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Iglesias, J. E.

Publications and source records attributed to Iglesias, J. E..

At least 19 recordsLinked to original sources

Improving racial fairness in brain age models using style-transfer synthesis

Brain age models can systematically mispredict age for specific demographic groups, risking biased estimates of neurological health. We present an approach to improve accuracy and reduce racial disparities using synthetic T1 images generated via style-transfer with SuperSynth, an open-source FreeSurfer tool that produces intensity harmonized isotropic images regardless of the input's contrast or resolution. We refer to the original scans as the real domain and their SuperSynth-derived counterparts as the synthetic domain. Because each synthetic image derives from the participant's own scan, comparisons between domains hold anatomy and demographic composition constant. We audited fairness by training a neural network across thirteen racial compositions on a diverse cohort (683 White, 605 Black, 431 Asian) in both domains. Our findings highlight three key insights. First, the synthetic domain enhanced both fairness and accuracy, and even models trained on a single demographic showed reduced racial disparity purely from switching domain. The same pattern appeared in two independently developed pretrained models. Second, models trained on synthetic data demonstrated superior out-of-distribution robustness in external clinical testing. Third, augmenting imbalanced datasets with synthetic minority images closed 61% of the fairness gap without requiring new data collection, and unlike explicitly supplying race labels, does not require race as a model input at deployment. Representational analyses indicated that appearance standardization changes which features drive age prediction rather than removing demographic information from the images. By utilizing synthetic data, our approach offers a robust pathway to more equitable and generalizable brain age models.

bioengineering↗

A hypothalamic-brainstem activity sequence underlies arousal fluctuations during daytime drowsiness

During monotonous tasks, struggling with drowsiness leads to dynamic fluctuations in vigilance and task performance. Whether these moment-to-moment fluctuations are regulated by sleep-wake control circuitry remains unknown. Here, we used high-resolution 7T fMRI optimized for subcortical imaging to resolve activity across the human arousal regulatory system, including the hypothalamus, brainstem nuclei, basal forebrain, and thalamus, during a sustained attention task as subjects spontaneously experienced drowsiness. We identified a coordinated activity pattern locked to behavioral failures: widespread transient suppression during arousal drops and reactivation during recovery across all arousal-promoting regions, with opposite responses in the sleep-promoting hypothalamic preoptic area. These changes unfolded over [~]10-15 s in a 30 consistent sequence, led by the hypothalamic nuclei. Furthermore, suppression of brainstem nuclei preceded cortical infraslow (<0.05 Hz) oscillations, implicating a role in global neurovascular dynamics. These findings provide a temporally resolved, network-level portrait of human subcortical dynamics during drowsiness and identify a hypothalamic-led, brainstem-mediated activity sequence underlying behavioral arousal fluctuations and global cortical hemodynamics.

neuroscience↗

On the accuracy of image registration in portable low-field 3D brain MRI

Portable low-field MRI offers an affordable and mobile alternative to conventional high-field scanners, enabling imaging in point-of-care and resource-limited settings. However, its lower signal-to-noise ratio, reduced resolution, and acquisition artifacts raise concerns about the accuracy of standard image registration methods. Reliable registration is critical for a wide range of emerging applications, including frequent brain monitoring, assessment of neurodegenerative disease progression, and evaluation of treatment effects such as those of Alzheimers therapeutics. In this work, we systematically evaluated state-of-the-art registration approaches on simulated low-field scans (obtained by downsampling high-field images) and on real low-field brain MRI data. We compared three representative approaches: classical optimization (NiftyReg), learning-based registration (SynthMorph), and synthesis-based registration (SynthSR+NiftyReg). Using downsampled high-field scans, all methods performed well, achieving high Dice scores and smooth deformation fields, indicating that reduced resolution alone does not hinder registration. In contrast, real low-field data exhibited lower accuracy, primarily due to geometric distortion and other acquisition-specific artifacts. Among the tested approaches, the synthesis-based pipeline achieved the most robust performance across subjects and modalities. Overall, existing algorithms can accommodate resolution limitations, however, future methods could further enhance coregistration by explicitly addressing the distortions present in low-field MRI scans.

