Structural and functional insights into the mouse hypothalamus are hampered by its small size and deep location. Here, we leverage ultra-high-field magnetic resonance imaging (UHF-MRI) at 17.2 Tesla to achieve unprecedented spatial resolution in structural, functional and neurochemical imaging of the mouse hypothalamus, including sexual dimorphism in certain nuclei. High-resolution ex vivo anatomical MRI enabled precise hypothalamic parcellation, improving on existing atlases and revealing nuclei previously unresolved by MRI. Diffusion MRI and tractography mapped intra- and extra-hypothalamic pathways, facilitating circuit-level exploration without a priori assumptions. Resting-state fMRI combined with independent component analysis identified novel hypothalamic networks, demonstrating the enhanced capacity of UHF MRI to detect deep-brain activity. Proton magnetic resonance spectroscopy quantified neurochemical profiles, revealing sexually dimorphic heterogeneity within the hypothalamus. Our comprehensive multimodal approach uncovers sex differences in hypothalamic anatomy, microstructure, and neurochemistry, emphasizing the importance of sex as a biological variable. This integrated pipeline offers a valuable resource for dissecting hypothalamic circuits and functions, advancing our understanding of neuroendocrine regulation, behavior, and disease mechanisms, with direct translational relevance. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-24-CE16-3311

Diffusion tractography is the prominent in-vivo technique to study and investigate white-matter pathways in the human brain. While tractography is a powerful method, recent work suggests that different tractography methods can produce strikingly different representations of the same white-matter pathway. This multitude of differing options and diverging pipelines makes tractography related group-effects difficult to generalize, as it is currently unclear whether group-level inferences made using one tractography pipeline can be expected to hold when a different, equally defensible pipeline is applied to the same data. Here, we test the generalizability of sex-related changes on tractography-derived features by analyzing the exact same datasets with two equally reasonable pipelines which differ in model fitting, tractography reconstruction, and microstructure and volumetric analysis. We found that despite differences in analysis, the resulting patterns and biological interpretations of sex effects rarely disagreed across methods. Microstructural effects between methods were remarkably consistent between protocols, only displaying one significant disagreement out of 343 comparisons (.29%). However, discrepancies were more common among volumetric effects, displaying 24% significant disagreement. Moreover, we found that reconstruction methods are differentially sensitive to tractography-derived features, as bundles derived from targeted tractography were much more sensitive to volumetric effects than tractogram-based tractography, potentially explaining the volumetric discrepancy between methods. This study indicates that reasonable methodological choices are unlikely to lead two investigators to fundamentally opposing conclusions about sex differences in white-matter, and that the robustness of tractography findings is similar to established fields of science. More broadly, this study presents an optimistic outlook on the future of tractography, as it provides an empirical benchmark for reproducibility and bolsters confidence in the generalizability and robustness of tractography-derived findings.

Social interactions shape both the physiological and behavioural development of offspring, and poor care/early caregiver loss is known to promote adverse outcomes during infancy in both animals and humans. How affiliative behaviours impact the future development of offspring remains an open question. Here, we used Equus caballus (domestic horse) as a model to investigate this question. By coupling magnetic resonance imaging, longitudinal biobehavioural assessments and advanced multivariate statistical modelling, we found that prolonged maternal presence during infancy promotes the maturation of brain regions involved in both social behaviour (anterior cingulate cortex and retrosplenial cortex) and physiological regulation (hypothalamus and amygdala). Additionally, offspring benefiting from a prolonged maternal presence showed higher default mode network connectivity, improved social competences and feeding behaviours, and higher concentrations of circulating lipids (triglyceride and cholesterol). The findings of the present study underscore the salient role of social interactions in the development of allostatic regulation in offspring.

