Comparing fully automated state-of-the-art cerebellum parcellation from magnetic resonance images

MR Imaging in Ataxias: Consensus Recommendations by the Ataxia Global Initiative Working Group on MRI Biomarkers

With many viable strategies in the therapeutic pipeline, upcoming clinical trials in hereditary and sporadic degenerative ataxias will benefit from non-invasive MRI biomarkers for patient stratification and the evaluation of therapies. The MRI Biomarkers Working Group of the Ataxia Global Initiative therefore devised guidelines to facilitate harmonized MRI data acquisition in clinical research and trials in ataxias. Recommendations are provided for a basic structural MRI protocol that can be used for clinical care and for an advanced multi-modal MRI protocol relevant for research and trial settings. The advanced protocol consists of modalities with demonstrated utility for tracking brain changes in degenerative ataxias and includes structural MRI, magnetic resonance spectroscopy, diffusion MRI, quantitative susceptibility mapping, and resting-state functional MRI. Acceptable ranges of acquisition parameters are provided to accommodate diverse scanner hardware in research and clinical contexts while maintaining a minimum standard of data quality. Important technical considerations in setting up an advanced multi-modal protocol are outlined, including the order of pulse sequences, and example software packages commonly used for data analysis are provided. Outcome measures most relevant for ataxias are highlighted with use cases from recent ataxia literature. Finally, to facilitate access to the recommendations by the ataxia clinical and research community, examples of datasets collected with the recommended parameters are provided and platform-specific protocols are shared via the Open Science Framework.

Structural deviations of the posterior fossa and the cerebellum and their cognitive links in a neurodevelopmental deletion syndrome

High-impact genetic variants associated with neurodevelopmental disorders provide biologically-defined entry points for mechanistic investigation. The 3q29 deletion (3q29Del) is one such variant, conferring a 40-100-fold increased risk for schizophrenia, as well as high risk for autism and intellectual disability. However, the mechanisms leading to neurodevelopmental disability remain largely unknown. Here, we report the first in vivo quantitative neuroimaging study in individuals with 3q29Del (N = 24) and neurotypical controls (N = 1608) using structural MRI. Given prior radiology reports of posterior fossa abnormalities in 3q29Del, we focused our investigation on the cerebellum and its tissue-types and lobules. Additionally, we compared the prevalence of cystic/cyst-like malformations of the posterior fossa between 3q29Del and controls and examined the association between neuroanatomical findings and quantitative traits to probe gene-brain-behavior relationships. 3q29Del participants had smaller cerebellar cortex volumes than controls, before and after correction for intracranial volume (ICV). An anterior-posterior gradient emerged in finer grained lobule-based and voxel-wise analyses. 3q29Del participants also had larger cerebellar white matter volumes than controls following ICV-correction and displayed elevated rates of posterior fossa arachnoid cysts and mega cisterna magna findings independent of cerebellar volume. Cerebellar white matter and subregional gray matter volumes were associated with visual-perception and visual-motor integration skills as well as IQ, while cystic/cyst-like malformations yielded no behavioral link. In summary, we find that abnormal development of cerebellar structures may represent neuroimaging-based biomarkers of cognitive and sensorimotor function in 3q29Del, adding to the growing evidence identifying cerebellar pathology as an intersection point between syndromic and idiopathic forms of neurodevelopmental disabilities.

Morphological changes in the cerebellum during aging: evidence from convolutional neural networks and shape analysis

The morphology and function of the cerebellum are associated with various developmental disorders and healthy aging. Changes in cerebellar morphology during the aging process have been extensively investigated, with most studies focusing on changes in cerebellar regional volume. The volumetric method has been used to quantitatively demonstrate the decrease in the cerebellar volume with age, but it has certain limitations in visually presenting the morphological changes of cerebellar atrophy from a three-dimensional perspective. Thus, we comprehensively described cerebellar morphological changes during aging through volume measurements of subregions and shape analysis. This study included 553 healthy participants aged 20-80 years. A novel cerebellar localized segmentation algorithm based on convolutional neural networks was utilized to analyze the volume of subregions, followed by shape analysis for localized atrophy assessment based on the cerebellar thickness. The results indicated that out of the 28 subregions in the absolute volume of the cerebellum, 15 exhibited significant aging trends, and 16 exhibited significant sex differences. Regarding the analysis of relative volume, only 11 out of the 28 subregions of the cerebellum exhibited significant aging trends, and 4 exhibited significant sex differences. The results of the shape analysis revealed region-specific atrophy of the cerebellum with increasing age. Regions displaying more significant atrophy were predominantly located in the vermis, the lateral portions of bilateral cerebellar hemispheres, lobules I-III, and the medial portions of the posterior lobe. This atrophy differed between sexes. Men exhibited slightly more severe atrophy than women in most of the cerebellar regions. Our study provides a comprehensive perspective for observing cerebellar atrophy during the aging process.

Neurodevelopmental trajectories of cerebellar grey matter associated with verbal abilities in males with autism spectrum disorder

Autism spectrum disorder (ASD) is a neurodevelopmental condition frequently associated with structural cerebellar abnormalities. Whether cerebellar grey matter volumes (GMV) are linked to verbal impairments remains controversial. Here, the association between cerebellar GMV and verbal abilities in ASD was examined across the lifespan. Lobular segmentation of the cerebellum was performed on structural MRI scans from the ABIDE I dataset in male individuals with ASD (N=144, age: 8.5-64.0 years) and neurotypical controls (N=188; age: 8.0-56.2 years). Stepwise linear mixed effects modeling including group (ASD vs. neurotypical controls), lobule-wise GMV, and age was performed to identify cerebellar lobules which best predicted verbal abilities as measured by verbal IQ (VIQ). An age-specific association between VIQ and GMV of bilateral Crus II was found in ASD relative to neurotypical controls. In children with ASD, higher VIQ was associated with larger GMV of left Crus II but smaller GMV of right Crus II. By contrast, in adults with ASD, higher VIQ was associated with smaller GMV of left Crus II and larger GMV of right Crus II. These findings indicate that relative to the contralateral hemisphere, an initial reliance on the language-nonspecific left cerebellar hemisphere is offset by more typical right-lateralization in adulthood.

