Biology subjects

Khan, A. R.

Publications and source records attributed to Khan, A. R..

At least 19 recordsLinked to original sources

bioRxiv2026

Phosphorylated -Synuclein shapes changes in brain structure, task-related activity and functional connectivity in M83 mice

Phosphorylated -synuclein at S129 (pS129) is the predominant form of -synuclein in the aggregates known as Lewy bodies (LB) and Lewy neurites (LN), the pathological hallmarks of Parkinson's disease (PD) and dementia with Lewy bodies (DLB), collectively known as synucleinopathies. The toxic nature of these inclusions remains contentious. To improve our understanding of these aggregates and their role in the structural and functional changes observed in synucleinopathies, we combined non-invasive structural and functional MRI in awake head-fixed M83 mice with whole-brain light-sheet fluorescence microscopy (LSFM) in the same animals following a unilateral injection of either human preformed fibrils of -synuclein (PFF) or PBS into the dorsal striatum. We developed a multimodal framework integrating the non-invasive, mesoscopic nature of MRI with the cellular-level details of LSFM to further our understanding of the underlying pathology of synucleinopathies. Using this framework, we show that four months after injection, animals injected with PFFs showed ubiquitous spread of pS129 pathology throughout the whole brain and spinal cord consistent with anatomical connectivity from the seeding region, with some structures such as the midbrain more susceptible to pS129 accumulation. Compared to controls, PFF-injected animals showed widespread atrophy as well as a decrease in functional connectivity, while evoked activity in the somatosensory/somatomotor areas in response to spontaneous paw movements showed significant hypoactivation. These cellular, structural and functional changes were significantly associated with the proportion of pS129 accumulation determined in the same animals. Our results demonstrate the deleterious effects of pS129 accumulation and argue in favor of a toxic role played by these aggregates.

neuroscience↗

bioRxiv2026

Hippocampal subfield macrostructure and myelination demonstrate distinct maturational signatures

The hippocampus is essential for learning and memory and undergoes prolonged development throughout childhood and adolescence. Evidence concerning hippocampal maturation is based primarily on volumetric measures. However, macrostructural growth and myelination processes may represent distinct biological processes. Using Hippunfold, we quantified hippocampal subfield volumes and myelin-sensitive tissue concentrations as proxies for tissue maturation using T1w/T2w ratios in 175 community-recruited participants aged 9 months to 21 years. Hippocampal subfield volumes were best described by quadratic developmental trajectories, whereas T1w/T2w ratios increased linearly with age across all subfields. Males exhibited larger hippocampal volumes, and females demonstrated higher and steeper age-related increases in T1w/T2w ratios. Sex-related hippocampal subfield differences were observed despite largely comparable cognitive and behavioural profiles. Hippocampal subfield volumes and myelin follow distinct developmental pathways, revealing sex-specific patterns of development that are not fully captured by morphology alone.

neuroscience↗

bioRxiv2026

AFIDs-Validator: An Open-Access AI-Guided Platform for Learning Anatomical Landmark Placement

Accurate localization of anatomical landmarks is a foundational skill in anatomy and imaging that is often taught informally through expert mentorship, requiring access to data and desktop software. There is no openly accessible, interactive resource that teaches neuroanatomy with quantitative feedback. We present the AFIDs-Validator (validator.afids.io), an open-access, browser-based platform that pairs guided instruction with quantitative assessment. The platform combines (1) a learning mode in which a language-model neuroanatomy tutor operates inside an MRI viewer, giving anatomy-first instruction that responds to the learner's current image slice, orientation, and cursor position; and (2) a validation engine that accepts a learner's landmark file and returns per-landmark Euclidean error against expert-annotated references spanning 21 brain templates. To make the feedback interpretable, we analyzed 15,000 landmark annotations across 132 human subjects and found that landmark difficulty varies fourfold (median error ranged from 0.37 mm at the anterior commissure to 1.50 mm at the temporal horns) with heavy-tailed distributions at every landmark. These distributions are compiled into per-landmark reliability priors, so learners are scored against the empirical spread of trained raters rather than an arbitrary threshold, and difficult landmarks are not mistaken for poor performance. The AFIDs-Validator requires no installation, licensed software, or local data, and all code, reference data, and tutor design are openly released.

scientific communication and education↗

bioRxiv2026

A surface-intrinsic framework for topology-preserving hippocampal alignment and precision morphometry