Abstract Background and aims Cerebral small vessel disease (SVD) contributes to stroke and cognitive decline and is identified by neuroimaging markers. However, clinical and radiological presentation varies widely between SVD etiologies, complicating the associations between neuroimaging markers and cognitive function. Processing speed is often impaired in individuals with SVD, but its relationship with neuroimaging markers of SVD remains poorly understood. We investigated these relationships in a multi-etiological SVD cohort. Methods We included 90 participants recruited at Assistance Publique – Hôpitaux de Paris (AP-HP): 30 with sporadic SVD, 30 with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) and 30 with cerebral amyloid angiopathy (CAA). All participants underwent multimodal neuroimaging at 3T and 7T and neuropsychological assessment. All analyzes were controlled for age, gender and education. Results Participants with sporadic SVD had a mean (SD) age of 62.4 (9.9) years, 57.7 (13.7) years in the CADASIL cohort, and 73.8 (8.4) years in the CAA cohort. Most neuroimaging markers showed significant differences across SVD etiologies (Figure 1). In contrast, processing speed performance did not differ between SVD etiologies. Only within the CAA group, higher PSMD (p-FDR = 0.04), higher free water fraction (p-FDR = 0.06), and lower diffusion tensor image analysis along the PVS (DTI-ALPS) index (p-FDR = 0.06) were associated with slower processing speed. Conclusions In a multi-etiological SVD cohort with comparable processing speed, our preliminary results suggest that neuroimaging-processing speed relationships are etiology-specific, highlighting that cognitive impairment in SVD arises from distinct pathologies rather than universal mechanisms. Exploring additional SVD markers may clarify processing speed-neuroimaging link. Conflict of interest Nothing to disclose Figure 1 - belongs to Results

Despite near-identical genetics, humans and chimpanzees display striking cognitive differences, thought to emerge from overall brain size variation and subtle divergences in brain connectivity. We present a comparative analysis of deep white matter bundle (DWMB) morphology in 39 in vivo chimpanzees and 39 humans, using diffusion MRI and a novel isomap-based shape analysis pipeline. After mapping DWMBs into a shared anatomical space via sulcus-informed diffeomorphic registration, we identified robust species-specific differences across key frontal tracts. We focused on four frontal tracts due to their roles in fronto-parietal and fronto-temporal connectivity supporting language, executive function, and socio-emotional processing, with the arcuate fasciculus serving as an internal control given its well-established species differences. Notably, the arcuate fasciculus in humans exhibited greater curvature, volume, and temporal extension-traits absent in chimpanzees and consistent with its role in language. The uncinate and inferior fronto-occipital fasciculus revealed distinct cross-species expansions and lateralization was observed for the frontal aslants and inferior fronto-occipital fasciculus in chimpanzees. These results provide the first high-dimensional morphological mapping of DWMBs across species, uncovering evolutionary adaptations in frontal connectivity and lateralization that likely underlie human-specific cognitive abilities.

Introduction Electroconvulsive therapy (ECT) is the most effective intervention for depression, yet no validated biomarkers reliably predict which patients will remit. Large-scale structural and functional dysconnectivity is well-established in major depressive disorder, motivating the use of graph-theoretical metrics to capture network architecture and identify treatment-sensitive markers. Methods In a prospective longitudinal study, 41 adult patients with a major depressive episode undergoing ECT and 24 healthy controls underwent anatomical, diffusion and resting-state functional MRI at baseline (V1). Patients were reassessed after five ECT sessions (V2, n = 31) and two weeks following treatment completion (V3, n = 29). Structural networks were constructed from multi-shell diffusion tractography and functional networks from rs-fMRI. Longitudinal change of global and local efficiency was assessed using linear mixed-effects models, and baseline predictors of remission (MADRS ≤10 at V3) were evaluated using ANOVAs and penalized binomial regression. Results Graph-theory metrics remained stable across timepoints, indicating no large-scale network reorganization during ECT. At baseline, patients showed reduced structural local efficiency relative to controls. Future remitters exhibited lower structural local and global efficiency in fractional anisotropy and neurite density index (NDI)-weighted networks at baseline compared with non-remitters, whereas non-remitters showed reduced functional local efficiency at baseline relative to controls. Penalized regression identified baseline NDI-weighted global efficiency as a significant predictor of remission. Conclusion Baseline structural and functional network profiles distinguished ECT remitters from non-remitters. These findings suggest that non-remission is characterized by reduced functional integration with relatively preserved structural connectivity, while remission is associated with preserved functional organization but lower baseline structural efficiency.

