LittleBrain: A gradient-based tool for the topographical interpretation of cerebellar neuroimaging findings

The Growing Little Brain: Cerebellar Functional Development from Cradle to School

Despite the cerebellum's crucial role in brain functions, its early development, particularly in relation to the cerebrum, remains poorly understood. Here, we examine cerebellocortical connectivity using over 1,000 high-quality resting-state functional MRI scans of children from birth to 60 months. By mapping cerebellar topography with fine temporal detail for the first time, we show the hierarchical and contralateral organization of cerebellocortical connectivity from birth. We observe dynamic shifts in cerebellar network gradients, which become more focal with age while maintaining stable anchor points similar to adults, highlighting the cerebellum's evolving yet stable role in functional integration during early development. Our findings provide the first evidence of cerebellar connections to higher-order networks at birth, which generally strengthen with age, emphasizing the cerebellum's early role in cognitive processing beyond sensory and motor functions. Our study provides insights into early cerebellocortical interactions, reveals functional asymmetry and sexual dimorphism in cerebellar development, and lays the groundwork for future research on cerebellum-related disorders in children.

aXonica: A support package for MRI based Neuroimaging

Magnetic Resonance Imaging (MRI) assists in studying the nervous system. MRI scans undergo significant processing before presenting the final images to medical practitioners. These processes are executed with ease due to excellent software pipelines. However, establishing software workstations is non-trivial and requires researchers in life sciences to be comfortable in downloading, installing, and scripting software that is non-user-friendly and may lack basic GUI. As researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines speeding up building software workstations and laboratories. Previous solutions include NeuroDebian, BIDS Apps, Flywheel, QMENTA, Boutiques, Brainlife and Neurodesk. Overall, all these solutions complement each other. NeuroDebian covers neuroscience and has a wider scope, providing only 51 tools for MRI. Whereas, BIDS Apps is committed to the BIDS format, covering only 45 software related to MRI. Boutiques is more flexible, facilitating its pipelines to be easily installed as separate containers, validated, published, and executed. Whereas, both Flywheel and Qmenta are propriety, leaving four for users looking for 'free for use' tools, i.e., NeuroDebian, Brainlife, Neurodesk, and BIDS Apps. This paper presents an extensive survey of 317 tools published in MRI-based neuroimaging in the last ten years, along with 'aXonica,' an MRI-based neuroimaging support package that is unbiased towards any formatting standards and provides 130 applications, more than that of NeuroDebian (51), BIDS App (45), Flywheel (70), and Neurodesk (85). Using a technology stack that employs GUI as the front-end and shell scripted back-end, aXonica provides (i) 130 tools that span the entire MRI-based neuroimaging analysis, and allow the user to (ii) select the software of their choice, (iii) automatically resolve individual dependencies and (iv) installs them. Hence, aXonica can serve as an important resource for researchers and teachers working in the field of MRI-based Neuroimaging to (a) develop software workstations, and/or (b) install newer tools in their existing workstations.

Population-wide cerebellar growth models of children and adolescents

In the past, the cerebellum has been best known for its crucial role in motor function. However, increasingly more findings highlight the importance of cerebellar contributions in cognitive functions and neurodevelopment. Using a total of 7240 neuroimaging scans from 4862 individuals, we describe and provide detailed, openly available models of cerebellar development in childhood and adolescence (age range: 6-17 years), an important time period for brain development and onset of neuropsychiatric disorders. Next to a traditionally used anatomical parcellation of the cerebellum, we generated growth models based on a recently proposed functional parcellation. In both, we find an anterior-posterior growth gradient mirroring the age-related improvements of underlying behavior and function, which is analogous to cerebral maturation patterns and offers evidence for directly related cerebello-cortical developmental trajectories. Finally, we illustrate how the current approach can be used to detect cerebellar abnormalities in clinical samples.