Sex Differences and Behavioral Associations with Typically Developing Pediatric Regional Cerebellar Gray Matter Volume

The cerebellum contributes to motor and higher-order control throughout neurodevelopment, with marked growth during childhood. Few studies have investigated differential associations of cerebellar morphometry with function in males and females. The present study examines sex differences in regional cerebellar gray matter volume (GMV) and the moderating effect of sex on the relationship between GMV and motor, cognitive, and emotional functions in a large cohort of typically developing (TD) children. Participants included 371 TD children (123 females, age 8-12 years). A convolutional neural network-based approach was employed for cerebellar parcellation. Volumes were harmonized using ComBat to adjust for hardware-induced variations. Regression analyses examined the effect of sex on GMV and whether sex moderated the relationship between GMV and motor, cognitive, and emotional functions. Males showed larger GMV in right lobules I-V, bilateral lobules VI, crus II/VIIb, and VIII, left lobule X, and vermis regions I-V and VIII-X. Greater motor function correlated with less vermis VI-VII GMV in females. Greater cognitive function correlated with greater left lobule VI GMV in females and less left lobule VI GMV in males. Finally, greater internalizing symptoms correlated with greater bilateral lobule IX GMV in females but less in males. These findings reveal sexually dimorphic patterns of cerebellar structure and associations with motor, cognitive, and emotional functions. Males generally show larger GMV than females. Larger GMV was associated with better cognitive functioning for females and better motor/emotional functioning for males.

Smaller Cerebellar Lobule VIIb is Associated with Tremor Severity in Parkinson's Disease

Alterations in the cerebellum's morphology in Parkinson's disease (PD) point to its pathophysiological involvement in this movement disorder. Such abnormalities have previously been attributed to different PD motor subtypes. The aim of the study was to relate volumes of specific cerebellar lobules to motor symptom severity, in particular tremor (TR), bradykinesia/rigidity (BR), and postural instability and gait disorders (PIGD) in PD. We performed a volumetric analysis based on T1-weighted MRI images of 55 participants with PD (22 females, median age 65 years, Hoehn and Yahr stage 2). Multiple regression models were fitted to investigate associations between volumes of cerebellar lobules with clinical symptom severity based on MDS-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) part III score and sub-scores for TR, BR, and PIGD; adjusted for age, sex, disease duration, and intercranial volume as cofactors. Smaller volume of lobule VIIb was associated with higher tremor severity (P = 0.004). No structure-function relationships were detected for other lobules or other motor symptoms. This distinct structural association denotes the involvement of the cerebellum in PD tremor. Characterizing morphological features of the cerebellum leads to a better understanding of its role in the spectrum of motor symptoms in PD and contributes further to identifying potential biological markers.

Patterns of subregional cerebellar atrophy across epilepsy syndromes: An ENIGMA-Epilepsy study

OBJECTIVE

The intricate neuroanatomical structure of the cerebellum is of longstanding interest in epilepsy, but has been poorly characterized within the current corticocentric models of this disease. We quantified cross-sectional regional cerebellar lobule volumes using structural magnetic resonance imaging in 1602 adults with epilepsy and 1022 healthy controls across 22 sites from the global ENIGMA-Epilepsy working group.

METHODS

A state-of-the-art deep learning-based approach was employed that parcellates the cerebellum into 28 neuroanatomical subregions. Linear mixed models compared total and regional cerebellar volume in (1) all epilepsies, (2) temporal lobe epilepsy with hippocampal sclerosis (TLE-HS), (3) nonlesional temporal lobe epilepsy, (4) genetic generalized epilepsy, and (5) extratemporal focal epilepsy (ETLE). Relationships were examined for cerebellar volume versus age at seizure onset, duration of epilepsy, phenytoin treatment, and cerebral cortical thickness.

RESULTS

Across all epilepsies, reduced total cerebellar volume was observed (d = .42). Maximum volume loss was observed in the corpus medullare (dmax = .49) and posterior lobe gray matter regions, including bilateral lobules VIIB (dmax = .47), crus I/II (dmax = .39), VIIIA (dmax = .45), and VIIIB (dmax = .40). Earlier age at seizure onset (η ρ max 2  = .05) and longer epilepsy duration (η ρ max 2  = .06) correlated with reduced volume in these regions. Findings were most pronounced in TLE-HS and ETLE, with distinct neuroanatomical profiles observed in the posterior lobe. Phenytoin treatment was associated with reduced posterior lobe volume. Cerebellum volume correlated with cerebral cortical thinning more strongly in the epilepsy cohort than in controls.

SIGNIFICANCE

We provide robust evidence of deep cerebellar and posterior lobe subregional gray matter volume loss in patients with chronic epilepsy. Volume loss was maximal for posterior subregions implicated in nonmotor functions, relative to motor regions of both the anterior and posterior lobe. Associations between cerebral and cerebellar changes, and variability of neuroanatomical profiles across epilepsy syndromes argue for more precise incorporation of cerebellar subregional damage into neurobiological models of epilepsy.

The Cerebellum and Cognitive Function: Anatomical Evidence from a Transdiagnostic Sample

Multiple lines of evidence across human functional, lesion, and animal data point to a cerebellar role, in particular of crus I, crus II, and lobule VIIB, in cognitive function. However, a mapping of distinct facets of cognitive function to cerebellar structure is missing. We analyzed structural neuroimaging data from the Healthy Brain Network (HBN). Cerebellar parcellation was performed with a validated automated segmentation pipeline (CERES) and stringent visual quality check (n = 662 subjects retained from initial n = 1452). Canonical correlation analyses (CCA) examined regional gray matter volumetric (GMV) differences in association to cognitive function (quantified with NIH Toolbox Cognition domain, NIH-TB), accounting for psychopathology severity, age, sex, scan location, and intracranial volume. Multivariate CCA uncovered a significant correlation between two components entailing a latent cognitive canonical (NIH-TB subscales) and a brain canonical variate (cerebellar GMV and intracranial volume, ICV), surviving bootstrapping and permutation procedures. The components correspond to partly shared cerebellar-cognitive function relationship with a first map encompassing cognitive flexibility (r = 0.89), speed of processing (r = 0.65), and working memory (r = 0.52) associated with regional GMV in crus II (r = 0.57) and lobule X (r = 0.59) and a second map including the crus I (r = 0.49) and lobule VI (r = 0.49) associated with working memory (r = 0.51). We show evidence for a structural subspecialization of the cerebellum topography for cognitive function in a transdiagnostic sample.