Accurate alignment of hippocampal anatomy across individuals remains challenging due to complex and highly variable folding patterns that are not well captured by conventional volumetric approaches. HippUnfold introduced a surface-based representation of the hippocampus, but key components--including coordinate estimation and inter-subject correspondence--were defined in the volumetric domain, making them susceptible to topological errors and interpolation artifacts. Here, we introduce a surface-intrinsic formulation of hippocampal unfolding in which geometry, intrinsic coordinates, and correspondence are defined directly on subject-specific surface manifolds. Intrinsic anterior-posterior and proximal-distal coordinates are computed by solving Laplace equations on the surface, and correspondence is established through surface-based resampling in unfolded space, replacing inverse volumetric warping. Relative to the original HippUnfold approach, this formulation improves test-retest consistency, subject identifiability, and mesh quality, while better preserving subject-specific gyral and sulcal morphology. Surface representations show reduced distortion between folded and unfolded spaces and eliminate misplaced or outlier vertices associated with volumetric warping. These improvements translate to enhanced sensitivity in a clinical application, improving lateralization of temporal lobe epilepsy. These results demonstrate that a surface-intrinsic formulation provides a principled and robust foundation for hippocampal unfolding, enabling topology-preserving alignment and more accurate characterization of inter-individual variability in health and disease.

neuroscience↗

bioRxiv2026

An anatomically distinct dopaminergic cell population of the zona incerta as evidence for the human A13 nucleus

The zona incerta (ZI) is a functionally and molecularly diverse deep brain region increasingly recognized as an integrative hub. The rodent ZI contains the dopaminergic A13 nucleus, with studies supporting a central role in modulating sensorimotor integration, nociception, and confers resilience in models of neurodegeneration; however, to date, no clear human homologue has been identified. Here, we identified a tyrosine hydroxylase-positive subregion in the human ZI consistent with the A13, and refined its borders using ex vivo MRI and histology. We translate these findings to in vivo MRI, demonstrating the A13 is distinguishable from surrounding regions by elevated T1 and T2* values. We further revealed a principal rostral-caudal axis of molecular and structural connectivity variation in the ZI, and identified the A13 as a localized molecular specialization. Altogether, we report a distinct ZI subregion corresponding to the A13 nucleus, providing an anatomical foundation for further mechanistic and translational investigation.

neuroscience↗

bioRxiv2026

Homoeo-alleles of wheat GNI2 fuel grain yields across input environments

Grain yield in wheat is frequently driven by pre-anthesis growth and how carbon is directed to reproductive parts, determining the potential size of the grain-producing sink. However, the genetic mechanisms controlling this carbon allocation remain unclear. In this study we discovered a series of loci in tetraploid and hexaploid wheats that, when combined, confer an average grain yield advantage in hexaploid winter wheat of approx. 5-7% under high-input farming while approx. 10-15% under low-input conditions. The responsible gene is GRAIN NUMBER INCREASE 2 (GNI2), ancestral to its duplicate GNI1, and represented by the homoeo-allelic series GNI-A2, GNI-B2, and GNI-D2. GNI1 and all GNI2 copies additively affect floral growth and fertility by modulating reproductive allocation and harvest index. Herewith, we describe a series of grain yield-relevant GNI2 homoeo-alleles with a proven track record for being beneficial in both high- and low-input environments. Their deployment offers a sustainable pathway to raise global grain yields in the future.

