized structural connectome, which underlies brain's cognitive abilities and influences its response to diseases and environmental factors. Hence, quantitative assessment of structural connectivity in the perinatal stage is useful for studying normal and abnormal neurodevelopment. However, estimation of the connectome from diffusion MRI data involves complex computations. For the perinatal period, these computations are further challenged by the rapid brain development, inherently low signal quality, imaging difficulties, and high inter-subject variability. These factors make it difficult to chart the normal development of the structural connectome. As a result, there is a lack of reliable normative baselines of structural connectivity metrics at this critical stage in brain development. In this study, we developed a computational method based on spatio-temporal averaging in the image space for determining such baselines. We used this method to analyze the structural connectivity between 33 and 44 postmenstrual weeks using data from 166 subjects. Our results unveiled clear and strong trends in the development of structural connectivity in the perinatal stage. We observed increases in measures of network integration and segregation, and widespread strengthening of the connections within and across brain lobes and hemispheres. We also observed asymmetry patterns that were consistent between different connection weighting approaches. Connection weighting based on fractional anisotropy and neurite density produced the most consistent results. Our proposed method also showed considerable agreement with an alternative technique based on connectome averaging. The new computational method and results of this study can be useful for assessing normal and abnormal development of the structural connectome early in life.

Advances in Fetal Brain Imaging.

Over the last 20 years, there have been remarkable developments in fetal brain MR imaging analysis methods. This article delves into the specifics of structural imaging, diffusion imaging, functional MR imaging, and spectroscopy, highlighting the latest advancements in motion correction, fetal brain development atlases, and the challenges and innovations. Furthermore, this article explores the clinical applications of these advanced imaging techniques in comprehending and diagnosing fetal brain development and abnormalities.

A detailed spatio-temporal atlas of the white matter tracts for the fetal brain.

This study presents the construction of a comprehensive spatiotemporal atlas detailing the development of white matter tracts in the fetal brain using diffusion magnetic resonance imaging (dMRI). Our research leverages data collected from fetal MRI scans conducted between 22 and 37 weeks of gestation, capturing the dynamic changes in the brain's microstructure during this critical period. The atlas includes 60 distinct white matter tracts, including commissural, projection, and association fibers. We employed advanced fetal dMRI processing techniques and tractography to map and characterize the developmental trajectories of these tracts. Our findings reveal that the development of these tracts is characterized by complex patterns of fractional anisotropy (FA) and mean diffusivity (MD), reflecting key neurodevelopmental processes such as axonal growth, involution of the radial-glial scaffolding, and synaptic pruning. This atlas can serve as a useful resource for neuroscience research and clinical practice, improving our understanding of the fetal brain and potentially aiding in the early diagnosis of neurodevelopmental disorders. By detailing the normal progression of white matter tract development, the atlas can be used as a benchmark for identifying deviations that may indicate neurological anomalies or predispositions to disorders.

Deep learning microstructure estimation of developing brains from diffusion MRI: A newborn and fetal study.

Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to assess the brain white matter. Fiber orientation distribution functions (FODs) are a common way of representing the orientation and density of white matter fibers. However, with standard FOD computation methods, accurate estimation requires a large number of measurements that usually cannot be acquired for newborns and fetuses. We propose to overcome this limitation by using a deep learning method to map as few as six diffusion-weighted measurements to the target FOD. To train the model, we use the FODs computed using multi-shell high angular resolution measurements as target. Extensive quantitative evaluations show that the new deep learning method, using significantly fewer measurements, achieves comparable or superior results than standard methods such as Constrained Spherical Deconvolution and two state-of-the-art deep learning methods. For voxels with one and two fibers, respectively, our method shows an agreement rate in terms of the number of fibers of 77.5% and 22.2%, which is 3% and 5.4% higher than other deep learning methods, and an angular error of 10° and 20°, which is 6° and 5° lower than other deep learning methods. To determine baselines for assessing the performance of our method, we compute agreement metrics using densely sampled newborn data. Moreover, we demonstrate the generalizability of the new deep learning method across scanners, acquisition protocols, and anatomy on two clinical external datasets of newborns and fetuses. We validate fetal FODs, successfully estimated for the first time with deep learning, using post-mortem histological data. Our results show the advantage of deep learning in computing the fiber orientation density for the developing brain from in-vivo dMRI measurements that are often very limited due to constrained acquisition times. Our findings also highlight the intrinsic limitations of dMRI for probing the developing brain microstructure.