Cerebellar Volume and Disease Staging in Parkinson's Disease: An ENIGMA-PD Study

BACKGROUND

Increasing evidence points to a pathophysiological role for the cerebellum in Parkinson's disease (PD). However, regional cerebellar changes associated with motor and non-motor functioning remain to be elucidated.

OBJECTIVE

To quantify cross-sectional regional cerebellar lobule volumes using three dimensional T1-weighted anatomical brain magnetic resonance imaging from the global ENIGMA-PD working group.

METHODS

Cerebellar parcellation was performed using a deep learning-based approach from 2487 people with PD and 1212 age and sex-matched controls across 22 sites. Linear mixed effects models compared total and regional cerebellar volume in people with PD at each Hoehn and Yahr (HY) disease stage, to an age- and sex- matched control group. Associations with motor symptom severity and Montreal Cognitive Assessment scores were investigated.

RESULTS

Overall, people with PD had a regionally smaller posterior lobe (dmax  = -0.15). HY stage-specific analyses revealed a larger anterior lobule V bilaterally (dmax  = 0.28) in people with PD in HY stage 1 compared to controls. In contrast, smaller bilateral lobule VII volume in the posterior lobe was observed in HY stages 3, 4, and 5 (dmax  = -0.76), which was incrementally lower with higher disease stage. Within PD, cognitively impaired individuals had lower total cerebellar volume compared to cognitively normal individuals (d = -0.17).

CONCLUSIONS

We provide evidence of a dissociation between anterior "motor" lobe and posterior "non-motor" lobe cerebellar regions in PD. Whereas less severe stages of the disease are associated with larger motor lobe regions, more severe stages of the disease are marked by smaller non-motor regions. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Examination of the Development and Asymmetry of the Cerebellum and Its Lobules in Individuals Aged 1-18 Years: A Retrospective MRI Study

Developmental studies of cerebellar lobules were limited. To our knowledge, structural asymmetry has not been studied in immature cerebellar lobules in the 1-18 age group. This study investigated the effect of age and gender on the volumetric development and asymmetry of the global cerebellum and cerebellar lobules in children and adolescents. In this retrospective study, we included 670 individuals [376 (56.1%) males] aged 1-18 years with normal brain MRIs between 2012 and 2021. volBrain CERES automatically segmented the right and left sides of the cerebellar lobules on three-dimensional T1-weighted MRIs. Volume and asymmetry data from individuals in 16 different age ranges were compared with SPSS (ver.28). The absolute volumetric development of the total cerebellum was consistent with the "S" development model in both sexes. The developmental trajectories of the cerebellar lobules were different from each other and showed sexual dimorphism. In the 1-18 age group, the absolute volumes of the total cerebellum and cerebellar lobules were significantly greater in males (p < 0.05). Absolute volumes of lobules IV, VIIB, VIIIA and VIIIB in the age groups had more gender differences. However, sexual dimorphism was insignificant in the cerebellum's total and lobular relative volume. Lobules IV, V, VI, VIIIA and VIIIB had left > right asymmetry and other lobules and total cerebellum had right > left asymmetry. This study confirmed the developmental heterogeneity and sexual dimorphism in the cerebellar lobules. It also provided volumetric data of the immature cerebellum to enable comparison in various neurological and neuropsychiatric diseases.

Patterns of subregional cerebellar atrophy across epilepsy syndromes: An ENIGMA-Epilepsy study

Objective

The intricate neuroanatomical structure of the cerebellum is of longstanding interest in epilepsy, but has been poorly characterized within the current cortico-centric models of this disease. We quantified cross-sectional regional cerebellar lobule volumes using structural MRI in 1,602 adults with epilepsy and 1,022 healthy controls across twenty-two sites from the global ENIGMA-Epilepsy working group.

Methods

A state-of-the-art deep learning-based approach was employed that parcellates the cerebellum into 28 neuroanatomical subregions. Linear mixed models compared total and regional cerebellar volume in i) all epilepsies; ii) temporal lobe epilepsy with hippocampal sclerosis (TLE-HS); iii) non-lesional temporal lobe epilepsy (TLE-NL); iv) genetic generalised epilepsy; and (v) extra-temporal focal epilepsy (ETLE). Relationships were examined for cerebellar volume versus age at seizure onset, duration of epilepsy, phenytoin treatment, and cerebral cortical thickness.

Results

Across all epilepsies, reduced total cerebellar volume was observed (d=0.42). Maximum volume loss was observed in the corpus medullare (dmax=0.49) and posterior lobe grey matter regions, including bilateral lobules VIIB (dmax= 0.47), Crus I/II (dmax= 0.39), VIIIA (dmax=0.45) and VIIIB (dmax=0.40). Earlier age at seizure onset (ηρ2max=0.05) and longer epilepsy duration (ηρ2max=0.06) correlated with reduced volume in these regions. Findings were most pronounced in TLE-HS and ETLE with distinct neuroanatomical profiles observed in the posterior lobe. Phenytoin treatment was associated with reduced posterior lobe volume. Cerebellum volume correlated with cerebral cortical thinning more strongly in the epilepsy cohort than in controls.