plant biology↗

bioRxiv2025

Hippocampal grey matter changes across scales in Alzheimer's Disease

Alzheimers disease (AD) is a progressive and debilitating neurodegenerative disease of the central nervous system, characterized by deterioration in cognitive function including extensive memory impairment. The hippocampus, a medial temporal lobe region, is a key orchestrator in the encoding and retrieval of memory and is believed to be one of the first regions to deteriorate in AD. In this work we examined hippocampal macrostructure (specifically gyrification and thickness) and microstructure in Alzheimers disease (AD) and mild cognitive impairment (MCI) relative to healthy aged controls in the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset. We first utilized an iterative training paradigm to adapt an existing deep learning approach for capturing hippocampal topology to elderly individuals as well as individuals with potential hippocampal degeneration. Using this new model, we found notable decreases in both thickness and gyrification in AD and MCI across both the subfields and anterior-posterior axis. Using the diffusion tensor representation derived from diffusion MRI data, we found significant increases in the mean diffusivity across the extent of the hippocampus in AD and MCI, which may be related to a number of changes such as loss of neuronal cells, decreased fiber density, demyelination, and increased presence of CSF. Examining the primary direction of diffusion relative to canonical hippocampal axes, we found distinct diffusion orientation shifts in AD and MCI throughout the anterior-posterior extent of the subiculum and CA1. Specifically, we found a decrease in diffusion oriented tangentially, and an increase in diffusion oriented along the long-axis. This could potentially be related to the known degeneration of the perforant path, which is greatly affected in AD and is a largely tangential oriented pathway. The AD-related changes in diffusion orientations were found to not have significant spatial overlap with AD-related changes in mean diffusivity, suggesting that they may be capturing distinct spatially-localized disease processes. Finally, we showed that the macro- and microstructure of the hippocampus in AD changed less across age relative to MCI and controls. As well, the age-related hippocampal macrostructure changes in MCI appeared indistinguishable from healthy aging.

neuroscience↗

bioRxiv2025

Leucine-rich repeat kinase 2 impairs the release sites of Parkinson's disease vulnerable dopamine axons

The end-stage pathology of Parkinsons disease (PD) involves the loss of dopamine-producing neurons in the substantia nigra pars compacta (SNc). However, synaptic deregulation of these neurons begins much earlier. Understanding the mechanisms behind synaptic deficits is crucial for early therapeutic intervention, yet these remain largely unknown. In the SNc, different dopamine neuron subtypes show varying susceptibility patterns to PD, complicating our understanding. This study uses intersectional genetic mouse models to uncover synaptic perturbations in vulnerable dopamine neurons, focusing on the LRRK2 kinase, a protein closely linked to PD. Through a combination of immunofluorescence and advanced proximity labeling methods, we found higher LRRK2 expression in the most vulnerable dopamine neuron subclusters. High-resolution imaging revealed that pathogenic LRRK2 disrupts release sites in vulnerable dopamine axons, leading to decreased in vivo spontaneous and evoked striatal dopamine release in mice with LRRK2 mutations. Proteomic and biochemical analyses indicate that mutant LRRK2 increases the phosphorylation of RAB3 proteins, reducing their interactions with RIM1and RIM2 effector proteins and impacting their synaptic functions. Overall, this research highlights the cell-autonomous dysfunctions caused by mutant LRRK2 in neurons, which are primarily affected by the disease. It also provides a framework for future therapeutic strategies for early nigrostriatal synaptic deficits in PD.

neuroscience↗

bioRxiv2025

Structural basis for binding of RILPL1 to TMEM55B reveals a lysosomal platform for adaptor assembly through a conserved TBM motif

Inherited mutations in VPS35 and the kinase LRRK2 lead to hyperphosphorylation of Rab GTPases and promote the formation of phospho-Rab signalling complexes. A subset of RH2 domain-containing proteins from the RILP-homology family, including RILP, RILPL1, RILPL2, JIP3, and JIP4 are Rab effectors that recognize the LRRK2-phosphorylated switch 2 threonine of phospho-Rab8A and phospho-Rab10. More recently, phospho-Rabs have been found on lysosomal membranes within multi-protein assemblies involving TMEM55B and RILPL1. TMEM55B is a 284-residue lysosomal membrane protein with no homology to known proteins. It comprises a 218-residue cytosolic N-terminal region and two predicted transmembrane -helices. Residues 80- 160, which face the cytosol, mediate binding to a C-terminal motif of RILPL1, formed after RILPL1 associates with phospho-Rab8A. Here, we report the crystal structures of TMEM55B alone and in complex with a C-terminal RILPL1 peptide, encompassing the TMEM55B interaction region, which we define as the TMEM55B Binding Motif (TBM). The cytosolic domain of TMEM55B adopts a rigid architecture of two tandem RING-like domains, each forming a Zn{superscript 2}-stabilized 40-residue {beta}-sandwich. TBM binding is mediated primarily by backbone hydrogen bonding and anchored by two glutamate residues from RILPL1. These findings support a model in which RILPL1 is recruited to phospho-Rab8A-positive lysosomes prior to TMEM55B engagement. Further co-immunoprecipitation and mutational analyses indicate that TMEM55B forms complexes independently of phospho-Rabs with proteins containing a conserved TBM, like that of RILPL1, including JIP3, JIP4, OCRL, WDR81, and TBC1D9B. Together, these findings uncover previously unrecognized regulatory networks associated with TMEM55B and lysosomal function and suggest that TMEM55B serves as a central hub for adaptor recruitment at the lysosomal membrane.

