Functional parcellation of human and macaque striatum reveals human-specific connectivity in the dorsal caudate

Altered corticostriatal connectivity in long-COVID patients is associated with cognitive impairment

BACKGROUND

The COVID-19 pandemic has had a significant impact on the health of millions of people worldwide, and many manifest new or persistent symptoms long after the initial onset of the infection. One of the leading symptoms of long-COVID is cognitive impairment, which includes memory loss, lack of concentration, and brain fog. Understanding the nature and underlying mechanisms of cognitive impairment in long-COVID is important for developing preventive and therapeutic interventions.

METHODS

Our present study investigated functional connectivity (FC) changes in patients with long-COVID and their associations with cognitive impairment. Resting-state functional MRI data from 60 long-COVID patients and 52 age- and sex-matched healthy controls were analyzed using seed-based functional connectivity analysis.

RESULTS

We found increased FC between the right caudate nucleus and both the left and right precentral gyri in long-COVID patients compared with healthy controls. In addition, elevated FC was observed between the right anterior globus pallidus and posterior cingulate cortex as well as the right temporal pole in long-COVID patients. Importantly, the magnitude of FC between the caudate and the left precentral gyrus showed a significant negative correlation with Montreal Cognitive Assessment (MoCA) scores and a negative correlation with Trail Making Test B performance in the patient group.

CONCLUSION

Patients with long-COVID present enhanced FC between the caudate and the left precentral gyrus. Furthermore, those FC alterations are related to the severity of cognitive impairment, particularly in the domain of executive functions.

Subcortical and insula functional connectivity aberrations and clinical implications in first-episode schizophrenia

INTRODUCTION

Schizophrenia is a complex mental disorder whose pathophysiology remains elusive, particularly in the roles of subcortex. This study aims to explore the role of subcortex and insula and their relationship with symptom changes in first-episode schizophrenia (FES) patients by utilizing machine learning algorithms and functional connectivity (FC).

METHODS

The study encompasses 261 participants, sourced from two independent samples of FES patients and their matched healthy controls (HC). The discovery dataset includes 77 FES patients at baseline (FES0W) and 77 matched HCs, with the patients undergoing a follow-up scan after eight weeks of antipsychotic treatment (FES8W, N = 34). A validation dataset from another region comprises 47 FES patients and 47 matched HCs.

RESULTS

Significant differences in subcortical FCs were observed between FES and controls, correlating with symptom severity and symptom changes. Machine learning models were developed to diagnose schizophrenia on an individual basis, achieving a balanced accuracy of 79.55 % across diverse centers.

CONCLUSIONS

These findings suggest that subcortical connectivity patterns offer potential as biomarkers for schizophrenia, enabling personalized treatment strategies and improving prognosis by facilitating early diagnosis.

Cross-species striatal hubs: Linking anatomy to resting-state connectivity

Corticostriatal connections are essential for motivation, cognition, and behavioral flexibility. There is broad interest in using resting-state functional magnetic resonance imaging (rs-fMRI) to link circuit dysfunction in these connections with neuropsychiatric disorders. In this paper, we used tract-tracing data from non-human primates (NHPs) to assess the likelihood of monosynaptic connections being represented in rs-fMRI data of NHPs and humans. We also demonstrated that existing hub locations in the anatomical data can be identified in the rs-fMRI data from both species. To characterize this in detail, we mapped the complete striatal projection zones from 27 tract-tracer injections located in the orbitofrontal cortex (OFC), dorsal anterior cingulate cortex (dACC), ventromedial prefrontal cortex (vmPFC), ventrolateral PFC (vlPFC), and dorsal PFC (dPFC) of macaque monkeys. Rs-fMRI seeds at the same regions of NHP and homologous regions of human brains showed connectivity maps in the striatum mostly consistent with those observed in the tracer data. We then examined the location of overlap in striatal projection zones. The medial rostral dorsal caudate connected with all five frontocortical regions evaluated in this study in both modalities (tract-tracing and rs-fMRI) and species (NHP and human). Other locations in the caudate also presented an overlap of four frontocortical regions, suggesting the existence of different locations with lower levels of input diversity. Small retrograde tracer injections and rs-fMRI seeds in the striatum confirmed these cortical input patterns. This study sets the ground for future studies evaluating rs-fMRI in clinical samples to measure anatomical corticostriatal circuit dysfunction and identify connectional hubs to provide more specific treatment targets for neurological and psychiatric disorders.