Significance

We provide robust evidence of deep cerebellar and posterior lobe subregional grey matter volume loss in patients with chronic epilepsy. Volume loss was maximal for posterior subregions implicated in non-motor functions, relative to motor regions of both the anterior and posterior lobe. Associations between cerebral and cerebellar changes, and variability of neuroanatomical profiles across epilepsy syndromes argue for more precise incorporation of cerebellum subregions into neurobiological models of epilepsy.

Radiological correlates of pseudobulbar affect: Corticobulbar and cerebellar components in primary lateral sclerosis

INTRODUCTION

Pseudobulbar affect (PBA) is a distressing symptom of a multitude of neurological conditions affecting patients with a rage of neuroinflammatory, neurovascular and neurodegenerative conditions. It manifests in disproportionate emotional responses to minimal or no contextual stimulus. It has considerable quality of life implications and treatment can be challenging.

METHODS

A prospective multimodal neuroimaging study was conducted to explore the neuroanatomical underpinnings of PBA in patients with primary lateral sclerosis (PLS). All participants underwent whole genome sequencing and screening for C9orf72 hexanucleotide repeat expansions, a comprehensive neurological assessment, neuropsychological screening (ECAS, HADS, FrSBe) and PBA was evaluated by the emotional lability questionnaire. Structural, diffusivity and functional MRI data were systematically evaluated in whole-brain (WB) data-driven and region of interest (ROI) hypothesis-driven analyses. In ROI analyses, functional and structural corticobulbar connectivity and cerebello-medullary connectivity alterations were evaluated separately.

RESULTS

Our data-driven whole-brain analyses revealed associations between PBA and white matter degeneration in descending corticobulbar as well as in commissural tracts. In our hypothesis-driven analyses, PBA was associated with increased right corticobulbar tract RD (p = 0.006) and decreased FA (p = 0.026). The left-hemispheric corticobulbar tract, as well as functional connectivity, showed similar tendencies. While uncorrected p-maps revealed both voxelwise and ROI trends for associations between PBA and cerebellar measures, these did not reach significance to unequivocally support the "cerebellar hypothesis".

CONCLUSIONS

Our data confirm associations between cortex-brainstem disconnection and the clinical severity of PBA. While our findings may be disease-specific, they are consistent with the classical cortico-medullary model of pseudobulbar affect.

Brain MRI detects early-stage alterations and disease progression in Friedreich ataxia

Friedreich ataxia is a progressive neurodegenerative disorder characterized by cerebellar and spinal atrophy. However, studies to elucidate the longitudinal progression of the pathology in the brain are somewhat inconsistent and limited, especially for early-stage Friedreich ataxia. Using a multimodal neuroimaging protocol, combined with advanced analysis methods, we sought to identify macrostructural and microstructural alterations in the brain of patients with early-stage Friedreich ataxia to better understand its distribution patterns and progression. We enrolled 28 patients with Friedreich ataxia and 20 age- and gender-matched controls. Longitudinal clinical and imaging data were collected in the patients at baseline, 12, 24 and 36 months. Macrostructural differences were observed in patients with Friedreich ataxia, compared to controls, including lower volume of the cerebellar white matter (but not cerebellar grey matter), superior cerebellar peduncle, thalamus and brainstem structures, and higher volume of the fourth ventricle. Diffusion tensor imaging and fixel-based analysis metrics also showed microstructural differences in several brain regions, especially in the cerebellum and corticospinal tract. Over time, many of these macrostructural and microstructural alterations progressed, especially cerebellar grey and white matter volumes, and microstructure of the superior cerebellar peduncle, posterior limb of the internal capsule and superior corona radiata. In addition, linear regressions showed significant associations between many of those imaging metrics and clinical scales. This study provides evidence of early-stage macrostructural and microstructural alterations and of progression over time in the brain in Friedreich ataxia. Moreover, it allows to non-invasively map such brain alterations over a longer period (3 years) than any previous study, and identifies several brain regions with significant involvement in the disease progression besides the cerebellum. We show that fixel-based analysis of diffusion MRI data is particularly sensitive to longitudinal change in the cerebellar peduncles, as well as motor and sensory white matter tracts. In combination with other morphometric measures, they may therefore provide sensitive imaging biomarkers of disease progression for clinical trials.

Genetic patterning for child psychopathology is distinct from that for adults and implicates fetal cerebellar development

Childhood psychiatric symptoms are often diffuse but can coalesce into discrete mental illnesses during late adolescence. We leveraged polygenic scores (PGSs) to parse genomic risk for childhood symptoms and to uncover related neurodevelopmental mechanisms with transcriptomic and neuroimaging data. In independent samples (Adolescent Brain Cognitive Development, Generation R) a narrow cross-disorder neurodevelopmental PGS, reflecting risk for attention deficit hyperactivity disorder, autism, depression and Tourette syndrome, predicted psychiatric symptoms through early adolescence with greater sensitivity than broad cross-disorder PGSs reflecting shared risk across eight psychiatric disorders, the disorder-specific PGS individually or two other narrow cross-disorder (Compulsive, Mood-Psychotic) scores. Neurodevelopmental PGS-associated genes were preferentially expressed in the cerebellum, where their expression peaked prenatally. Further, lower gray matter volumes in cerebellum and functionally coupled cortical regions associated with psychiatric symptoms in mid-childhood. These findings demonstrate that the genetic underpinnings of pediatric psychiatric symptoms differ from those of adult illness, and implicate fetal cerebellar developmental processes that endure through childhood.