biochemistry↗

bioRxiv2025

Multiplexed BOLD oscillations reveal the interplay of normalization and attention

Monkey electrophysiology has linked attention to divisive normalization, yet noninvasive evidence in humans remains limited. We use frequency-tagged fMRI to isolate visual cortical populations that simultaneously encode multiple competing inputs. We show that responses of these sites are suppressed during inattention and enhanced during attention - consistent with the normalization model, which predicts that attention selectively disinhibits competing inputs - offering a noninvasive translational bridge to study fine-grained computations underlying attentional selection.

neuroscience↗

bioRxiv2025

Attentional enhancement and suppression of stimulus-synchronized BOLD oscillations

Visual cortical neurons synchronize their firing rates to periodic visual stimuli. EEG is commonly used to study directed attention by frequency-tagging brain responses to multiple stimuli oscillating at different frequencies, but is limited by its coarse spatial resolution. Here we leverage frequency-tagging fMRI (ft-fMRI) to study the influence of directed attention on the fine-grained spatiotemporal dynamics of competing stimulus-driven visual cortical oscillations. Our analysis reveals that distinct populations of visual cortical neurons exhibit in-phase (enhancing) or anti-phase (suppressive) synchronization with the oscillating stimuli. Directed attention homogeneously increases the amplitude of anti-phase BOLD oscillations across the visual hierarchy, consistent with a distributed suppressive field. In contrast, attentional modulation of in-phase BOLD oscillations increases hierarchically from V1 to hV4. The strength of anti-phase, but not in-phase, modulation predicted psychophysical correlates of attentional performance. Our results strongly corroborate the biased competition model of attention and unveil a novel BOLD correlate of attentional suppression.

neuroscience↗

bioRxiv2024

Frequency-tagged fMRI: A platform for fine-grained spatiotemporal analysis of cortical function

Frequency tagging with functional MRI (ft-fMRI) enables precise mapping of neural dynamics by synchronizing oscillatory stimuli to stimulus-driven blood-oxygen-level-dependent (BOLD) responses. We developed and validated a dual-frequency tagging protocol to dissociate fundamental, multiplexed, and nonlinear intermodulation frequency responses across the human visual cortex at high spatial resolution. Using 3T and 7T fMRI, we reliably detected frequency-tagged BOLD responses at the level of individual vertices, revealing fine-grained cortical topographies and robust temporal synchronization to driving frequencies. Multiplexed responses, encoding multiple frequencies simultaneously, and nonlinear intermodulation components, were spatially dissociable and exhibited reproducible dynamics within and across experimental sessions. These findings establish ft-fMRI as a powerful tool for investigating fine-grained cortical computations, previously inaccessible to traditional fMRI. By bridging the spatiotemporal resolution gap between electrophysiology and fMRI, ft-fMRI provides a versatile platform for studying perception, attention, and multisensory integration in health and disease.

neuroscience↗

bioRxiv2024

Converging effects of cannabis and psychosis on the dopamine system: A longitudinal neuromelanin-sensitive MRI study in cannabis use disorder and first episode schizophrenia.