neuroscience↗

Fast segmentation with the NextBrain histological atlas

Structural brain analysis at the subregion level offers critical insights into healthy aging and neurodegenerative diseases. The NextBrain histological atlas was recently introduced to support such fine-grained investigations, but its existing Bayesian segmentation framework remains computationally prohibitive, particularly for large-scale studies. We present a new, open-source tool that dramatically accelerates segmentation using a hybrid approach combining: machine learning, contrast-adaptive segmentation; target-specific image synthesis; and fast diffeomorphic registration (all three with GPU support). Our method enables highly granular segmentation of brain MRI scans of any resolution and contrast (in vivo or ex vivo) at a fraction of the computational cost of the original method (<5 minutes on a GPU). We validate our tool on four different modalities (in vivo MRI, ex vivo MRI, HiP-CT, and photography) across a total of approximately 4,000 brain scans. Our results demonstrate that the accelerated approach achieves comparable accuracy to the original method in terms of Dice scores, while reducing runtime by over an order of magnitude. This work enables high-resolution anatomical analysis at unprecedented scale and flexibility, providing a practical solution for large neuroimaging studies. Our tool is publicly available in FreeSurfer (https://surfer.nmr.mgh.harvard.edu/fswiki/HistoAtlasSegmentation).

neuroscience↗

Progressive changes in functional connectivity between thalamic nuclei and cortical networks across learning

The thalamus is connected to cerebral cortex and subcortical regions, serving as a node within cognitive networks. It is a heterogeneous structure formed of functionally distinct nuclei with unique connectivity patterns. However, their contributions to cognitive functioning within networks is poorly understood. Recent animal research suggests that thalamic nuclei such as the mediodorsal nucleus play critical roles in goal-directed behaviour. Our aim was to investigate how functional integration of thalamic nuclei within cortical and subcortical networks changes whilst transitioning from more controlled goal-directed behaviour towards more automatic or habitual behaviour in humans. We analysed functional magnetic resonance imaging (fMRI) data from a stimulus-response learning study to investigate functional connectivity (FC) changes across learning between thalamic nuclei with cortical networks and subcortical structures in healthy subjects. We defined subcortical regions-of-interest (ROIs) individually in native space, segmenting the thalamus into 47 nuclei and segmenting 38 subregions within the basal ganglia and hippocampus. Additionally, we defined 12 cerebral cortex ROIs via maximum-probability network templates. Learning-related connectivity changes were examined via ROI-to-ROI functional network analysis. Our results showed that learning was associated with: 1) decreasing FC between the frontoparietal network and higher order thalamic nuclei; 2) increasing FC between the cingulo-opercular network and pulvinar nuclei, 3) decreasing FC between the default mode network (DMN) and right mediodorsal nuclei; 4) increasing FC between the DMN and left mediodorsal nuclei; 5) altered functional connectivity between thalamic nuclei and putamen subregions, and 6) increasing intrathalamic FC. Together, this suggests that several thalamic nuclei are involved in the learning-related transition from controlled to more automatic behaviour.

neuroscience↗

Mapping the Cerebrovascular Abnormality in Transgenic Alzheimer's Disease (AD) Mice with deep-learning-based super-resolution cerebral blood volume (CBV)-MRI

To measure the brain-wide vascular density (VD) alteration in degenerated brains with Alzheimers Disease (AD), deep learning-based super-resolution approach was developed to assist the segmentation of micro-vessels from the Monocrystalline Iron Oxide Nanoparticle (MION)-based CBV MRI images of transgenic mouse brains. Iron-induced T2* amplification effect well separated micro-vessels with tens of microns from capillary-enriched parenchyma voxels, enabling vascular compartment-specific VD differential analysis between AD and wildtype control mice. The differential maps based on segmented micro-vessels identified decreased VD in the anterior cingulate cortex (ACC) and medial entorhinal cortex (mEC) and increased VD in several highlighted brain regions, including dentate gyrus (DG) of the hippocampus, central and geniculate thalamus, medial septal area (MS), ventral tegmental area (VTA), and lateral entorhinal cortex (lEC). In contrast, the T2*-weighted capillary density mapping from parenchyma voxels showed increased VD in several cortical regions, including somatosensory and visual cortex, retrosplenial cortex, as well as piriform area and lEC in AD brains. However, dramatic capillary VD decrease was observed in the subcortical areas including hippocampus, thalamus, hypothalamus, and pontine areas. These high-resolution MION-based CBV MRI elucidates altered vascular compartments in degenerated AD brains, reconciling the various region-specific vascular impairment and angiogenesis in functional areas critical for cognitive decline of AD.