Divergent growth of the transient brain compartments in fetuses with nonsyndromic isolated clefts involving the primary and secondary palate.

Cleft lip/palate is a common orofacial malformation that often leads to speech/language difficulties as well as developmental delays in affected children, despite surgical repair. Our understanding of brain development in these children is limited. This study aimed to analyze prenatal brain development in fetuses with cleft lip/palate and controls. We examined in utero MRIs of 30 controls and 42 cleft lip/palate fetal cases and measured regional brain volumes. Cleft lip/palate was categorized into groups A (cleft lip or alveolus) and B (any combination of clefts involving the primary and secondary palates). Using a repeated-measures regression model with relative brain hemisphere volumes (%), and after adjusting for multiple comparisons, we did not identify significant differences in regional brain growth between group A and controls. Group B clefts had significantly slower weekly cerebellar growth compared with controls. We also observed divergent brain growth in transient brain structures (cortical plate, subplate, ganglionic eminence) within group B clefts, depending on severity (unilateral or bilateral) and defect location (hemisphere ipsilateral or contralateral to the defect). Further research is needed to explore the association between regional fetal brain growth and cleft lip/palate severity, with the potential to inform early neurodevelopmental biomarkers and personalized diagnostics.

Characterizing microstructural development in the fetal brain using diffusion MRI from 23 to 36 weeks of gestation.

We utilized motion-corrected diffusion tensor imaging (DTI) to evaluate microstructural changes in healthy fetal brains during the late second and third trimesters. Data were derived from fetal magnetic resonance imaging scans conducted as part of a prospective study spanning from 2013 March to 2019 May. The study included 44 fetuses between the gestational ages (GAs) of 23 and 36 weeks. We reconstructed fetal brain DTI using a motion-tracked slice-to-volume registration framework. Images were segmented into 14 regions of interest (ROIs) through label propagation using a fetal DTI atlas, with expert refinement. Statistical analysis involved assessing changes in fractional anisotropy (FA) and mean diffusivity (MD) throughout gestation using mixed-effects models, and identifying points of change in trajectory for ROIs with nonlinear trends. Results showed significant GA-related changes in FA and MD in all ROIs except in the thalamus' FA and corpus callosum's MD. Hemispheric asymmetries were found in the FA of the periventricular white matter (pvWM), intermediate zone, and subplate and in the MD of the ganglionic eminence and pvWM. This study provides valuable insight into the normal patterns of development of MD and FA in the fetal brain. These changes are closely linked with cytoarchitectonic changes and display indications of early functional specialization.

Improving Calibration and Out-of-Distribution Detection in Deep Models for Medical Image Segmentation.

Convolutional Neural Networks (CNNs) have proved to be powerful medical image segmentation models. In this study, we address some of the main unresolved issues regarding these models. Specifically, training of these models on small medical image datasets is still challenging, with many studies promoting techniques such as transfer learning. Moreover, these models are infamous for producing over-confident predictions and for failing silently when presented with out-of-distribution (OOD) test data. In this paper, for improving prediction calibration we advocate for multi-task learning, i.e., training a single model on several different datasets, spanning different organs of interest and different imaging modalities. We show that multi-task learning can significantly improve model confidence calibration. For OOD detection, we propose a novel method based on spectral analysis of CNN feature maps. We show that different datasets, representing different imaging modalities and/or different organs of interest, have distinct spectral signatures, which can be used to identify whether or not a test image is similar to the images used for training. We show that our proposed method is more accurate than several competing methods, including methods based on prediction uncertainty and image classification.

Population Atlas Analysis of Emerging Brain Structural Connections in the Human Fetus.