Variations on the theme: focus on cerebellum and emotional processing

The cerebellum operates exploiting a complex modular organization and a unified computational algorithm adapted to different behavioral contexts. Recent observations suggest that the cerebellum is involved not just in motor but also in emotional and cognitive processing. It is therefore critical to identify the specific regional connectivity and microcircuit properties of the emotional cerebellum. Recent studies are highlighting the differential regional localization of genes, molecules, and synaptic mechanisms and microcircuit wiring. However, the impact of these regional differences is not fully understood and will require experimental investigation and computational modeling. This review focuses on the cellular and circuit underpinnings of the cerebellar role in emotion. And since emotion involves an integration of cognitive, somatomotor, and autonomic activity, we elaborate on the tradeoff between segregation and distribution of these three main functions in the cerebellum.

Functional Gradients of the Cerebellum: a Review of Practical Applications

Gradient-based analyses have contributed to the description of cerebellar functional neuroanatomy. More recently, functional gradients of the cerebellum have been used as a multi-purpose tool for neuroimaging research. Here, we provide an overview of the many practical applications of cerebellar functional gradient analyses. These practical applications include examination of intra-cerebellar and cerebellar-extracerebellar organization; transformation of functional gradients into parcellations with discrete borders; projection of functional gradients calculated within cerebellar structures to other extracerebellar structures; interpretation of cerebellar neuroimaging findings using qualitative and quantitative methods; detection of differences in patient populations; and other more complex practical applications of cerebellar gradient-based analyses. This review may serve as an introduction and catalog of options for neuroscientists who wish to design and analyze imaging studies using functional gradients of the cerebellum.

Neural connectome features of procrastination: Current progress and future direction

Procrastination refers to an irrationally delay for intended courses of action despite of anticipating a negative consequence due to this delay. Previous studies tried to reveal the neural substrates of procrastination in terms of connectome-based biomarkers. Based on this, we proposed a unified triple brain network model for procrastination and pinpointed out what challenges we are facing in understanding neural mechanism of procrastination. Specifically, based on neuroanatomical features, the unified triple brain network model proposed that connectome-based underpinning of procrastination could be ascribed to the abnormalities of self-control network (i.e., dorsolateral prefrontal cortex, DLPFC), emotion-regulation network (i.e., orbital frontal cortex, OFC), and episodic prospection network (i.e., para-hippocampus cortex, PHC). Moreover, based on the brain functional features, procrastination had been attributed to disruptive neural circuits on FPN (frontoparietal network)-SCN (subcortical network) and FPN-SAN (salience network), which led us to hypothesize the crucial roles of interplay between these networks on procrastination in unified triple brain network model. Despite of these findings, poor interpretability and computational model limited further understanding for procrastination from theoretical and neural perspectives. On balance, the current study provided an overview to show current progress on the connectome-based biomarkers for procrastination, and proposed the integrative neurocognitive model of procrastination.

Distinct alterations in cerebellar connectivity with substantia nigra and ventral tegmental area in Parkinson's disease

In Parkinson's disease (PD), neurodegeneration of dopaminergic neurons occurs in the midbrain, specifically targeting the substantia nigra (SN), while leaving the ventral tegmental area (VTA) relatively spared in early phases of the disease. Although the SN and VTA are known to be functionally dissociable in healthy adults, it remains unclear how this dissociation is altered in PD. To examine this issue, we performed a whole-brain analysis to compare functional connectivity in PD to healthy adults using resting-state functional magnetic resonance imaging (rs-fMRI) data compiled from three independent datasets. Our analysis showed that across the sample, the SN had greater connectivity with the precuneus, anterior cingulate gyrus, and areas of the occipital cortex, partially replicating our previous work in healthy young adults. Notably, we also found that, in PD, VTA-right cerebellum connectivity was higher than SN-right cerebellum connectivity, whereas the opposite trend occurred in healthy controls. This double dissociation may reflect a compensatory role of the cerebellum in PD and could provide a potential target for future study and treatment.