Enhancing fetal alcohol spectrum disorders diagnosis with a classifier based on the intracerebellar gradient of volumetric undersizing

In fetal alcohol spectrum disorders (FASD), brain growth deficiency is a hallmark of subjects both with fetal alcohol syndrome (FAS) and with non-syndromic FASD (NS-FASD, i.e., those without specific diagnostic features). However, although the cerebellum was suggested to be more severely undersized than the rest of the brain, it has not yet been given a specific place in the FASD diagnostic criteria where neuroanatomical features still count for little if anything in diagnostic specificity. We applied a combination of cerebellar segmentation tools on a 1.5 T 3DT1 brain MRI dataset from a monocentric population of 89 FASD (52 FAS, 37 NS-FASD) and 126 typically developing controls (6-20 years old), providing 8 volumes: cerebellum, vermis and 3 lobes (anterior, posterior, inferior), plus total brain volume. After adjustment of confounders, the allometric scaling relationship between these cerebellar volumes (V_i ) and the total brain or cerebellum volume (V_t ) was fitted (V_i  = bV_t ^a ), and the effect of group (FAS, control) on allometric scaling was evaluated. We then estimated for each cerebellar volume in the FAS population the deviation from the typical scaling (_v DTS) learned in the controls. Lastly, we trained and tested two classifiers to discriminate FAS from controls, one based on the total cerebellum _v DTS only, the other based on all the cerebellar _v DTS, comparing their performance both in the FAS and the NS-FASD group. Allometric scaling was significantly different between FAS and control group for all the cerebellar volumes (p < .001). We confirmed the excess of total cerebellum volume deficit (_v DTS = -10.6%) and revealed an antero-inferior-posterior gradient of volumetric undersizing in the hemispheres (-12.4%, 1.1%, 2.0%, repectively) and the vermis (-16.7%, -9.2%, -8.6%, repectively). The classifier based on the intracerebellar gradient of _v DTS performed more efficiently than the one based on total cerebellum _v DTS only (AUC = 92% vs. 82%, p = .001). Setting a high probability threshold for >95% specificity of the classifiers, the gradient-based classifier identified 35% of the NS-FASD to have a FAS cerebellar phenotype, compared to 11% with the cerebellum-only classifier (p_FISHER  = 0.027). In a large series of FASD, this study details the volumetric undersizing within the cerebellum at the lobar and vermian level using allometric scaling, revealing an anterior-inferior-posterior gradient of vulnerability to prenatal alcohol exposure. It also strongly suggests that this intracerebellar gradient of volumetric undersizing may be a reliable neuroanatomical signature of FAS that could be used to improve the specificity of the diagnosis of NS-FASD.

Understanding the relationship between cerebellar structure and social abilities

BACKGROUND

The cerebellum contains more than 50% of all neurons in the brain and is involved in a broad range of cognitive functions, including social communication and social cognition. Inconsistent atypicalities in the cerebellum have been reported in individuals with autism compared to controls suggesting the limits of categorical case control comparisons. Alternatively, investigating how clinical dimensions are related to neuroanatomical features, in line with the Research Domain Criteria approach, might be more relevant. We hypothesized that the volume of the "cognitive" lobules of the cerebellum would be associated with social difficulties.

METHODS

We analyzed structural MRI data from a large pediatric and transdiagnostic sample (Healthy Brain Network). We performed cerebellar parcellation with a well-validated automated segmentation pipeline (CERES). We studied how social communication abilities-assessed with the social component of the Social Responsiveness Scale (SRS)-were associated with the cerebellar structure, using linear mixed models and canonical correlation analysis.

RESULTS

In 850 children and teenagers (mean age 10.8 ± 3 years; range 5-18 years), we found a significant association between the cerebellum, IQ and social communication performance in our canonical correlation model.

LIMITATIONS

Cerebellar parcellation relies on anatomical boundaries, which does not overlap with functional anatomy. The SRS was originally designed to identify social impairments associated with autism spectrum disorders.

CONCLUSION

Our results unravel a complex relationship between cerebellar structure, social performance and IQ and provide support for the involvement of the cerebellum in social and cognitive processes.

Morphometric evaluation of cerebellar lobules in individuals with unilateral vertebral artery hypoplasia

PURPOSE

Vertebral arteries (VAs) provide blood circulation to the posterior fossa in general and are the main blood supply of the posterior fossa structures of the brain. Our aim in this study is to analyze the segmental volumetric values of cerebellar structures with the voxel-based volumetric analysis system in individuals with unilateral vertebral artery hypoplasia.

METHODS

In this retrospective study, segmental volumetric values/percentile ratios of cerebellar lobules were calculated using 3D fast spoiled gradient recall acquisition in steady-state (3D T1 FSPGR) MRI sequence images of the brain in individuals with unilateral vertebral artery hypoplasia (VAH) and in those without bilateral VAH and any symptoms of vertebrobasilar insufficiency as the control group was evaluated in volBrain ( http://volbrain.upv.es/ ).

RESULTS

The VAH group consisted of 50 (19 males/31 females) and the control group had 50 (21 males/29 females) individuals. The cerebellar lobule III, IV, VIIIA and X total volumes and the cerebellar lobule I-II, III, IV, VIIIA and X gray matter volumes were lower in the hypoplastic side than the non-hypoplastic cases and also than the contralateral side of the hypoplastic cases in the VAH group. In addition, it was found that that lobules IV and V had lower cortical thickness and lobules I-II had a higher coverage rate in the intracranial cavity in the hypoplastic side than the non-hypoplastic cases and also than the contralateral side of the hypoplastic cases (p < 0.05).

CONCLUSION

In this study, it was found that cerebellar lobule III, IV, VIIIA, X total volumes and cerebellar lobule I-II, III, IV, VIIIA, X gray matter volumes in addition to lobule IV, V cortical thicknesses were low in individuals with unilateral VAH. Being aware of these variations and taking them into account during future volumetric studies on the cerebellum are very important.

Altered brain white matter structural motor network in spinocerebellar ataxia type 3

OBJECTIVES

Spinocerebellar ataxia type 3 is a disorder within the brain network. However, the relationship between the brain network and disease severity is still unclear. This study aims to investigate changes in the white matter (WM) structural motor network, both in preclinical and ataxic stages, and its relationship with disease severity.

METHODS

For this study, 20 ataxic, 20 preclinical SCA3 patients, and 20 healthy controls were recruited and received MRI scans. Disease severity was quantified using the SARA and ICARS scores. The WM motor structural network was created using probabilistic fiber tracking and was analyzed using graph theory and network-based statistics at global, nodal, and edge levels. In addition, the correlations between network topological measures and disease duration or clinical scores were analyzed.