Striatum and globus pallidus structural abnormalities in schizophrenia: A retrospective study of the different stages of the disease

BACKGROUND

The basal ganglia are important structures for the release of dopamine in the limbic circuits of the midbrain, and the striatum and globus pallidus are the major nuclei of the basal ganglia, and the dysfunction of these regions has been the basis of many models that have attempted to explain the underlying mechanisms of schizophrenia symptoms. The purpose of this study was to investigate the changes in the volume of the striatum subregion and globus pallidus in three different stages of schizophrenia, and to analyze whether these volume changes were related to antipsychotic drugs and schizophrenia symptoms.

METHODS

In this study, we investigated the volume of the striatum and globus pallidus in patients with schizophrenia at three different stages. The study included 57 patients with first-episode schizophrenia (FSZ), 51 patients with early-stage schizophrenia (ESZ), 86 patients with chronic schizophrenia (CSZ), and 191 healthy controls (HC), all of whom underwent structured magnetic resonance imaging (MRI) scans. Covariance analysis was performed using SPSS 26.0 was used for covariance analysis to determine whether there were significant differences in striatal subregion and globus pallidus volume between groups, and stratified analysis was used to further eliminate the effect of age on brain volume. Finally, the correlation analysis between the region of interest and the cumulative dose of antipsychotic drugs and psychotic symptoms was performed.

RESULTS

The comparison between the different stages of the illness showed significant volume differences in the left caudate nucleus (lCAU) (F = 2.665, adjusted p = 0.048), left putamen (lPUT) (F = 12.749, adjusted p < 0.001), left pallidum (lPAL) (F = 41.111, adjusted p < 0.001), and right pallidum (rPAL) (F = 14.479, adjusted p < 0.001). Post-hoc analysis with corrections showed that the volume differences in the lCAU subregion disappeared. Further stratified analysis controlling for age showed that compared with the HC, the lPAL (t = 4.347, p < 0.001) was initially significantly enlarged in the FSZ group, the lPUT (t = 4.493, p < 0.001), rPUT (t = 2.190, p = 0.031), lPAL (t = 7.894, p < 0.001), and rPAL (t = 4.983, p < 0.001) volumes were all significantly increased in the ESZ group, and the lPUT (t = 3.314, p = 0.002), lPAL (t = 6.334, p < 0.001), and rPAL (t = 3.604, p < 0.001) subregion volumes were also significantly increased in the CSZ group. Correlation analysis showed that lPUT and bilateral globus pallidus were associated with cumulative dose of antipsychotics, but were not associated with clinical symptoms in each subregion.

CONCLUSION

The findings suggest that different subregions of the striatum and globus pallidus show significant volume differences at different stages of schizophrenia compared to HC. These volume differences may be strong radiographic evidence for schizophrenia. In addition, the lPAL was the only significantly different brain region observed in the FSZ group, suggesting that it may be a sensitive indicator of early brain structural changes in schizophrenia. Finally, our findings support the hypothesis that antipsychotic drugs have an effect on the volume of brain structures.

Genetically modified non-human primate models for research on neurodegenerative diseases

Neurodegenerative diseases (NDs) are a group of debilitating neurological disorders that primarily affect elderly populations and include Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). Currently, there are no therapies available that can delay, stop, or reverse the pathological progression of NDs in clinical settings. As the population ages, NDs are imposing a huge burden on public health systems and affected families. Animal models are important tools for preclinical investigations to understand disease pathogenesis and test potential treatments. While numerous rodent models of NDs have been developed to enhance our understanding of disease mechanisms, the limited success of translating findings from animal models to clinical practice suggests that there is still a need to bridge this translation gap. Old World non-human primates (NHPs), such as rhesus, cynomolgus, and vervet monkeys, are phylogenetically, physiologically, biochemically, and behaviorally most relevant to humans. This is particularly evident in the similarity of the structure and function of their central nervous systems, rendering such species uniquely valuable for neuroscience research. Recently, the development of several genetically modified NHP models of NDs has successfully recapitulated key pathologies and revealed novel mechanisms. This review focuses on the efficacy of NHPs in modeling NDs and the novel pathological insights gained, as well as the challenges associated with the generation of such models and the complexities involved in their subsequent analysis.