ImportanceDespite evidence that individuals who use cannabis early in life are at elevated risk of psychosis and that the neurotransmitter dopamine has a role in both conditions, the mechanism linking the two conditions remains unclear. ObjectiveTo use neuromelanin-sensitive MRI (neuromelanin-MRI), a practical, proxy measure of dopamine function, to assess whether a common alteration in the dopamine system may be implicated in cannabis use and psychosis and whether this alteration can be observed in cannabis users whether or not they have a diagnosis of first-episode schizophrenia. Design, Setting, and ParticipantsThis longitudinal observational study recruited participants from 2019 to 2023 from an early intervention service for psychosis in London, Ontario, Canada. The sample consisted of 25 participants with cannabis use disorder (CUD) and 36 participants without CUD (nCUD), of which 28 had first-episode schizophrenia (FES). One-year follow-up was completed for 12 CUD and 25 nCUD participants. Main Outcomes and MeasuresNeuromelanin-MRI contrast within the substantia nigra (SN) and within a subregion previously linked to psychosis severity (a priori psychosis region of interest) and diagnoses of schizophrenia-spectrum disorder and cannabis use disorder derived from the Structured Clinical Interview for DSM-5. Linear mixed effects analyses were performed relating neuromelanin-MRI contrast to clinical measures. ResultsWe found that CUD was associated with elevated neuromelanin-MRI signal in a cluster of ventral SN voxels (387 of 2060 SN voxels, pcorrected=0.027, permutation test). Furthermore, CUD was associated with elevated neuromelanin-MRI signal in an SN subregion previously documented to have elevated signal in relation to untreated psychotic symptoms (t92 =2.12, p=0.037). In contrast, FES was not associated with a significant alteration in neuromelanin-MRI signal (241 SN voxels had elevated signal, pcorrected=0.094). Conclusions and RelevanceThese findings suggest that elevated dopamine function in a critical SN subregion may contribute to the risk of psychosis in people with CUD. Thus, cannabis affects the long-suspected final common pathway for the clinical expression of psychotic symptoms. Imaging the dopamine system with neuromelanin-MRI may index long-term dopamine turnover. Key PointsO_ST_ABSQuestionC_ST_ABSIs the same midbrain dopamine pathway impacted by cannabis as in psychosis? FindingsCannabis use disorder participants had elevated neuromelanin-MRI signal in a cluster of ventral substantia nigra voxels and in a subregion previously documented to have elevated signal in relation to untreated psychotic symptoms. MeaningIncreased dopamine functioning in the ventral substantia nigra may contribute to the risk of psychosis in people with cannabis use disorders.

neuroscience↗

bioRxiv2024

Mapping the topographic organization of the human zona incerta using diffusion MRI

The zona incerta (ZI) is a deep brain region originally described by Auguste Forel as an "immensely confusing area about which nothing can be said." Despite the elusive nature of this structure, mounting evidence supports the role of the ZI and surrounding regions across a diverse range of brain functions and as a candidate target for neuromodulatory therapies. Using in vivo diffusion MRI and data-driven connectivity, we identify a topographic organization between the ZI and neocortex. Specifically, our methods identify a rostral-caudal gradient predominantly connecting the frontopolar and ventral prefrontal cortices with the rostral ZI, and the primary sensorimotor cortices with the caudal ZI. Moreover, we demonstrate how clustering and gradient approaches build complementary evidence including facilitating the mapping of a central region of the ZI, connected with the dorsal prefrontal cortex. These results were shown to be replicable across multiple datasets and at the individual subject level, building evidence for the important role of the ZI in mediating frontal lobe-associated tasks, ranging from motor to cognitive to emotional control. Finally, we consider the impact of this topographic organization on the refinement of neuromodulatory targets. These results pave the way for an increasingly detailed understanding of ZI substructures, and considerations for in vivo targeting of the ZI for neuromodulation.

neuroscience↗

bioRxiv2024

Neurite Density and Free Water in the Gray and White Matter of Early Psychosis Patients

Diffusion weighted imaging has been frequently used to characterize the white matter in patients with schizophrenia, but the most commonly used model, diffusion tensor imaging (DTI), is not specific to the histological nature of microstructural changes. This is particularly true in the more complex grey matter tissue. Furthermore, DTI changes have not been consistently reported in early schizophrenia populations, but this does not exclude more subtle changes that may not affect the model fit. Recently developed biophysical models of diffusion, such as the neurite orientation dispersion and density imaging (NODDI) model, may overcome these issues by quantifying specific tissue subcompartments, capturing diffusion profiles characteristic of intra-neurite, extra-neurite, and free water space. We applied the NODDI model to early schizophrenia patients (n=54) and healthy controls (n=51) from the Human Connectome Project - Early Psychosis dataset, investigating both the grey and white matter. We observed a diffuse, increased free water fraction throughout the grey matter, especially in the left insula, though there were not notable changes in the white matter. The spatial variation in the grey matter free water was not fully explained by the partial volume effects from the cerebrospinal fluid, indicating a role for tissue edema. The role of vasogenic processes in early stages of psychosis that may precede white matter anomalies documented in later disease stages warrant further investigation.