neuroscience↗

A next-generation, histological atlas of the human brain and its application to automated brain MRI segmentation

Magnetic resonance imaging (MRI) is the standard tool to image the human brain in vivo. In this domain, digital brain atlases are essential for subject-specific segmentation of anatomical regions of interest (ROIs) and spatial comparison of neuroanatomy from different subjects in a common coordinate frame. High-resolution, digital atlases derived from histology (e.g., Allen atlas [7], BigBrain [13], Julich [15]), are currently the state of the art and provide exquisite 3D cytoarchitectural maps, but lack probabilistic labels throughout the whole brain. Here we present NextBrain, a next - generation probabilistic atlas of human brain anatomy built from serial 3D histology and corresponding highly granular delineations of five whole brain hemispheres. We developed AI techniques to align and reconstruct [~]10,000 histological sections into coherent 3D volumes with joint geometric constraints (no overlap or gaps between sections), as well as to semi-automatically trace the boundaries of 333 distinct anatomical ROIs on all these sections. Comprehensive delineation on multiple cases enabled us to build the first probabilistic histological atlas of the whole human brain. Further, we created a companion Bayesian tool for automated segmentation of the 333 ROIs in any in vivo or ex vivo brain MRI scan using the NextBrain atlas. We showcase two applications of the atlas: automated segmentation of ultra-high-resolution ex vivo MRI and volumetric analysis of Alzheimers disease and healthy brain ageing based on [~]4,000 publicly available in vivo MRI scans. We publicly release: the raw and aligned data (including an online visualisation tool); the probabilistic atlas; the segmentation tool; and ground truth delineations for a 100 m isotropic ex vivo hemisphere (that we use for quantitative evaluation of our segmentation method in this paper). By enabling researchers worldwide to analyse brain MRI scans at a superior level of granularity without manual effort or highly specific neuroanatomical knowledge, NextBrain holds promise to increase the specificity of MRI findings and ultimately accelerate our quest to understand the human brain in health and disease.

neuroscience↗

Segmentation of supragranular and infragranular layers in ultra-high resolution 7T ex vivo MRI of the human cerebral cortex

Accurate labeling of specific layers in the human cerebral cortex is crucial for advancing our understanding of neurodevelopmental and neurodegenerative disorders. Lever-aging recent advancements in ultra-high resolution ex vivo MRI, we present a novel semi-supervised segmentation model capable of identifying supragranular and infragranular layers in ex vivo MRI with unprecedented precision. On a dataset consisting of 17 whole-hemisphere ex vivo scans at 120 {micro}m, we propose a multi-resolution U-Nets framework (MUS) that integrates global and local structural information, achieving reliable segmentation maps of the entire hemisphere, with Dice scores over 0.8 for supra- and infragranular layers. This enables surface modeling, atlas construction, anomaly detection in disease states, and cross-modality validation, while also paving the way for finer layer segmentation. Our approach offers a powerful tool for comprehensive neuroanatomical investigations and holds promise for advancing our mechanistic understanding of progression of neurodegenerative diseases.

neuroscience↗

Three-dimensional histology reveals dissociable human hippocampal long axis gradients of Alzheimer's pathology