Functional division of the dorsal striatum based on a graph neural network

The dorsal striatum, an essential nucleus in subcortical areas, has a crucial role in controlling a variety of complex cognitive behaviors; however, few studies have been conducted in recent years to explore the functional subregions of the dorsal striatum that are significantly activated when performing multiple tasks. To explore the differences and connections between the functional subregions of the dorsal striatum that are significantly activated when performing different tasks, we propose a framework for functional division of the dorsal striatum based on a graph neural network model. First, time series information for each voxel in the dorsal striatum is extracted from acquired functional magnetic resonance imaging data and used to calculate the connection strength between voxels. Then, a graph is constructed using the voxels as nodes and the connection strengths between voxels as edges. Finally, the graph data are analyzed using the graph neural network model to functionally divide the dorsal striatum. The framework was used to divide functional subregions related to the four tasks including olfactory reward, "0-back" working memory, emotional picture stimulation, and capital investment decision-making. The results were further subjected to conjunction analysis to obtain 15 functional subregions in the dorsal striatum. The 15 different functional subregions divided based on the graph neural network model indicate that there is functional differentiation in the dorsal striatum when the brain performs different cognitive tasks. The spatial localization of the functional subregions contributes to a clear understanding of the differences and connections between functional subregions.

Mapping and comparing fMRI connectivity networks across species

Technical advances in neuroimaging, notably in fMRI, have allowed distributed patterns of functional connectivity to be mapped in the human brain with increasing spatiotemporal resolution. Recent years have seen a growing interest in extending this approach to rodents and non-human primates to understand the mechanism of fMRI connectivity and complement human investigations of the functional connectome. Here, we discuss current challenges and opportunities of fMRI connectivity mapping across species. We underscore the critical importance of physiologically decoding neuroimaging measures of brain (dys)connectivity via multiscale mechanistic investigations in animals. We next highlight a set of general principles governing the organization of mammalian connectivity networks across species. These include the presence of evolutionarily conserved network systems, a dominant cortical axis of functional connectivity, and a common repertoire of topographically conserved fMRI spatiotemporal modes. We finally describe emerging approaches allowing comparisons and extrapolations of fMRI connectivity findings across species. As neuroscientists gain access to increasingly sophisticated perturbational, computational and recording tools, cross-species fMRI offers novel opportunities to investigate the large-scale organization of the mammalian brain in health and disease.

From Computation to Clinic

Theory-driven and data-driven computational approaches to psychiatry have enormous potential for elucidating mechanism of disease and providing translational linkages between basic science findings and the clinic. These approaches have already demonstrated utility in providing clinically relevant understanding, primarily via back translation from clinic to computation, revealing how specific disorders or symptoms map onto specific computational processes. Nonetheless, forward translation, from computation to clinic, remains rare. In addition, consensus regarding specific barriers to forward translation-and on the best strategies to overcome these barriers-is limited. This perspective review brings together expert basic and computationally trained researchers and clinicians to 1) identify challenges specific to preclinical model systems and clinical translation of computational models of cognition and affect, and 2) discuss practical approaches to overcoming these challenges. In doing so, we highlight recent evidence for the ability of computational approaches to predict treatment responses in psychiatric disorders and discuss considerations for maximizing the clinical relevance of such models (e.g., via longitudinal testing) and the likelihood of stakeholder adoption (e.g., via cost-effectiveness analyses).

Mapping cross-species connectome atlas of human and macaque striatum

Cross-species connectome atlas (CCA) that can provide connectionally homogeneous and homologous brain nodes is essential and customized for cross-species neuroscience. However, existing CCAs were flawed in design and coarse-grained in results. In this study, a normative mapping framework of CCA was proposed and applied on human and macaque striatum. Specifically, all striatal voxels in the 2 species were mixed together and classified based on their represented and characterized feature of within-striatum resting-state functional connectivity, which was shared between the species. Six pairs of striatal parcels in these species were delineated in both hemispheres. Furthermore, this striatal parcellation was demonstrated by the best-matched whole-brain functional and structural connectivity between interspecies corresponding subregions. Besides, detailed interspecies differences in whole-brain multimodal connectivities and involved brain functions of these subregions were described to flesh out this CCA of striatum. In particular, this flexible and scalable mapping framework enables reliable construction of CCA of the whole brain, which would enable reliable findings in future cross-species research and advance our understandings into how the human brain works.

Altered regional brain activity and functional connectivity in resting-state brain networks associated with psychological erectile dysfunction

Introduction

Erectile dysfunction (ED), especially psychological ED (pED), is usually accompanied with psychological factors, which are related to abnormal activity in brain regions involved in sexual behavior. However, the mechanisms underlying functional changes in the brain of pED are still unclear. The present study aimed to explore the abnormalities of brain function, as well as their relationships with sexual behavior and emotion in pED patients.