BACKGROUND: A lack of in utero imaging data hampers our understanding of the connections in the human fetal brain. Generalizing observations from postmortem subjects and premature newborns is inaccurate due to technical and biological differences. PURPOSE: To evaluate changes in fetal brain structural connectivity between 23 and 35 weeks postconceptional age using a spatiotemporal atlas of diffusion tensor imaging (DTI). STUDY TYPE: Retrospective. POPULATION: Publicly available diffusion atlases, based on 60 healthy women (age 18-45 years) with normal prenatal care, from 23 and 35 weeks of gestation. FIELD STRENGTH/SEQUENCE: 3.0 Tesla/DTI acquired with diffusion-weighted echo planar imaging (EPI). ASSESSMENT: We performed whole-brain fiber tractography from DTI images. The cortical plate of each diffusion atlas was segmented and parcellated into 78 regions derived from the Edinburgh Neonatal Atlas (ENA33). Connectivity matrices were computed, representing normalized fiber connections between nodes. We examined the relationship between global efficiency (GE), local efficiency (LE), small-worldness (SW), nodal efficiency (NE), and betweenness centrality (BC) with gestational age (GA) and with laterality. STATISTICAL TESTS: Linear regression was used to analyze changes in GE, LE, NE, and BC throughout gestation, and to assess changes in laterality. The t-tests were used to assess SW. P-values were corrected using Holm-Bonferroni method. A corrected P-value <0.05 was considered statistically significant. RESULTS: Network analysis revealed a significant weekly increase in GE (5.83%/week, 95% CI 4.32-7.37), LE (5.43%/week, 95% CI 3.63-7.25), and presence of SW across GA. No significant hemisphere differences were found in GE (P = 0.971) or LE (P = 0.458). Increasing GA was significantly associated with increasing NE in 41 nodes, increasing BC in 3 nodes, and decreasing BC in 2 nodes. DATA CONCLUSION: Extensive network development and refinement occur in the second and third trimesters, marked by a rapid increase in global integration and local segregation. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 2.

Atypical fetal brain development in fetuses with non-syndromic isolated musculoskeletal birth defects (niMSBDs).

Non-syndromic, isolated musculoskeletal birth defects (niMSBDs) are among the leading causes of pediatric hospitalization. However, little is known about brain development in niMSBDs. Our study aimed to characterize prenatal brain development in fetuses with niMSBDs and identify altered brain regions compared to controls. We retrospectively analyzed in vivo structural T2-weighted MRIs of 99 fetuses (48 controls and 51 niMSBDs cases). For each group (19-31 and >31 gestational weeks (GW)), we conducted repeated-measures regression analysis with relative regional volume (% brain hemisphere) as a dependent variable (adjusted for age, side, and interactions). Between 19 and 31GW, fetuses with niMSBDs had a significantly (P < 0.001) smaller relative volume of the intermediate zone (-22.9 ± 3.2%) and cerebellum (-16.1 ± 3.5%,) and a larger relative volume of proliferative zones (38.3 ± 7.2%), the ganglionic eminence (34.8 ± 7.3%), and the ventricles (35.8 ± 8.0%). Between 32 and 37 GW, compared to the controls, niMSBDs showed significantly smaller volumes of central regions (-9.1 ± 2.1%) and larger volumes of the cortical plate. Our results suggest there is altered brain development in fetuses with niMSBDs compared to controls (13.1 ± 4.2%). Further basic and translational neuroscience research is needed to better visualize these differences and to characterize the altered development in fetuses with specific niMSBDs.

Characterizing normal perinatal development of the human brain structural connectivity.

Early brain development is characterized by the formation of a highly organized structural connectome. The interconnected nature of this connectome underlies the brain's cognitive abilities and influences its response to diseases and environmental factors. Hence, quantitative assessment of structural connectivity in the perinatal stage is useful for studying normal and abnormal neurodevelopment. However, estimation of the connectome from diffusion MRI data involves complex computations. For the perinatal period, these computations are further challenged by the rapid brain development and imaging difficulties. Combined with high inter-subject variability, these factors make it difficult to chart the normal development of the structural connectome. As a result, there is a lack of reliable normative baselines of structural connectivity metrics at this critical stage in brain development. In this study, we developed a computational framework, based on spatio-temporal averaging, for determining such baselines. We used this framework to analyze the structural connectivity between 33 and 44 postmenstrual weeks using data from 166 subjects. Our results unveiled clear and strong trends in the development of structural connectivity in perinatal stage. Connection weighting based on fractional anisotropy and neurite density produced the most consistent results. We observed increases in global and local efficiency, a decrease in characteristic path length, and widespread strengthening of the connections within and across brain lobes and hemispheres. We also observed asymmetry patterns that were consistent between different connection weighting approaches. The new computational method and results are useful for assessing normal and abnormal development of the structural connectome early in life.

LigaNET: A multi-modal deep learning approach to predict the risk of subsequent anterior cruciate ligament injury after surgery.