INTRODUCTIONThree-dimensional (3D) histology analyses are essential to overcome sampling variability and understand pathological differences beyond the dissection axis. We present Path2MR, the first pipeline allowing 3D reconstruction of sparse human histology without an MRI reference. We implemented Path2MR with post-mortem hippocampal sections to explore pathology gradients in Alzheimers Disease. METHODSBlockface photographs of brain hemisphere slices are used for 3D reconstruction, from which an MRI-like image is generated using machine learning. Histology sections are aligned to the reconstructed hemisphere and subsequently to an atlas in standard space. RESULTSPath2MR successfully registered histological sections to their anatomical position along the hippocampal longitudinal axis. Combined with histopathology quantification, we found an expected peak of tau pathology at the anterior end of the hippocampus, while amyloid-{beta} displayed a quadratic anterior-posterior distribution. CONCLUSIONPath2MR, which enables 3D histology using any brain bank dataset, revealed significant differences along the hippocampus between tau and amyloid-{beta}.

neuroscience↗

Sustaining wakefulness: Brainstem connectivity in human consciousness

Consciousness is comprised of arousal (i.e., wakefulness) and awareness. Substantial progress has been made in mapping the cortical networks that modulate awareness in the human brain, but knowledge about the subcortical networks that sustain arousal is lacking. We integrated data from ex vivo diffusion MRI, immunohistochemistry, and in vivo 7 Tesla functional MRI to map the connectivity of a subcortical arousal network that we postulate sustains wakefulness in the resting, conscious human brain, analogous to the cortical default mode network (DMN) that is believed to sustain self-awareness. We identified nodes of the proposed default ascending arousal network (dAAN) in the brainstem, hypothalamus, thalamus, and basal forebrain by correlating ex vivo diffusion MRI with immunohistochemistry in three human brain specimens from neurologically normal individuals scanned at 600-750 {micro}m resolution. We performed deterministic and probabilistic tractography analyses of the diffusion MRI data to map dAAN intra-network connections and dAAN-DMN internetwork connections. Using a newly developed network-based autopsy of the human brain that integrates ex vivo MRI and histopathology, we identified projection, association, and commissural pathways linking dAAN nodes with one another and with cortical DMN nodes, providing a structural architecture for the integration of arousal and awareness in human consciousness. We release the ex vivo diffusion MRI data, corresponding immunohistochemistry data, network-based autopsy methods, and a new brainstem dAAN atlas to support efforts to map the connectivity of human consciousness. One sentence summaryWe performed ex vivo diffusion MRI, immunohistochemistry, and in vivo 7 Tesla functional MRI to map brainstem connections that sustain wakefulness in human consciousness.

neuroscience↗

3D analysis of dissection photographs with surface scanning and machine learning for quantitative neuropathology

We present open-source tools for 3D analysis of photographs of dissected slices of human brains, which are routinely acquired in brain banks but seldom used for quantitative analysis. Our tools can: (i) 3D reconstruct a volume from the photographs and, optionally, a surface scan; and (ii) produce a high-resolution 3D segmentation into 11 brain regions per hemisphere (22 in total), independently of the slice thickness. Our tools can be used as a substitute for ex vivo magnetic resonance imaging (MRI), which requires access to an MRI scanner, ex vivo scanning expertise, and considerable financial resources. We tested our tools on synthetic and real data from two NIH Alzheimers Disease Research Centers. The results show that our methodology yields accurate 3D reconstructions, segmentations, and volumetric measurements that are highly correlated to those from MRI. Our method also detects expected differences between post mortem confirmed Alzheimers disease cases and controls. The tools are available in our widespread neuroimaging suite "FreeSurfer" (https://surfer.nmr.mgh.harvard.edu/fswiki/PhotoTools).

neuroscience↗

Hippocampal sclerosis of aging at post-mortem is evident on MRI more than a decade prior

INTRODUCTIONHippocampal sclerosis of aging (HS) is an important component of combined dementia neuropathology. However, the temporal evolution of its histologically-defined features is unknown. We investigated pre-mortem longitudinal hippocampal atrophy associated with HS, as well as with other dementia-associated pathologies. METHODSWe analyzed hippocampal volumes from MRI segmentations in 64 dementia patients with longitudinal MRI follow-up and post-mortem neuropathological evaluation, including HS assessment in the hippocampal head and body. RESULTSSignificant HS-associated hippocampal volume changes were observed thoughout the evaluated timespan, up to 11.75 years before death. These changes were independent of age and Alzheimers Disease (AD) burden, and specifically driven by CA1 and subiculum. AD burden, but not HS, significantly associated with the rate of hippocampal atrophy. DISCUSSIONHS-associated volume changes are detectable on MRI earlier than 10 years before death. These findings could contribute to the derivation of volumetric cut-offs for in vivo differentiation between HS and AD.

neuroscience↗

A novel histological staging of hippocampal sclerosis that is evident in grey matter loss in vivo.