Increased resting-state activity in the cerebellum with mothers having less adaptive sensory processing and trait anxiety

Child‐rearing mothers with high levels of trait anxiety have a tendency for less adaptive sensory processing, which causes parenting stress. However, the neural mechanisms underlying this sensory processing and trait anxiety remain unclear. We aimed to determine the whole‐brain spontaneous neural activity and sensory processing characteristics in mothers with varying parenting stress levels. Using resting‐state functional magnetic resonance imaging, we assessed mothers caring for more than one preschool aged (2–5 years) child and presenting with varying levels of sensory processing, trait anxiety, and parenting stress. Spontaneous neural activities in select brain regions were evaluated by whole‐brain correlation analyses based on the fractional amplitude of low‐frequency fluctuations (fALFF). We found significant positive correlations between levels of sensory processing with trait anxiety and parenting stress. Mothers having less adaptive sensory processing had significantly increased resting‐state network activities in the left lobule VI of the cerebellum. Increased fALFF values in the left lobule VI confirmed the mediation effect on the relationship between trait anxiety and sensory processing. A tendency for less adaptive sensory processing involving increased brain activity in lobule VI could be an indicator of maternal trait anxiety and the risk of parenting stress.

Structural and resting state functional connectivity beyond the cortex

Mapping the structural and functional connectivity of the central nervous system has become a key area within neuroimaging research. While detailed network structures across the entire brain have been probed using animal models, non-invasive neuroimaging in humans has thus far been dominated by cortical investigations. Beyond the cortex, subcortical nuclei have traditionally been less accessible due to their smaller size and greater distance from radio frequency coils. However, major neuroimaging developments now provide improved signal and the resolution required to study these structures. Here, we present an overview of the connectivity between the amygdala, brainstem, cerebellum, spinal cord and the rest of the brain. While limitations to their imaging and analyses remain, we also provide some recommendations and considerations for mapping brain connectivity beyond the cortex.

Differential vulnerability of the cerebellum in healthy ageing and Alzheimer's disease

Recent findings challenge the prior notion that the cerebellum remains unaffected by Alzheimer's disease (AD). Yet, it is unclear whether AD exacerbates age-related cerebellar grey matter decline or engages distinct structural and functional territories. We performed a meta-analysis of cerebellar grey matter loss in normal ageing and AD. We mapped voxels with structural decline onto established brain networks, functional parcellations, and along gradients that govern the functional organisation of the cerebellum. Importantly, these gradients track continuous changes in cerebellar specialisation providing a more nuanced measure of the functional profile of regions vulnerable to ageing and AD. Gradient 1 progresses from motor to cognitive territories; Gradient 2 isolates attentional processing; Gradient 3 captures lateralisation differences in cognitive functions. We identified bilateral and right-lateralised posterior cerebellar atrophy in ageing and AD, respectively. Age- and AD-related structural decline only showed partial spatial overlap in right lobule VI/Crus I. Despite the seemingly distinct patterns of AD- and age-related atrophy, the functional profiles of these regions were similar. Both participate in the same macroscale networks (default mode, frontoparietal, attention), support executive functions and language processing, and did not exhibit a difference in relative positions along Gradients 1 or 2. However, Gradient 3 values were significantly different in ageing vs. AD, suggesting that the roles of left and right atrophied cerebellar regions exhibit subtle functional differences despite their membership in similar macroscale networks. These findings provide an unprecedented characterisation of structural and functional differences and similarities in cerebellar grey matter loss between normal ageing and AD.

The detailed organization of the human cerebellum estimated by intrinsic functional connectivity within the individual