Studies on the human brain have emphasized the loss of gray matter volume and decreased thickness during normal aging, along with variations in the density of small axon fibers across different regions of the corpus callosum (CC). Here, we investigated age-related changes in white matter connectivity in the CC and their association with handedness and cognitive decline in chimpanzees. To this end, microstructural measures of CC morphology were obtained from a sample of 49 chimpanzees. Initial assessments included quantifying streamline density, fractional anisotropy (FA), axial diffusivity (AD), and radial diffusivity (RD) values, which were then correlated with age and cognitive measures using the Primate Cognition Test Battery. We found an inverse association between streamline density and age in chimpanzees, particularly in the anterior and central CC regions. We also found an inverse association between FA and age in the splenium. Lastly, after controlling for age and sex, chimpanzees with higher cognition values also had higher FA values in anterior regions of the CC. Collectively, our results show that chimpanzees diverged from the typical human pattern, suggesting stronger interhemispheric connectivity integrity in frontal cortical brain regions compared to humans.

Background: MRI markers, including visible perivascular spaces (PVS), diffusion tensor image analysis along the perivascular space (DTI-ALPS) index, and peak width of skeletonized mean diffusivity (PSMD) may capture the earliest pathogenesis of cerebral small vessel disease (SVD). This study aimed to elucidate the association between these markers and cognitive decline in sporadic and hereditary SVD. Methods: We included individuals from two cohorts: (1) participants with sporadic SVD from the Radboud University Nijmegen Diffusion tensor Magnetic resonance imaging Cohort (RUNDMC) and (2) participants with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) followed at the French National Referral Center. Individuals in both cohorts underwent neuroimaging and cognitive assessment over 14 years. We quantified baseline PVS burden, DTI-ALPS index and PSMD. We used linear mixed models to test their associations with longitudinal cognitive function, and Fine-and-Gray models to assess their association with incident all-cause dementia. Results: Cohort 1 included 446 individuals (mean age (SD) 65.2 years (8.9); 203 women), Cohort 2 included 164 individuals (mean age (SD) 49.9 years (12.6); 88 women). Baseline DTI-ALPS index was independently associated with better longitudinal processing speed (Cohort 1:β=0.11, 95 %CI 0.03–0.19) and cognitive index (Cohort 2:β=0.20, 95 %CI 0.06–0.33). Neither PVS burden, DTI-ALPS index nor PSMD were significantly associated with increased risk of all-cause dementia. Conclusion: These findings suggest that DTI-ALPS index may serve as a marker for cognitive decline. However, these markers have limited association with all-cause dementia risk. Future studies are needed to validate DTI-ALPS index and its link to cognitive decline.

Using diffusion-weighted imaging, we quantified the microstructure of U-shaped fiber bundles connecting the primary motor and somatosensory cortices in chimpanzees. We tested for sex and age effects, lateralization, and associations with manual and orofacial motor functions. Manual skills were assessed with a tool-use task; orofacial communication was assessed by individual variation in attention-getting sound production. Chimpanzees showed population-level leftward asymmetries in fractional anisotropy in U-fibers connecting central and inferior cortices, especially in females. Age was inversely associated with radial, axial, and mean diffusivity in these bundles. Right-handed motor skill was linked to stronger leftward fractional anisotropy asymmetries in superior regions. In contrast, more frequent attention-getting sound production was associated with increased leftward asymmetries in inferior regions. These findings show that different motor functions in chimpanzees are linked to region-specific variation in U-fiber integrity along the dorsal-ventral axis, aligning with previous representations of the chimpanzee motor "homunculus." The observed association between orofacial skill and leftward asymmetry in inferior sensorimotor regions suggests a potential preadaptation for the lateralized speech functions found in modern humans.