RESULTS

Preclinical patients showed increasing assortativity of the motor network, altered subnetwork including 12 edges of 11 nodes, and 5 brain regions presenting reduced nodal strength. In ataxic patients assortativity of the motor network also increased, but global efficiency, global strength, and transitivity decreased. Ataxic patients showed a wider altered subnetwork and a higher number of reduced nodal strengths. A negative correlation between the transitivity of the motor network and SARA and ICARS scores was observed in ataxic patients.

INTERPRETATION

Changes to the WM motor network in SCA3 start before ataxia onset, and WM motor network involvement increases with disease progression. Global network topological measures of the WM motor network appear to be a promising image biomarker for disease severity. This study provides new insights into the pathophysiology of disease in SCA3/MJD.

CerebNet: A fast and reliable deep-learning pipeline for detailed cerebellum sub-segmentation

Quantifying the volume of the cerebellum and its lobes is of profound interest in various neurodegenerative and acquired diseases. Especially for the most common spinocerebellar ataxias (SCA), for which the first antisense oligonculeotide-base gene silencing trial has recently started, there is an urgent need for quantitative, sensitive imaging markers at pre-symptomatic stages for stratification and treatment assessment. This work introduces CerebNet, a fully automated, extensively validated, deep learning method for the lobular segmentation of the cerebellum, including the separation of gray and white matter. For training, validation, and testing, T1-weighted images from 30 participants were manually annotated into cerebellar lobules and vermal sub-segments, as well as cerebellar white matter. CerebNet combines FastSurferCNN, a UNet-based 2.5D segmentation network, with extensive data augmentation, e.g. realistic non-linear deformations to increase the anatomical variety, eliminating additional preprocessing steps, such as spatial normalization or bias field correction. CerebNet demonstrates a high accuracy (on average 0.87 Dice and 1.742mm Robust Hausdorff Distance across all structures) outperforming state-of-the-art approaches. Furthermore, it shows high test-retest reliability (average ICC >0.97 on OASIS and Kirby) as well as high sensitivity to disease effects, including the pre-ataxic stage of spinocerebellar ataxia type 3 (SCA3). CerebNet is compatible with FreeSurfer and FastSurfer and can analyze a 3D volume within seconds on a consumer GPU in an end-to-end fashion, thus providing an efficient and validated solution for assessing cerebellum sub-structure volumes. We make CerebNet available as source-code (https://github.com/Deep-MI/FastSurfer).

Age-volume associations in cerebellar lobules by sex and reproductive stage

The cerebellum has established associations with motor function and a well-recognized role in cognition. In advanced age, cognitive and motor impairments contribute to reduced quality of life and are more common. Regional cerebellar volume is associated with performance across these domains and sex hormones may influence this volume. Examining sex differences in regional cerebellar volume in conjunction with age, and in the context of reproductive stage stands to improve our understanding of cerebellar aging and pathology. Data from 508 healthy adults (ages 18-88; 47% female) from the Cambridge Centre for Ageing and Neuroscience database were used here. CERES was used to assess lobular volume in T1-weighted images. We examined sex differences in adjusted regional cerebellar volume while controlling for age. A subgroup of participants (n = 370, 50% female) was used to assess group differences in female reproductive stages as compared to age-matched males. Sex differences in adjusted volume were seen across most anterior and posterior cerebellar lobules. Most of these lobules had significant linear relationships with age in males and females. While there were no interactions between sex and reproductive stage groups, exploratory analyses in females alone revealed multiple regional differences by reproductive stage. We found sex differences in volume across much of the cerebellum, linear associations with age, and did not find an interaction for sex and reproductive stage on regional cerebellar volume. Longitudinal investigation into hormonal influences on cerebellar structure and function is warranted as hormonal changes with menopause may impact cerebellar volume over time.

vol2Brain: A New Online Pipeline for Whole Brain MRI Analysis

Automatic and reliable quantitative tools for MR brain image analysis are a very valuable resource for both clinical and research environments. In the past few years, this field has experienced many advances with successful techniques based on label fusion and more recently deep learning. However, few of them have been specifically designed to provide a dense anatomical labeling at the multiscale level and to deal with brain anatomical alterations such as white matter lesions (WML). In this work, we present a fully automatic pipeline (vol2Brain) for whole brain segmentation and analysis, which densely labels (N &gt; 100) the brain while being robust to the presence of WML. This new pipeline is an evolution of our previous volBrain pipeline that extends significantly the number of regions that can be analyzed. Our proposed method is based on a fast and multiscale multi-atlas label fusion technology with systematic error correction able to provide accurate volumetric information in a few minutes. We have deployed our new pipeline within our platform volBrain (www.volbrain.upv.es), which has been already demonstrated to be an efficient and effective way to share our technology with the users worldwide.

Altered Coupling of Cerebral Blood Flow and Functional Connectivity Strength in First-Episode Schizophrenia Patients With Auditory Verbal Hallucinations

Objective

Auditory verbal hallucinations (AVHs) are a major symptom of schizophrenia and are connected with impairments in auditory and speech-related networks. In schizophrenia with AVHs, alterations in resting-state cerebral blood flow (CBF) and functional connectivity have been described. However, the neurovascular coupling alterations specific to first-episode drug-naïve schizophrenia (FES) patients with AVHs remain unknown.

Methods

Resting-state functional MRI and arterial spin labeling (ASL) was performed on 46 first-episode drug-naïve schizophrenia (FES) patients with AVHs (AVH), 39 FES drug-naïve schizophrenia patients without AVHs (NAVH), and 48 healthy controls (HC). Then we compared the correlation between the CBF and functional connection strength (FCS) of the entire gray matter between the three groups, as well as the CBF/FCS ratio of each voxel. Correlation analyses were performed on significant results between schizophrenia patients and clinical measures scale.