INTRODUCTIONHippocampal sclerosis of aging (HS) is defined by end-stage histological findings, strongly associated with limbic-predominant age-related TDP-43 encephalopathy (LATE). We aimed to characterize features of early HS to refine the understanding of its role within combined pathology. METHODSWe studied 159 brain donations from the multimodal Vallecas Alzheimers Center Study. A staging system (0 to IV) was developed to account for HS progression and analyzed in relation to pre-mortem cognitive and MRI data. RESULTSOur HS staging system displayed a significant correlation with disease duration, cognitive performance and combined neuropathologies, especially with LATE. Two-level assessment along the hippocampal longitudinal axis revealed an anterior-posterior gradient of HS severity. In vivo MRI showed focally reduced hippocampal grey matter density as a function of HS staging. DISCUSSIONThe association of this staging system with clinical progression and structural differences supports its utility in the characterization and potential in vivo monitoring of HS.

neuroscience↗

Accurate Bayesian segmentation of thalamic nuclei using diffusion MRI and an improved histological atlas

The human thalamus is a highly connected brain structure, which is key for the control of numerous functions and is involved in several neurological disorders. Recently, neuroimaging studies have increasingly focused on the volume and connectivity of the specific nuclei comprising this structure, rather than looking at the thalamus as a whole. However, accurate identification of cytoarchitectonically designed histological nuclei on standard in vivo structural MRI is hampered by the lack of image contrast that can be used to distinguish nuclei from each other and from surrounding white matter tracts. While diffusion MRI may offer such contrast, it has lower resolution and lacks some boundaries visible in structural imaging. In this work, we present a Bayesian segmentation algorithm for the thalamus. This algorithm combines prior information from a probabilistic atlas with likelihood models for both structural and diffusion MRI, allowing label boundaries to be informed by both modalities. We present an improved probabilistic atlas, incorporating 26 thalamic nuclei identified from histology and 45 white matter tracts identified in ultra-high gradient strength diffusion imaging. We present a family of likelihood models for diffusion tensor imaging, ensuring compatibility with the vast majority of neuroimaging datasets that include diffusion MRI data. The use of these diffusion likelihood models greatly improves identification of nuclei versus segmentation based solely on structural MRI. Dice comparison of 5 manually identifiable groups of nuclei to ground truth segmentations show improvements of up to 10 percentage points. Additionally, our chosen model shows a high degree of reliability, with median test-retest Dice scores above 0.85 for four out of five nuclei groups, whilst also offering improved detection of differential thalamic involvement in Alzheimers disease (AUROC 83.36%). The probabilistic atlas and segmentation tool will be made publicly available as part of the neuroimaging package FreeSurfer.

neuroscience↗

A multimodal imaging and analysis pipeline for creating a cellular census of the human cerebral cortex

Cells are not uniformly distributed in the human cerebral cortex. Rather, they are arranged in a regional and laminar fashion that span a range of scales. Here we demonstrate an innovative imaging and analysis pipeline to construct a reliable cell census across the human cerebral cortex. Magnetic resonance imaging (MRI) is used to establish a macroscopic reference coordinate system of laminar and cytoarchitectural boundaries. Cell counting is obtained with both traditional immunohistochemistry, to provide a stereological gold-standard, and with a custom-made inverted confocal light-sheet fluorescence microscope (LSFM) for 3D imaging at cellular resolution. Finally, mesoscale optical coherence tomography (OCT) enables the registration of the distorted histological cell typing obtained with LSFM to the MRI-based atlas coordinate system.

neuroscience↗

Quantification of volumetric morphometry and optical property in the cortex of human cerebellum at micrometer resolution