Anterior cruciate ligament (ACL) injuries are a common cause of soft tissue injuries in young active individuals, leading to a significant risk of premature joint degeneration. Postoperative management of such injuries, in particular returning patients to athletic activities, is a challenge with immediate and long-term implications including the risk of subsequent injury. In this study, we present LigaNET, a multi-modal deep learning pipeline that predicts the risk of subsequent ACL injury following surgical treatment. Postoperative MRIs (n=1,762) obtained longitudinally between 3 to 24 months after ACL surgery from a cohort of 159 patients along with 11 non-imaging outcomes were used to train and test: 1) a 3D CNN to predict subsequent ACL injury from segmented ACLs, 2) a 3D CNN to predict injury from the whole MRI, 3) a logistic regression classifier predict injury from non-imaging data, and 4) a multi-modal pipeline by fusing the predictions of each classifier. The CNN using the segmented ACL achieved an accuracy of 77.6% and AUROC of 0.84, which was significantly better than the CNN using the whole knee MRI (accuracy: 66.6%, AUROC: 0.70; P<.001) and the non-imaging classifier (accuracy: 70.1%, AUROC: 0.75; P=.039). The fusion of all three classifiers resulted in highest classification performance (accuracy: 80.6%, AUROC: 0.89), which was significantly better than each individual classifier (P<.001). The developed multi-modal approach had similar performance in predicting the risk of subsequent ACL injury from any of the imaging sequences (P>.10). Our results demonstrate that a deep learning approach can achieve high performance in identifying patients at high risk of subsequent ACL injury after surgery and may be used in clinical decision making to improve postoperative management (e.g., safe return to sports) of ACL injured patients.

Deep learning microstructure estimation of developing brains from diffusion MRI: a newborn and fetal study.

Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to assess the brain white matter. Fiber orientation distribution functions (FODs) are a common way of representing the orientation and density of white matter fibers. However, with standard FOD computation methods, accurate estimation of FODs requires a large number of measurements that usually cannot be acquired for newborns and fetuses. We propose to overcome this limitation by using a deep learning method to map as few as six diffusion-weighted measurements to the target FOD. To train the model, we use the FODs computed using multi-shell high angular resolution measurements as target. Extensive quantitative evaluations show that the new deep learning method, using significantly fewer measurements, achieves comparable or superior results to standard methods such as Constrained Spherical Deconvolution. We demonstrate the generalizability of the new deep learning method across scanners, acquisition protocols, and anatomy on two clinical datasets of newborns and fetuses. Additionally, we compute agreement metrics within the HARDI newborn dataset, and validate fetal FODs with post-mortem histological data. The results of this study show the advantage of deep learning in inferring the microstructure of the developing brain from in-vivo dMRI measurements that are often very limited due to subject motion and limited acquisition times, but also highlight the intrinsic limitations of dMRI in the analysis of the developing brain microstructure. These findings, therefore, advocate for the need for improved methods that are tailored to studying the early development of human brain.

TBSS++: A novel computational method for Tract-Based Spatial Statistics.

Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to assess the brain white matter. One of the most common computations in dMRI involves cross-subject tract-specific analysis, whereby dMRI-derived biomarkers are compared between cohorts of subjects. The accuracy and reliability of these studies hinges on the ability to compare precisely the same white matter tracts across subjects. This is an intricate and error-prone computation. Existing computational methods such as Tract-Based Spatial Statistics (TBSS) suffer from a host of shortcomings and limitations that can seriously undermine the validity of the results. We present a new computational framework that overcomes the limitations of existing methods via (i) accurate segmentation of the tracts, and (ii) precise registration of data from different subjects/scans. The registration is based on fiber orientation distributions. To further improve the alignment of cross-subject data, we create detailed atlases of white matter tracts. These atlases serve as an unbiased reference space where the data from all subjects is registered for comparison. Extensive evaluations show that, compared with TBSS, our proposed framework offers significantly higher reproducibility and robustness to data perturbations. Our method promises a drastic improvement in accuracy and reproducibility of cross-subject dMRI studies that are routinely used in neuroscience and medical research.

Direct segmentation of brain white matter tracts in diffusion MRI.

The brain white matter consists of a set of tracts that connect distinct regions of the brain. Segmentation of these tracts is often needed for clinical and research studies. Diffusion-weighted MRI offers unique contrast to delineate these tracts. However, existing segmentation methods rely on intermediate computations such as tractography or estimation of fiber orientation density. These intermediate computations, in turn, entail complex computations that can result in unnecessary errors. Moreover, these intermediate computations often require dense multi-shell measurements that are unavailable in many clinical and research applications. As a result, current methods suffer from low accuracy and poor generalizability. Here, we propose a new deep learning method that segments these tracts directly from the diffusion MRI data, thereby sidestepping the intermediate computation errors. Our experiments show that this method can achieve segmentation accuracy that is on par with the state of the art methods (mean Dice Similarity Coefficient of 0.826). Compared with the state of the art, our method offers far superior generalizability to undersampled data that are typical of clinical studies and to data obtained with different acquisition protocols. Moreover, we propose a new method for detecting inaccurate segmentations and show that it is more accurate than standard methods that are based on estimation uncertainty quantification. The new methods can serve many critically important clinical and scientific applications that require accurate and reliable non-invasive segmentation of white matter tracts.