Materials and methods

Resting state functional magnetic resonance imaging (rs-fMRI) data were collected from 31 pED patients to 31 healthy controls (HCs). The values of amplitude of fractional amplitude of low-frequency fluctuation (fALFF) and functional connectivity (FC) were calculated and compared between groups. In addition, the associations between abnormal brain regions and clinical features were evaluated by Pearson correlation analyses.

Results

Compared to HCs, pED patients demonstrated decreased fALFF values in the left medial superior frontal gyrus (had decreased FC values with the left dorsolateral superior frontal gyrus), the left lingual gyrus (had decreased FC values with the left parahippocamal gyrus and insula), the left putamen (had decreased FC values with the right caudate) and the right putamen (had decreased FC values with the left putamen and the right caudate). The fALFF values of the left medial superior frontal gyrus were negatively correlated with the fifth item scores of International Index of Erectile Function (IIEF-5). Negative relationships were found between fALFF values of the left putamen and the second item scores of Arizona Sexual Scale (ASEX). FC values between the right putamen and caudate were negatively related to the state scores of State-Trait Anxiety Inventory (STAI-S).

Conclusion

Altered brain function were found in the medial superior frontal gyrus and caudate-putamen of pED patients, which were associated with sexual function and psychological condition. These findings provided new insights into the central pathological mechanisms of pED.

Disrupted functional connectivity of the brain reward system in substance use problems: A meta-analysis of functional neuroimaging studies

Extensive literature suggests that the brain reward system is crucial in understanding the neurobiology of substance use disorders. However, evidence of reliable deficits in functional connectivity across studies on substance use problems remains limited. Therefore, a voxel-wise seed-based meta-analysis using brain regions of the reward system as seeds of interest was conducted on 96 studies representing 5757 subjects with substance use problems. The ventromedial prefrontal cortex exhibited hyperconnectivity with the ventral striatum and hypoconnectivity with the amygdala and hippocampus. The executive striatum showed hyperconnectivity with the motor thalamus and dorsolateral prefrontal cortex and hypoconnectivity with the anterior cingulate cortex and anterior insula. Finally, the limbic striatum was found to be hyperconnected to the orbitofrontal cortex and hypoconnected to the precuneus compared with healthy subjects. The current study provided meta-analytical evidence of deficient functional connectivity between brain regions of the reward system and cortico-striato-thalamocortical loops in addiction. These results are consistent with deficits in motivation and habit formation occurring in addiction, and they highlight alterations in brain regions involved in socio-emotional processing and attention salience.

[Reduced numerical density of oligodendrocytes and oligodendrocyte clusters in the head of the caudate nucleus in schizophrenia]

OBJECTIVE

Morphometric estimation of the numerical density of oligodendrocytes (NcOl) and numerical density of oligodendrocyte clusters (NvOlC) in the rostral part of the caudate head nucleus associated with the cortical regions of the default network in the norm and in schizophrenia.

MATERIAL AND METHODS

NcOl and NvOlC were determined in the gray matter of the rostral part of the head of the caudate nucleus in Nissl-stained sections using optical dissector in postmortem brains in 18 schizophrenia and 18 healthy control cases.

RESULTS

The NvOl (-20%, p<0.001) and NvOlC (-28%, p<0.001) were decreased in the schizophrenia group as compared to the control groups. The NvOl correlated with the NvOlC (R≥0.88, p<0.001) in both groups while a lack of correlations was previously found in the central part of the caudate head.

CONCLUSION

The detected deficits of the NcOl and NvOlC is an agreement with prominent suppressing of cortico-striatal connections and reduced density of gray matter in this part of the caudate in schizophrenia. The differences in the pattern of correlations as compared to the central part of this structure might be associated with the specific features of functional activity of default-mode and fronto-parietal networks associated with these parts of caudate nucleus.

Nigral Iron Deposition Influences Disease Severity by Modulating the Effect of Parkinson's Disease on Brain Networks

BACKGROUND

In Parkinson's disease (PD), excessive iron deposition in the substantia nigra may exacerbate α-synuclein aggregation, facilitating the degeneration of dopaminergic neurons and their neural projection.

OBJECTIVE

To investigate the interaction effect between nigral iron deposition and PD status on brain networks.

METHODS

Eighty-five PD patients and 140 normal controls (NC) were included. Network function and nigral iron were measured using multi-modality magnetic resonance imaging. According to the median of nigral magnetic susceptibility of NC (0.095 ppm), PD and NC were respectively divided into high and low nigral iron group. The main and interaction effects were investigated by mixed effect analysis.