The surface of the human cerebellar cortex is much more tightly folded than the cerebral cortex. Volumetric analysis of cerebellar morphometry in magnetic resonance imaging studies suffers from insufficient resolution, and therefore has had limited impact on disease assessment. Automatic serial polarization-sensitive optical coherence tomography (as-PSOCT) is an emerging technique that offers the advantages of microscopic resolution and volumetric reconstruction of large-scale samples. In this study, we reconstructed multiple cubic centimeters of ex vivo human cerebellum tissue using as-PSOCT. The morphometric and optical properties of the cerebellar cortex across five subjects were quantified. While the molecular and granular layers exhibited similar mean thickness in the five subjects, the thickness varied greatly between the crown of the folium and the depth of the fissure in the granular layer within subjects. Layer-specific optical property remained homogenous within individual subjects but showed higher cross-subject variability than layer thickness. High-resolution volumetric morphometry and optical property maps of human cerebellar cortex revealed by as-PSOCT have great potential to advance our understanding of cerebellar function and diseases. HighlightsWe reconstructed cubic centimeters of human cerebellar samples at micrometer resolution in five subjects. Thickness of the granular layer varies greatly between the crowns and depths of cerebellar fissures. Cross-subject variability is higher in optical property than cortical morphology. Our results suggest homogenous cell and myelin density in the cortical layers of human cerebellum despite the highly convoluted folding patterns.

neuroscience↗

Reliability and sensitivity of two whole-brain segmentation approaches included in FreeSurfer - ASEG and SAMSEG

An accurate and reliable whole-brain segmentation is a key aspect of longitudinal neuroimaging studies. The ability to measure structural changes reliably is fundamental to detect confidently biological effects, especially when these affects are small. In this work, we undertake a thorough comparative analysis of reliability, bias, sensitivity to detect longitudinal change and diagnostic sensitivity to Alzheimers disease of two subcortical segmentation methods, Automatic Segmentation (ASEG) and Sequence Adaptive Multimodal Segmentation (SAMSEG). These are provided by the recently released version 7.1 of the open-source neuroimaging package FreeSurfer, with ASEG being the default segmentation method. First, we use a large sample of participants (n = 1629) distributed across the lifespan (age range = 4-93 years) to assess the within-session test-retest reliability in eight bilateral subcortical structures: amygdala, caudate, hippocampus, lateral ventricles, nucleus accumbens, pallidum, putamen and thalamus. We performed the analyses separately for a sub-sample scanned on a 1.5T Siemens Avanto (n = 774) and a sub-sample scanned on a 3T Siemens Skyra (n = 855). The absolute symmetrized percent differences across the lifespan indicated relatively constant reliability trajectories across age except for the younger children in the Avanto dataset for ASEG. Although both methods showed high reliability (ICC > 0.95), SAMSEG yielded significantly lower volumetric differences between repeated measures for all subcortical segmentations (p < 0.05) and higher spatial overlap in all structures except putamen, which had significantly higher spatial overlap for ASEG. Second, we tested how well each method was able to detect neuroanatomic volumetric change using longitudinal follow up scans (n = 491 for Avanto and n = 245 for Skyra; interscan interval = 1-10 years). Both methods showed excellent ability to detect longitudinal change, but yielded age-trajectories with notable differences for most structures, including the hippocampus and the amygdala. For instance, ASEG hippocampal volumes showed a steady age-decline from subjects in their twenties, while SAMSEG hippocampal volumes were stable until their sixties. Finally, we tested sensitivity of each method to clinically relevant change. We compared annual rate of hippocampal atrophy in a group of cognitively normal older adults (n = 20), patients with mild cognitive impairment (n = 20) and patients with Alzheimers disease (n = 20). SAMSEG was more sensitive to detect differences in atrophy between the groups, demonstrating ability to detect clinically relevant longitudinal changes. Both ASEG and SAMSEG were reliable and led to detection of within-person longitudinal change. However, SAMSEG yielded more consistent measurements between repeated scans without a lack of sensitivity to changes.

neuroscience↗

A multimodal computational pipeline for 3D histology of the human brain

Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of a whole human hemisphere.

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