Introduction Electroconvulsive therapy (ECT) induces an increase in hippocampal volume presumed to reflect neurogenesis in severely depressed patients. We hypothesized that Neurite Orientation Dispersion and Density Imaging (NODDI) provides in vivo evidence of hippocampal neurogenesis following ECT. Methods This prospective longitudinal study included 43 depressed patients treated by ECT. Three sequential evaluations (V1: baseline, V2: at 2 weeks into ECT, V3: 14 days within completing ECT) included a 3T MR-scan with 3D T1-weighted and multi-shell diffusion (b = 200/1500/2500 s/mm2, 30/45/60 directions) sequences and clinical assessment with depression scales. Q-ball, Diffusion Tensor and NODDI models provided the following metrics: axial (AD), radial (RD) and mean diffusivity (MD), fractional anisotropy (FA) and generalized FA (GFA), neurite density index (NDI), isotropic fraction (Fiso), neurite orientation and dispersion index (ODI). FreeSurfer was used to extract whole hippocampal and subfields volumes from T1-weighted images. A linear mixed-effect model assessed the changes over time in hippocampal volumes and mean diffusion metrics, and their relationship with clinical response was analyzed with ANOVA. Bonferroni corrections were applied. Results 107 MRI were obtained at V1 (n = 43), V2 (n = 34) and V3 (n = 30) from 43 patients. Mean (± SD) interval between V1-V3 was 70 ± 25 days. Diffusion metrics in the hippocampus were: at V2, a decrease in left GFA, right AD, bilateral Fiso, and a bilateral ODI increase. Additionally, at V3, we observed a left MD decrease, bilateral AD decrease, right NDI increase, and bilateral ODI increase. Notably, NDI and Fiso changes were localized to the dentate gyrus but not to the hippocampal tail. ECT-responders showed a significant right hippocampus volume increase at 2 weeks into ECT. Conclusion After ECT, the observed increase in hippocampal volume is accompanied by bilateral changes in NODDI parameters, consistent with hippocampal neuroplasticity.

Introduction Severe depressive disorder is associated with smaller hippocampal volumes. We hypothesized that Neurite Orientation Dispersion and Density Imaging (NODDI) could provide in vivo evidence of decreased hippocampal neuroplasticity in patients with depression. Methods This cross-sectional study evaluated 43 patients with treatment-resistant depression eligible for electroconvulsive therapy and 24 controls. MRI evaluations included a 3T scan with 3DT1-weighted and multi-shell diffusion sequences (b = 200/1500/2500 s/mm², 30/45/60 directions). Q-ball, diffusion tensor, and NODDI models were used to obtain axial diffusivity (AD), radial diffusivity (RD), mean diffusivity (MD), fractional anisotropy (FA), generalized FA (GFA), neurite density index (NDI), isotropic fraction (Fiso), and orientation dispersion index (ODI). Hippocampal volumes were extracted using FreeSurfer from T1-weighted images. Pearson correlations adjusted for sex and group analyzed the relationship between age and bilateral hippocampal diffusion. Mixed-effects models assessed the impact of depression, hemisphere, sex, and age on eight diffusion metrics. Correlation matrices and group-specific correlograms analyzed diffusion metrics across both hippocampi. Principal component analysis (PCA) reduced these metrics to components explaining ‘95% of the variance. Results A total of 107 MRIs from patients and 24 MRIs from controls were analyzed. Hippocampal NDI was negatively correlated with age (r = -0.41, p = 0.002), while hippocampal Fiso was positively correlated (r = 0.45, p = 0.001). FA, GFA, AD, NDI, and ODI showed significant differences between patients and controls, despite comparable hippocampal volumes. PCA analysis effectively distinguished the two groups, achieving a diagnostic accuracy of 1. Conclusion Diffusion microstructural analyses reveal hippocampal alterations in severely depressed patients, potentially reflecting decreased neuroplasticity.