RESULTS

The main effect of disease was observed in basal ganglia network (BGN) and visual network (VN). The interaction effect between nigral iron and PD status was observed in left inferior frontal gyrus and left insular lobe in BGN, as well as right middle occipital gyrus, right superior temporal gyrus, and bilateral cuneus in VN. Furthermore, multiple mediation analysis revealed that the functional connectivity of interaction effect clusters in BGN and medial VN partially mediated the relationship between nigral iron and Unified Parkinson's Disease Rating Scale II score.

CONCLUSION

Our study demonstrates an interaction of nigral iron deposition and PD status on brain networks, that is, nigral iron deposition is associated with the change of brain network configuration exclusively when in PD. We identified a potential causal mediation pathway for iron to affect disease severity that was mediated by both BGN dysfunction and VN hyperfunction in PD.

Connectivity of the corticostriatal and thalamostriatal systems in normal and parkinsonian states: An update

The striatum receives abundant glutamatergic afferents from the cortex and thalamus. These inputs play a major role in the functions of the striatal neurons in normal conditions, and are significantly altered in pathological states, such as Parkinson's disease. This review summarizes the current knowledge of the connectivity of the corticostriatal and thalamostriatal pathways, with emphasis on the most recent advances in the field. We also discuss novel findings regarding structural changes in cortico- and thalamostriatal connections that occur in these connections as a consequence of striatal loss of dopamine in parkinsonism.

Concurrent mapping of brain ontogeny and phylogeny within a common space: Standardized tractography and applications

Developmental and evolutionary effects on brain organization are complex, yet linked, as evidenced by the correspondence in cortical area expansion across these vastly different time scales. However, it is still not possible to study concurrently the ontogeny and phylogeny of cortical areal connections, which is arguably more relevant to brain function than allometric measurements. Here, we propose a novel framework that allows the integration of structural connectivity maps from humans (adults and neonates) and nonhuman primates (macaques) onto a common space. We use white matter bundles to anchor the common space and use the uniqueness of cortical connection patterns to these bundles to probe area specialization. This enabled us to quantitatively study divergences and similarities in connectivity over evolutionary and developmental scales, to reveal brain maturation trajectories, including the effect of premature birth, and to translate cortical atlases between diverse brains. Our findings open new avenues for an integrative approach to imaging neuroanatomy.

Topographic organization of the human caudate functional connectivity and age-related changes with resting-state fMRI

The striatum is postulated to play a central role in gating cortical processing during goal-oriented behavior. While many human neuroimaging studies have treated the striatum as an undivided whole or several homogeneous compartments, some recent studies showed that its circuitry is topographically organized and has more complex relations with the cortical networks than previously assumed. Here, we took a gradient functional connectivity mapping approach that utilizes the entire anatomical space of the caudate nucleus to examine the organization of its functional relationship with the rest of the brain and how its topographic mapping changes with age. We defined the topography of the caudate functional connectivity using three publicly available resting-state fMRI datasets. We replicated and extended previous findings. First, we found two stable gradients of caudate connectivity patterns along its medial-lateral (M-L) and anterior-posterior (A-P) axes, supporting findings from previous tract-tracing studies of non-human primates that there are at least two main organizational principles within the caudate nucleus. Second, unlike previous emphasis of the A-P topology, we showed that the differential connectivity patterns along the M-L gradient of caudate are more clearly organized with the large-scale neural networks; such that brain networks associated with internal vs. external orienting behavior are respectively more closely linked to the medial vs. lateral extent of the caudate. Third, the caudate's M-L organization showed greater age-related reduction in integrity, which was further associated with age-related changes in behavioral measures of executive functions. In sum, our analysis confirmed a sometimes overlooked M-L functional connectivity gradient within the caudate nucleus, with its lateral longitudinal zone more closely linked to the frontoparietal cortical circuits and age-related changes in cognitive control. These findings provide a more precise mapping of the human caudate functional connectivity, both in terms of the gradient organization with cortical networks and age-related changes in such organization.

Changes in corticostriatal connectivity and striatal tissue iron associated with efficacy of clozapine for treatment‑resistant schizophrenia

RATIONALE

Though numerous studies demonstrate the superiority of clozapine (CLZ) for treatment of persistent psychotic symptoms that are characteristic of treatment-refractory schizophrenia (TRS), what remains unknown are the neural and molecular mechanisms underlying CLZ's efficacy. Recent work implicates increased corticostriatal functional connectivity as a marker of response to non-CLZ, dopamine (DA) D2-receptor blocking antipsychotic drugs. However, it is undetermined whether this connectivity finding also relates to CLZ's unique efficacy, or if response to CLZ is associated with changes in striatal DA functioning.