Distinct regions of the cerebellum connect to separate regions of the cerebral cortex forming a complex topography. Although cerebellar organization has been examined in group-averaged data, study of individuals provides an opportunity to discover features that emerge at a higher spatial resolution. Here, functional connectivity MRI was used to examine the cerebellum of two intensively sampled individuals (each scanned 31 times). Connectivity to somatomotor cortex showed the expected crossed laterality and topography of the body maps. A surprising discovery was connectivity to the primary visual cortex along the vermis with evidence for representation of the central field. Within the hemispheres, each individual displayed a hierarchical progression from the inverted anterior lobe somatomotor map through to higher-order association zones. The hierarchy ended at Crus I/II and then progressed in reverse order through to the upright somatomotor map in the posterior lobe. Evidence for a third set of networks was found in the most posterior extent of the cerebellum. Detailed analysis of the higher-order association networks revealed robust representations of two distinct networks linked to the default network, multiple networks linked to cognitive control, as well as a separate representation of a language network. Although idiosyncratic spatial details emerged between subjects, each network could be detected in both individuals, and seed regions placed within the cerebellum recapitulated the full extent of the spatially specific cerebral networks. The observation of multiple networks in juxtaposed regions at the Crus I/II apex confirms the importance of this zone to higher-order cognitive function and reveals new organizational details.NEW & NOTEWORTHY Stable, within-individual maps of cerebellar organization reveal orderly macroscale representations of the cerebral cortex with local juxtaposed zones representing distinct networks. In addition, individuals reveal idiosyncratic organizational features.

Neurodevelopmental and Psychiatric Symptoms in Patients with a Cyst Compressing the Cerebellum: an Ongoing Enigma

A patient diagnosed with developmental delay, intellectual disability, and autistic and obsessive-compulsive symptoms was found to have a posterior fossa arachnoid cyst (PFAC) compressing the cerebellum. The patient was referred to our Ataxia Unit for consideration of surgical drainage of the cyst to improve his clinical constellation. This scenario led to an in-depth analysis including a literature review, functional resting-state MRI analysis of our patient compared to a group of controls, and genetic testing. While it is reasonable to consider that there may be a causal relationship between PFAC and neurodevelopmental or psychiatric symptoms in some patients, there is also a nontrivial prevalence of PFAC in the asymptomatic population and a significant possibility that many PFAC are incidental findings in the context of primary cognitive or psychiatric symptoms. Our functional MRI analysis is the first to examine brain function, and to report cerebellar dysfunction, in a patient presenting with cognitive/psychiatric symptoms found to have a structural abnormality compressing the cerebellum. These neuroimaging findings are inherently limited due to their correlational nature but provide unprecedented evidence suggesting that cerebellar compression may be associated with cerebellar dysfunction. Exome gene sequencing revealed additional etiological possibilities, highlighting the complexity of this field of cerebellar clinical and scientific practice. Our findings and discussion may guide future investigations addressing an important knowledge gap-namely, is there a link between cerebellar compression (including arachnoid cysts and possibly other forms of cerebellar compression such as Chiari malformation), cerebellar dysfunction (including fMRI abnormalities reported here), and neuropsychiatric symptoms?

Cerebellar Functional Anatomy: a Didactic Summary Based on Human fMRI Evidence

The cerebellum is relevant for virtually all aspects of behavior in health and disease. Cerebellar findings are common across all kinds of neuroimaging studies of brain function and dysfunction. A large and expanding body of literature mapping motor and non-motor functions in the healthy human cerebellar cortex using fMRI has served as a tool for interpreting these findings. For example, results of cerebellar atrophy in Alzheimer's disease in caudal aspects of Crus I/II and medial lobule IX can be interpreted by consulting a large number of task, resting-state, and gradient-based reports that describe the functional characteristics of these specific aspects of the cerebellar cortex. Here, we provide a concise summary that outlines organizational principles observed consistently across these studies of normal cerebellar organization. This basic framework may be useful for investigators performing or reading experiments that require a functional interpretation of human cerebellar topography.