Fetal brain tissue annotation and segmentation challenge results.

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, gray matter, white matter, ventricles, cerebellum, brainstem, deep gray matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero.

Heterogeneous growth of the insula shapes the human brain.

The human cerebrum consists of a precise and stereotyped arrangement of lobes, primary gyri, and connectivity that underlies human cognition [P. Rakic, Nat. Rev. Neurosci. 10, 724-735 (2009)]. The development of this arrangement is less clear. Current models explain individual primary gyrification but largely do not account for the global configuration of the cerebral lobes [T. Tallinen, J. Y. Chung, J. S. Biggins, L. Mahadevan, Proc. Natl. Acad. Sci. U.S.A. 111, 12667-12672 (2014) and D. C. Van Essen, Nature 385, 313-318 (1997)]. The insula, buried in the depths of the Sylvian fissure, is unique in terms of gyral anatomy and size. Here, we quantitatively show that the insula has unique morphology and location in the cerebrum and that these key differences emerge during fetal development. Finally, we identify quantitative differences in developmental migration patterns to the insula that may underlie these differences. We calculated morphologic data in the insula and other lobes in adults (N = 107) and in an in utero fetal brain atlas (N = 81 healthy fetuses). In utero, the insula grows an order of magnitude slower than the other lobes and demonstrates shallower sulci, less curvature, and less surface complexity both in adults and progressively throughout fetal development. Spherical projection analysis demonstrates that the lenticular nuclei obstruct 60 to 70% of radial pathways from the ventricular zone (VZ) to the insula, forcing a curved migration to the insula in contrast to a direct radial pathway. Using fetal diffusion tractography, we identify radial glial fascicles that originate from the VZ and curve around the lenticular nuclei to form the insula. These results confirm existing models of radial migration to the cortex and illustrate findings that suggest differential insular and cerebral development, laying the groundwork to understand cerebral malformations and insular function and pathologies.

Abnormal prenatal brain development in Chiari II malformation.

Introduction: The Chiari II is a relatively common birth defect that is associated with open spinal abnormalities and is characterized by caudal migration of the posterior fossa contents through the foramen magnum. The pathophysiology of Chiari II is not entirely known, and the neurobiological substrate beyond posterior fossa findings remains unexplored. We aimed to identify brain regions altered in Chiari II fetuses between 17 and 26 GW. Methods: We used in vivo structural T2-weighted MRIs of 31 fetuses (6 controls and 25 cases with Chiari II). Results: The results of our study indicated altered development of diencephalon and proliferative zones (ventricular and subventricular zones) in fetuses with a Chiari II malformation compared to controls. Specifically, fetuses with Chiari II showed significantly smaller volumes of the diencephalon and significantly larger volumes of lateral ventricles and proliferative zones. Discussion: We conclude that regional brain development should be taken into consideration when evaluating prenatal brain development in fetuses with Chiari II.

A computational framework for characterizing normative development of structural brain connectivity in the perinatal stage.

Quantitative assessment of the brain's structural connectivity in the perinatal stage is useful for studying normal and abnormal neurodevelopment. However, estimation of the structural connectome from diffusion MRI data involves a series of complex and ill-posed computations. For the perinatal period, this analysis is further challenged by the rapid brain development and difficulties of imaging subjects at this stage. These factors, along with high inter-subject variability, have made it difficult to chart the normative development of the structural connectome. Hence, there is a lack of baseline trends in connectivity metrics that can be used as reliable references for assessing normal and abnormal brain development at this critical stage. In this paper we propose a computational framework, based on spatio-temporal atlases, for determining such baselines. We apply the framework on data from 169 subjects between 33 and 45 postmenstrual weeks. We show that this framework can unveil clear and strong trends in the development of structural connectivity in the perinatal stage. Some of our interesting findings include that connection weighting based on neurite density produces more consistent trends and that the trends in global efficiency, local efficiency, and characteristic path length are more consistent than in other metrics.