Results

The CBF/FCS ratio was reduced in the cognitive and emotional brain regions in both the AVH and NAVH groups, primarily in the crus I/II, vermis VI/VII, and cerebellum VI. In the AVH group compared with the HC group, the CBF/FCS ratio was higher in auditory perception and language-processing areas, primarily the left superior and middle temporal gyrus (STG/MTG). The CBF/FCS ratio in the left STG and left MTG positively correlates with the score of the Auditory Hallucination Rating Scale in AVH patients.

Conclusion

These findings point to the difference in neurovascular coupling failure between AVH and NAVH patients. The dysfunction of the forward model based on the predictive and computing role of the cerebellum may increase the excitability in the auditory cortex, which may help to understand the neuropathological mechanism of AVHs.

Effects of the Intermittent Theta Burst Stimulation of the Cerebellar Vermis on Balance Recovery After Stroke: A Study Protocol for a Randomized Controlled Trial

Background

The recovery of balance function is a critical segment in the rehabilitation treatment of stroke. The cerebellum is considered as the key structure involved in balance and motor control. The cerebellar vermis plays an important role in integrating vision, proprioception, and sensory skin input and may be a candidate stimulation target for regulating the motor network related with balance. However, evidence that the intermittent theta burst stimulation (iTBS) of cerebellar vermis can promote the recovery of balance function after stroke remains insufficient. Therefore, this study aims to explore the efficacy of the cerebellar vermis iTBS for the treatment of balance function in patients with stroke.

Methods and Analysis

Forty patients with stroke will be recruited in this prospective, randomized, sham-controlled trial. Participants will be randomized in a 1:1 ratio to receive either 15 sessions of cerebellar vermis iTBS (600 pulses) or sham stimulation. Additionally, a routine rehabilitation therapy follows the intervention. The primary outcome is the Berg Balance Scale, and the secondary outcomes are the Fugl–Meyer assessment of the lower extremity and modified Barthel index. The above outcomes will be assessed before intervention and at the end of each week. Pre- and post-iTBS resting-state functional magnetic resonance imaging (rs-fMRI) will be acquired, and the regional homogeneity, fractional amplitude of low-frequency fluctuation and functional connectivity will be calculated and analyzed.

Discussion

This protocol holds promise as a potential method to improve balance function in patients with stroke. If the outcomes of patients improve after the intervention, the study will provide new insights into improving balance function.

Ethics and Dissemination

This study has been approved by the Medical Research Ethics Committee of Wuxi Mental Health Center (Wuxi Tongren Rehabilitation Hospital). Results will be disseminated through (open-access) peer-reviewed publications, networks of scientists, professionals, and the public and presented at conferences.

Clinical Trial Registration Number

www.chictr.org.cn, identifier ChiCTR2100052590.

Convolutional Neural Networks for Segmenting Cerebellar Fissures from Magnetic Resonance Imaging

The human cerebellum plays an important role in coordination tasks. Diseases such as spinocerebellar ataxias tend to cause severe damage to the cerebellum, leading patients to a progressive loss of motor coordination. The detection of such damages can help specialists to approximate the state of the disease, as well as to perform statistical analysis, in order to propose treatment therapies for the patients. Manual segmentation of such patterns from magnetic resonance imaging is a very difficult and time-consuming task, and is not a viable solution if the number of images to process is relatively large. In recent years, deep learning techniques such as convolutional neural networks (CNNs or convnets) have experienced an increased development, and many researchers have used them to automatically segment medical images. In this research, we propose the use of convolutional neural networks for automatically segmenting the cerebellar fissures from brain magnetic resonance imaging. Three models are presented, based on the same CNN architecture, for obtaining three different binary masks: fissures, cerebellum with fissures, and cerebellum without fissures. The models perform well in terms of precision and efficiency. Evaluation results show that convnets can be trained for such purposes, and could be considered as additional tools in the diagnosis and characterization of neurodegenerative diseases.

Diagnosis of early mild cognitive impairment using a multiobjective optimization algorithm based on T1-MRI data

Alzheimer's disease (AD) is the most prevalent form of dementia. The accurate diagnosis of AD, especially in the early phases is very important for timely intervention. It has been suggested that brain atrophy, as measured with structural magnetic resonance imaging (sMRI), can be an efficacy marker of neurodegeneration. While classification methods have been successful in diagnosis of AD, the performance of such methods have been very poor in diagnosis of those in early stages of mild cognitive impairment (EMCI). Therefore, in this study we investigated whether optimisation based on evolutionary algorithms (EA) can be an effective tool in diagnosis of EMCI as compared to cognitively normal participants (CNs). Structural MRI data for patients with EMCI (n = 54) and CN participants (n = 56) was extracted from Alzheimer's disease Neuroimaging Initiative (ADNI). Using three automatic brain segmentation methods, we extracted volumetric parameters as input to the optimisation algorithms. Our method achieved classification accuracy of greater than 93%. This accuracy level is higher than the previously suggested methods of classification of CN and EMCI using a single- or multiple modalities of imaging data. Our results show that with an effective optimisation method, a single modality of biomarkers can be enough to achieve a high classification accuracy.

Cerebellar Volumes and Sensorimotor Behavior in Autism Spectrum Disorder

Background

Sensorimotor issues are common in autism spectrum disorder (ASD), though their neural bases are not well understood. The cerebellum is vital to sensorimotor control and reduced cerebellar volumes in ASD have been documented. Our study examined the extent to which cerebellar volumes are associated with multiple sensorimotor behaviors in ASD.

Materials and Methods

Fifty-eight participants with ASD and 34 typically developing (TD) controls (8-30 years) completed a structural MRI scan and precision grip testing, oculomotor testing, or both. Force variability during precision gripping as well as absolute error and trial-to-trial error variability of visually guided saccades were examined. Volumes of cerebellar lobules, vermis, and white matter were quantified. The relationships between each cerebellar region of interest (ROI) and force variability, saccade error, and saccade error variability were examined.