At temperate and polar latitudes, animals and humans experience seasonal changes that impact physiology and behavior. In these habitats, the prevalence and severity of certain psychiatric disorders fluctuate seasonally. Such patterns imply that an adaptive system fine-tunes brain physiology in response to annual environmental changes, and alterations to this system may adversely affect mental health. To date, the core neuronal circuitry of the seasonal control of brain functioning is still largely unknown. To address this question, we identified brain regions sensitive to seasonal changes, using neuroimaging in the domestic sheep (Ovis aries), an animal model commonly used to study seasonality. Here, we developed MRI neuroinformatics resources (templates and atlas) dedicated to the analysis of the sheep brain and revealed that seasons broadly modify grey matter organization and volume of both cortical and subcortical regions involved in the control of homeostasis, sensory processing, learning, memory, behavior control, and social cognition. Many of these regions were not previously known to be affected by seasonal variations, highlighting that the seasonal control of brain function involves plasticity mechanisms across multiple brain sites.

Diffusion MRI tractography (dMRI) has fundamentally transformed our ability to investigate white matter pathways in the human brain. While long-range connections have extensively been studied, superficial white matter bundles (SWMBs) have remained a relatively underexplored aspect of brain connectivity. This study undertakes a comprehensive examination of SWMB connectivity in both the human and chimpanzee brains, employing a novel combination of empirical and geometric methodologies to classify SWMB morphology in an objective manner. Leveraging two anatomical atlases, the Ginkgo Chauvel chimpanzee atlas and the Ginkgo Chauvel human atlas, comprising respectively 844 and 1375 superficial bundles, this research focuses on sparse representations of the morphology of SWMBs to explore the little-understood superficial connectivity of the chimpanzee brain and facilitate a deeper understanding of the variability in shape of these bundles. While similar, already well-known in human U-shape fibers were observed in both species, other shapes with more complex geometry such as 6 and J shapes were encountered. The localisation of the different bundle morphologies, putatively reflecting the brain gyrification process, was different between humans and chimpanzees using an isomap-based shape analysis approach. Ultimately, the analysis aims to uncover both commonalities and disparities in SWMBs between chimpanzees and humans, shedding light on the evolution and organization of these crucial neural structures.

Manual segmentation is an essential tool in the researcher's technical arsenal. It is a frequent practice necessary for image analysis in many protocols, especially in neuroimaging and comparative brain anatomy. In the framework of emergence of studies focusing on alternative animal models, manual segmentation procedures play a critical role. Nevertheless, this critical task is often assigned to students, a process that, unfortunately, tends to be time-consuming and repetitive. Well-conducted and well-described segmentation procedures can potentially guide novice and even expert operators and enhance research works' internal and external validity, making it possible to harmonize studies and facilitate data sharing. Furthermore, recent advances in neuroimaging, such as ex vivo imaging or ultra-high-field MRI, enable new acquisition modalities and the identification of minute structures that are barely visible with typical approaches. In this context of increasingly detailed and multimodal brain studies, reflecting on methodology is relevant and necessary. Because it is crucial to implement good practices in manual segmentation per se but also in the description of the segmentation procedures in research papers, we propose a general roadmap for optimizing the technique, its process and the reporting of manual segmentation. For each of them, the relevant elements of the literature have been collected and cited. The article is accompanied by a checklist that the reader can use to verify that the critical steps are being followed.

In this study, we investigated the controversial presence of the inferior fronto-occipital fasciculus (IFOF) in the macaque species ( Macaca fascicularis ) using ultra-high field MRI (11.7 T) diffusion data. Thanks to a fiber clustering approach, we were able to reconstruct the IFOF in both hemispheres. We observed thin frontal connections and a more developed fasciculus on the right hemisphere compared to the left. The presence of this special fasciculus, known in Humans as being part of the ventral pathways for multi-modal language processing, is a new step forward concerning the comprehension of the macaque brain, and the primate brain in general.