A tutorial and tool for exploring feature similarity gradients with MRI data

There has been an increasing interest in examining organisational principles of the cerebral cortex (and subcortical regions) using different MRI features such as structural or functional connectivity. Despite the widespread interest, introductory tutorials on the underlying technique targeted for the novice neuroimager are sparse in the literature. Articles that investigate various "neural gradients" (for example based on region studied "cortical gradients," "cerebellar gradients," "hippocampal gradients" etc … or feature of interest "functional gradients," "cytoarchitectural gradients," "myeloarchitectural gradients" etc …) have increased in popularity. Thus, we believe that it is opportune to discuss what is generally meant by "gradient analysis". We introduce basics concepts in graph theory, such as graphs themselves, the degree matrix, and the adjacency matrix. We discuss how one can think about gradients of feature similarity (the similarity between timeseries in fMRI, or streamline in tractography) using graph theory and we extend this to explore such gradients across the whole MRI scale; from the voxel level to the whole brain level. We proceed to introduce a measure for quantifying the level of similarity in regions of interest. We propose the term "the Vogt-Bailey index" for such quantification to pay homage to our history as a brain mapping community. We run through the techniques on sample datasets including a brain MRI as an example of the application of the techniques on real data and we provide several appendices that expand upon details. To maximise intuition, the appendices contain a didactic example describing how one could use these techniques to solve a particularly pernicious problem that one may encounter at a wedding. Accompanying the article is a tool, available in both MATLAB and Python, that enables readers to perform the analysis described in this article on their own data. We refer readers to the graphical abstract as an overview of the analysis pipeline presented in this work.

Functional Connectivity Changes in Retired Rugby League Players: A Data-Driven Functional Magnetic Resonance Imaging Study

There is considerable interest in the long-term brain health of retired contact and collision sport athletes; however, little is known about possible underlying changes in functional brain connectivity in this group. We evaluated whole-brain functional connectivity patterns using multi-voxel pattern analysis (MVPA) to determine whether alterations in functional connectivity distinguish retired professional athletes from a matched group of healthy community control subjects. Thirty-two retired athletes with a history of multiple self-reported sport-related concussions and 36 healthy community control subjects who were similar in age and education, completed functional magnetic resonance imaging. We identified brain regions with abnormal functional connectivity patterns using whole-brain MVPA as implemented in the Conn toolbox. First-level MVPA was performed using 64 principal component analysis (PCA) components. Second-level F test was performed using the first three MVPA components for retired athletes > controls group contrast. Post hoc seed-to-voxel analyses using the MVPA cluster results as seeds were performed to characterize functional connectivity abnormalities from brain regions identified by MVPA. MVPA revealed one cluster of abnormal functional connectivity located in cerebellar lobule V. This region of lobule V corresponded to the ventral attention network. Post hoc seed-to-voxel analysis using the cerebellar MVPA cluster as a seed revealed multiple areas of cerebral cortical hyper-connectivity and hypo-connectivity in retired athletes when compared with controls. This initial report suggests that cerebellar dysfunction might be present and clinically important in some retired athletes.

Intrinsic Functional Connectivity of Dentate Nuclei in Autism Spectrum Disorder

Cerebellar abnormalities are commonly reported in autism spectrum disorder (ASD). Dentate nuclei (DNs) are key structures in the anatomical circuits linking the cerebellum to the extracerebellum. Previous resting-state functional connectivity (RsFc) analyses reported DN abnormalities in high-functioning ASD (HF-ASD). This study examined the RsFc of the DN in young adults with HF-ASD compared with healthy controls (HCs) with the aim to expand upon previous findings of DNs in a dataset using advanced, imaging acquisition methods that optimize spatiotemporal resolution and statistical power. Additional seed-to-voxel analyses were carried out using motor and nonmotor DN coordinates reported in previous studies as seeds. We report abnormal dentato-cerebral and dentato-cerebellar functional connectivity in ASD. Our results expand and, in part, replicate previous descriptions of DN RsFc abnormalities in this disorder and reveal correlations between DN-cerebral RsFc and ASD symptom severity.