OBJECTIVE

In a cohort of 22 individuals with TRS, we examined response to CLZ in relation to the following: (1) change in corticostriatal functional connectivity; and (2) change in a magnetic resonance-based measure of striatal tissue iron (R2'), which demonstrates utility as a proxy measure for elements of DA functioning.

METHODS

Participants underwent scanning while starting CLZ and after 12 weeks of CLZ treatment. We used both cortical and striatal regions of interest to examine changes in corticostriatal interactions and striatal R2' in relation to CLZ response (% reduction of psychotic symptoms).

RESULTS

We first found that response to CLZ was associated with an increase in corticostriatal connectivity between the dorsal caudate and regions of the frontoparietal network (P < 0.05, corrected). Secondly, we observed no significant changes in striatal R2' across CLZ treatment.

CONCLUSION

Overall, these results indicate that changes in corticostriatal networks without gross shifts in striatal DA functioning underlies CLZ response. Our results provide novel mechanistic insight into response to CLZ treatment.

Don't forget the little brain: A framework for incorporating the cerebellum into the understanding of cognitive aging

With the rapidly growing population of older adults, an improved understanding of brain and cognitive aging is critical, given the impacts on health, independence, and quality of life. To this point, we have a well-developed literature on the cortical contributions to cognition in advanced age. However, while this work has been foundational for our understanding of brain and behavior in older adults, subcortical contributions, particularly those from the cerebellum, have not been integrated into these models and frameworks. Incorporating the cerebellum into models of cognitive aging is an important step for moving the field forward. There has also been recent interest in this structure in Alzheimer's dementia, indicating that such work may be beneficial to our understanding of neurodegenerative disease. Here, I provide an updated overview of the cerebellum in advanced age and propose that it serves as a critical source of scaffolding or reserve for cortical function. Age-related impacts on cerebellar function further impact cortical processing, perhaps resulting in many of the activation patterns commonly seen in aging.

Brain intrinsic connection patterns underlying tool processing in human adults are present in neonates and not in macaques

Tool understanding and use are supported by a dedicated left-lateralized, intrinsically connected network in the human adult brain. To examine this network’s phylogenetic and ontogenetic origins, we compared resting-state functional connectivity (rsFC) among regions subserving tool processing in human adults to rsFC among homologous regions in human neonates and macaque monkeys (adolescent and mature). These homologous regions formed an intrinsic network in human neonates, but not in macaques. Network topological patterns were highly similar between human adults and neonates, and significantly less so between humans and macaques. The premotor-parietal rsFC had most significant contribution to the formation of the neonatal tool network. These results suggest that an intrinsic brain network potentially supporting tool processing exists in the human brain prior to individual tool use experiences, and that the premotor-parietal functional connection in particular offers a brain basis for complex tool behaviors specific to humans.

Striatal Subdivisions Estimated via Deep Embedded Clustering With Application to Parkinson's Disease

Recent fMRI connectivity-based parcellation (CBP) methods have been developed to obtain homogeneous and functionally coherent brain parcels. However, most of these studies utilize traditional clustering methods that neglect hidden nonlinear features. To enhance parcellation performance, here we propose a deep embedded connectivity-based parcellation (DECBP) framework and apply it to determine functional subdivisions of the striatum in public resting state fMRI data sets. This framework integrates fMRI connectivity features into deep embedded clustering (DEC), a deep neural network based on a stacked autoencoder. Compared to three prevalent clustering methods and their combinations with principal component analysis (PCA), the DECBP exhibited a significantly higher similarity between scans, individuals, and groups, indicating enhanced reproducibility. The generated reliable parcellations were also largely consistent with other public atlases. We further explored the functional subunits in the striatum in a data set from 23 Parkinson's disease (PD) subjects and 27 age-matched healthy controls (HC). All putaminal subregions of PD demonstrated lower interhemispheric connectivity than those of HC, which might reflect imbalance in the pathological progression of PD. Such hypo-connectivity was also observed between putaminal subregions and other brain regions, reflecting neuroimaging manifestations of the altered cortico-striato-thalamo-cortical circuit. These observed weaker couplings were associated with PD severity and duration. Our results support the utilization of the DECBP framework and suggest that abnormal connectivity in putaminal subregions may be a potential indicator of PD.