Background and purpose Cerebral small vessel diseases (SVDs) are characterized by early white matter (WM) changes, whose pathological underpinnings are yet poorly understood. CADASIL is a monogenic and archetypal SVD, providing an ideal model for investigating these changes. Here, we used multicompartment microscopic diffusion imaging and relaxometry to elucidate microstructural changes underlying early WM abnormalities in CADASIL. Methods We acquired diffusion MRI data with a multiple-shell Q-space sampling strategy, and relaxometry T1 and T2 data, with a 160 and 80-μm isotropic resolution respectively, ex vivo , in CADASIL and control mice. Diffusion datasets were computed with the Neurite Orientation Dispersion and Density Imaging model to extract the neurite density index, the extracellular free water and the orientation dispersion index. Relaxometry datasets were computed with a 3-compartment myelin water imaging model to extract the myelin content. MRI metrics were compared between CADASIL and control mice using voxel and WM tract-based analyses and with electron microscopy analysis. Results WM in CADASIL mice displayed a widespread reduction in general fractional anisotropy, a large increase in extracellular free water, a reduction in the myelin content, but no reduction in neurite density. Electron microscopy analysis showed a ∽2-fold increase in the extracellular spaces and an elevation of the g-ratio indicative of myelin sheath thinning in CADASIL WM. Conclusion Our findings suggest that accumulation of interstitial fluid and myelin damage are 2 major factors underlying early WM changes in CADASIL. Advanced diffusion MRI and relaxometry are promising approaches to decipher the underpinnings of WM alterations in SVDs.

Mapping the chimpanzee brain connectome and comparing it to that of humans is key to our understanding of similarities and differences in primate evolution that occurred after the split from their common ancestor around 6 million years ago. In contrast to studies on macaque species' brains, fewer studies have specifically addressed the structural connectivity of the chimpanzee brain and its comparison with the human brain. Most comparative studies in the literature focus on the anatomy of the cortex and deep nuclei to evaluate how their morphology and asymmetry differ from that of the human brain, and some studies have emerged concerning the study of brain connectivity among humans, monkeys, and apes. In this work, we established a new white matter atlas of the deep and superficial white matter structural connectivity in chimpanzees. In vivo anatomical and diffusion-weighted magnetic resonance imaging (MRI) data were collected on a 3-Tesla MRI system from 39 chimpanzees. These datasets were subsequently processed using a novel fiber clustering pipeline adapted to the chimpanzee brain, enabling us to create two novel deep and superficial white matter connectivity atlases representative of the chimpanzee brain. These atlases provide the scientific community with an important and novel set of reference data for understanding the commonalities and differences in structural connectivity between the human and chimpanzee brains. We believe this study to be innovative both in its novel approach and in mapping the superficial white matter bundles in the chimpanzee brain, which will contribute to a better understanding of hominin brain evolution.

The brainstem plays an essential role in many vital functions, such as autonomic control, consciousness and sleep, motricity, somatic afferent function, and cognition. Its involvement in several neurological diseases and the definition of brainstem targets for deep brain stimulation (DBS) explain the need for brainstem atlases describing its structural organization and connectivity from several modalities, from histology to ultrahigh field ex vivo MRI. Nonetheless, these atlases are often limited to a subpart of the brainstem or only include a single subject, the brainstem variability being considered low. This paper proposes a pipeline to create a high-resolution multisubject probabilistic atlas of the whole human brainstem based on four ultrahigh field ex vivo MRI datasets. The variability of the brainstem structures appears higher than usually considered, both for the volume and position of the central gray matter structures of the brainstem. This justifies the creation of atlases that capture the anatomical variability across subjects. The one we present here only included four specimens, but can easily be incremented due to its highly flexible design.