Altered resting-state functional connectivity in young children at familial high risk for psychotic illness: A preliminary study

Multiple lines of evidence suggest that illness development in schizophrenia and other psychotic disorders predates the first psychotic episode by many years. In this study, we examined a sample of 15 pre-adolescent children, ages 7 through 12 years, who are at familial high-risk (FHR) because they have a parent or sibling with a history of schizophrenia or related psychotic disorder. Using multi-voxel pattern analysis (MVPA), a data-driven fMRI analysis, we assessed whole-brain differences in functional connectivity in the FHR sample as compared to an age- and sex-matched control (CON) group of 15 children without a family history of psychosis. MVPA analysis yielded a single cluster in right posterior superior temporal gyrus (pSTG/BA 22) showing significant group-differences in functional connectivity. Post-hoc characterization of this cluster through seed-to-voxel analysis revealed mostly reduced functional connectivity of the pSTG seed to a set of language and default mode network (DMN) associated brain regions including Heschl's gyrus, inferior temporal gyrus extending into fusiform gyrus, (para)hippocampus, thalamus, and a cerebellar cluster encompassing mainly Crus I/II. A height-threshold of whole-brain p < .001 (two-sided), and FDR-corrected cluster-threshold of p < .05 (non-parametric statistics) was used for post-hoc characterization. These findings suggest that abnormalities in functional communication in a network encompassing right STG and associated brain regions are present before adolescence in at-risk children and may be a risk marker for psychosis. Subsequent changes in this functional network across development may contribute to either disease manifestation or resilience in children with a familial vulnerability for psychosis.

Convergence of three parcellation approaches demonstrating cerebellar lobule volume deficits in Alcohol Use Disorder

Recent advances in robust and reliable methods of MRI-derived cerebellar lobule parcellation volumetry present the opportunity to assess effects of Alcohol Use Disorder (AUD) on selective cerebellar lobules and relations with indices of nutrition and motor functions. In pursuit of this opportunity, we analyzed high-resolution MRI data acquired in 24 individuals with AUD and 20 age- and sex-matched controls with a 32-channel head coil using three different atlases: the online automated analysis pipeline volBrain Ceres, SUIT, and the Johns Hopkins atlas. Participants had also completed gait and balance examination and hematological analysis of nutritional and liver status, enabling testing of functional meaningfulness of each cerebellar parcellation scheme. Compared with controls, each quantification approach yielded similar patterns of group differences in regional volumes: All three approaches identified AUD-related deficits in total tissue and total gray matter, but only Ceres identified a total white matter volume deficit. Convergent volume differences occurred in lobules I-V, Crus I, VIIIB, and IX. Coefficients of variation (CVs) were <20% for 46 of 56 regions measured and in general were graded: Ceres<SUIT<Hopkins. The most robust correlations were identified between poorer stability in balancing on one leg and smaller lobule VI and Crus I volumes from the Ceres atlas. Lower values of two essential vitamins-thiamine (vitamin B1) and serum folate (vitamin B9)-along with lower red blood cell count, which are dependent on adequate levels of B vitamins, correlated with smaller gray matter volumes of lobule VI and Crus I. Higher γ-glutamyl transferase (GGT) levels, possibly reflecting compromised liver function, correlated with smaller volumes of lobules VI and X. These initial results based on high resolution data produced with clinically practical imaging procedures hold promise for expanding our knowledge about the relevance of focal cerebellar morphology in AUD and other neuropsychiatric conditions.

The Theory and Neuroscience of Cerebellar Cognition

Cerebellar neuroscience has undergone a paradigm shift. The theories of the universal cerebellar transform and dysmetria of thought and the principles of organization of cerebral cortical connections, together with neuroanatomical, brain imaging, and clinical observations, have recontextualized the cerebellum as a critical node in the distributed neural circuits subserving behavior. The framework for cerebellar cognition stems from the identification of three cognitive representations in the posterior lobe, which are interconnected with cerebral association areas and distinct from the primary and secondary cerebellar sensorimotor representations linked with the spinal cord and cerebral motor areas. Lesions of the anterior lobe primary sensorimotor representations produce dysmetria of movement, the cerebellar motor syndrome. Lesions of the posterior lobe cognitive-emotional cerebellum produce dysmetria of thought and emotion, the cerebellar cognitive affective/Schmahmann syndrome. The notion that the cerebellum modulates thought and emotion in the same way that it modulates motor control advances the understanding of the mechanisms of cognition and opens new therapeutic opportunities in behavioral neurology and neuropsychiatry.