neuroscience↗

bioRxiv2024

Stable White Matter Structure in the First Three Years after Psychosis Onset

BackgroundWhite matter alterations observed using diffusion weighted imaging have become a hallmark of chronic schizophrenia, but it is unclear when these changes arise over the course of the disease. Nearly all studies thus far have been cross-sectional, so despite their large sample sizes, they cannot determine if changes accumulate as a degenerative process, or if patients with pre-existing white matter damage are predisposed to more chronic forms of schizophrenia. MethodsWe examined 160 scans comprising two years of annual follow-up data from n=42 controls and n=28 schizophrenia patients recruited in the first two years since their diagnosis, totalling two to three scans per subject. We additionally examined six-month follow-up data obtained from an ultra-high field (7 Tesla) scanner (n=68 scans; n=19 first-episode schizophrenia patients; n=15 controls) as a validation dataset. A longitudinal model was used to compare the trajectory of diffusion tenor parameters between patients and controls. Positive and negative symptom scores were correlated with diffusion parameters using ROI- and clustering-based approaches. ResultsWe failed to observe any longitudinal differences in any diffusion tensor imaging parameters between patients and controls in either dataset. We did, however, observe consistent associations between white matter alterations and negative symptoms in both datasets. ConclusionsWhite matter does not appear susceptible to schizophrenia-linked degeneration in the early stages of disease, but pre-existing pathology may be linked to disease severity.

neuroscience↗

bioRxiv2024

The developing hippocampus: Microstructural evolution through childhood and adolescence

The hippocampus is a structure in the medial temporal lobe which serves multiple cognitive functions. While important, the development of the hippocampus in the formative period of childhood and adolescence has not been extensively investigated, with most contemporary research focusing on macrostructural measures of volume. Thus, there has been little research on the development of the micron-scale structures (i.e., microstructure) of the hippocampus, which engender its cognitive functions. The current study examined age-related changes of hippocampal microstructure using diffusion MRI data acquired with an ultra-strong gradient (300 mT/m) MRI scanner in a sample of children and adolescents (N=88; 8-19 years). Surface-based hippocampal modelling was combined with established microstructural approaches, such as Diffusion Tensor Imaging (DTI) and Neurite Orientation Dispersion Density Imaging (NODDI), and a more advanced gray matter diffusion model Soma And Neurite Density Imaging (SANDI). No significant changes in macrostructural measures (volume, gyrification, and thickness) were found between 8-19 years, while significant changes in microstructure measures related to neurites (from NODDI and SANDI), soma (from SANDI), and mean diffusivity (from DTI) were found. In particular, there was a significant increase across age in neurite MR signal fraction and a significant decrease in extracellular MR signal fraction and mean diffusivity across the hippocampal subfields and long-axis. A significant negative correlation between age and MR apparent soma radius was found in the subiculum and CA1 throughout the anterior and body of the hippocampus. Further surface-based analyses uncovered variability in age-related microstructural changes between the subfields and long-axis, which may reflect ostensible developmental differences along these two axes. Finally, correlation of hippocampal surfaces representing age-related changes of microstructure with maps derived from histology allowed for postulation of the potential underlying microstructure that diffusion changes across age may be capturing. Overall, distinct neurite and soma developmental profiles in the human hippocampus during late childhood and adolescence are reported for the first time.

neuroscience↗

bioRxiv2024

HippoMaps: Multiscale cartography of the human hippocampal formation

The hippocampus has a unique microarchitecture, is situated at the nexus of multiple macroscale functional networks, contributes to numerous cognitive as well as affective processes, and is highly susceptible to brain pathology across common disorders. These features make the hippocampus a model to understand how brain structure covaries with function, in both health and disease. Here, we introduce HippoMaps, an open access toolbox and online data warehouse for the mapping and contextualization of subregional hippocampal data in the human brain (http://hippomaps.readthedocs.io). HippoMaps capitalizes on a unified hippocampal unfolding approach as well as shape intrinsic registration capabilities to allow for cross-subject and cross-modal data aggregation. We initialize this repository with an unprecedented combination of hippocampal data spanning 3D ex-vivo histology, ex-vivo 9.4 Tesla MRI, as well as in-vivo structural MRI and resting-state functional MRI (rsfMRI) obtained at 3 and 7 Tesla, together with intracranial encephalography (iEEG) recordings in epilepsy patients. HippoMaps also contains validated tools for spatial map association analysis in the hippocampus that correct for autocorrelation. All code and data are compliant with community standards, and comprehensive online tutorials facilitate broad adoption. Applications of this work span methodologies and modalities, spatial scales, as well as clinical and basic research contexts, and we encourage community feedback and contributions in the spirit of open and iterative scientific resource development.

neuroscience↗