Results

Relative to TD controls, individuals with ASD showed increased force variability. Individuals with ASD showed a reduced volume of cerebellar vermis VI-VII relative to TD controls. Relative to TD females, females with ASD showed a reduced volume of bilateral cerebellar Crus II/lobule VIIB. Increased volume of Crus I was associated with increased force variability. Increased volume of vermal lobules VI-VII was associated with reduced saccade error for TD controls but not individuals with ASD. Increased right lobule VIII and cerebellar white matter volumes as well as reduced right lobule VI and right lobule X volumes were associated with greater ASD symptom severity. Reduced volumes of right Crus II/lobule VIIB were associated with greater ASD symptom severity in only males, while reduced volumes of right Crus I were associated with more severe restricted and repetitive behaviors only in females.

Conclusion

Our finding that increased force variability in ASD is associated with greater cerebellar Crus I volumes indicates that disruption of sensory feedback processing supported by Crus I may contribute to skeletomotor differences in ASD. Results showing that volumes of vermal lobules VI-VII are associated with saccade precision in TD but not ASD implicates atypical organization of the brain systems supporting oculomotor control in ASD. Associations between volumes of cerebellar subregions and ASD symptom severity suggest cerebellar pathological processes may contribute to multiple developmental challenges in ASD.

The Immediate Effects of Intermittent Theta Burst Stimulation of the Cerebellar Vermis on Cerebral Cortical Excitability During a Balance Task in Healthy Individuals: A Pilot Study

Objective: This pilot study aimed to investigate the immediate effects of single-session intermittent theta-burst stimulation (iTBS) on the cerebellar vermis during a balance task, which could unveil the changes of cerebral cortical excitability in healthy individuals.

Subjects: A total of seven right-handed healthy subjects (26.86 ± 5.30 years) were included in this study.

Interventions: Each subject received single-session iTBS on cerebellar vermis in a sitting position.

Main Measures: Before and after the intervention, all subjects were asked to repeat the balance task of standing on the left leg three times. Each task consisted of 15 s of standing and 20 s of resting. Real-time changes in cerebral cortex oxygen concentrations were monitored with functional near-infrared spectroscopy (fNIRS). During the task, changes in blood oxygen concentration were recorded and converted into the mean HbO₂ for statistical analysis.

Results: After stimulation, the mean HbO₂ in the left SMA (P = 0.029) and right SMA (P = 0.043) significantly increased compared with baseline. However, no significant changes of mean HbO₂ were found in the bilateral dorsolateral prefrontal lobe (P > 0.05).

Conclusion: Single-session iTBS on the cerebellar vermis in healthy adults can increase the excitability of the cerebral cortex in the bilateral supplementary motor areas during balance tasks.

Clinical Trial Registration: [www.ClinicalTrials.gov], identifier [ChiCTR2100048915].

Chronic cluster headache: A study of the telencephalic and cerebellar cortical thickness

PURPOSE

Previous studies on brain morphological alterations in chronic cluster headache revealed inconsistent findings.

METHOD

The present cross-sectional explorative study determined telencephalic and cerebellar cortex thickness alterations in a relatively wide sample of chronic cluster headache patients (n = 28) comparing them to matched healthy individuals.

RESULTS

The combination of two highly robust state-of-the-art approaches for thickness estimation (Freesurfer, CERES), strengthened by functional characterization of the identified abnormal regions, revealed four main results: chronic cluster headache patients show 1) cortical thinning in the right middle cingulate cortex, left posterior insula, and anterior cerebellar lobe, regions involved in nociception's sensory and sensory-motor aspects and possibly in autonomic functions; 2) cortical thinning in the left anterior superior temporal sulcus and the left collateral/lingual sulcus, suggesting neuroplastic maladaptation in areas possibly involved in social cognition, which may promote psychiatric comorbidity; 3) abnormal functional connectivity among some of these identified telencephalic areas; 4) the identified telencephalic areas of cortical thinning present robust interaction, as indicated by the functional connectivity results, with the left posterior insula possibly playing a pivotal role.

CONCLUSION

The reported results constitute a coherent and robust picture of the chronic cluster headache brain. Our study paves the way for hypothesis-driven studies that might impact our understanding of the pathophysiology of this condition.

Automated segmentation of deep brain nuclei using convolutional neural networks and susceptibility weighted imaging

The advent of susceptibility-sensitive MRI techniques, such as susceptibility weighted imaging (SWI), has enabled accurate in vivo visualization and quantification of iron deposition within the human brain. Although previous approaches have been introduced to segment iron-rich brain regions, such as the substantia nigra, subthalamic nucleus, red nucleus, and dentate nucleus, these methods are largely unavailable and manual annotation remains the most used approach to label these regions. Furthermore, given their recent success in outperforming other segmentation approaches, convolutional neural networks (CNN) promise better performances. The aim of this study was thus to evaluate state-of-the-art CNN architectures for the labeling of deep brain nuclei from SW images. We implemented five CNN architectures and considered ensembles of these models. Furthermore, a multi-atlas segmentation model was included to provide a comparison not based on CNN. We evaluated two prediction strategies: individual prediction, where a model is trained independently for each region, and combined prediction, which simultaneously predicts multiple closely located regions. In the training dataset, all models performed with high accuracy with Dice coefficients ranging from 0.80 to 0.95. The regional SWI intensities and volumes from the models' labels were strongly correlated with those obtained from manual labels. Performances were reduced on the external dataset, but were higher or comparable to the intrarater reliability and most models achieved significantly better results compared to multi-atlas segmentation. CNNs can accurately capture the individual variability of deep brain nuclei and represent a highly useful tool for their segmentation from SW images.

Unique Morphometric Features of the Cerebellum and Cerebellocerebral Structural Correlation Between Autism Spectrum Disorder and Schizophrenia

Background

Although cerebellar morphological involvement has been increasingly recognized in autism spectrum disorder (ASD) and schizophrenia (SZ), the extent to which there are morphological differences between them has not been definitively quantified. Furthermore, although previous studies have demonstrated increased anatomical cerebellocerebral correlations in both conditions, differences between their associations have not been well characterized.

Methods

We compared cerebellar volume between males with ASD (n = 31), males with SZ (n = 28), and typically developing males (n = 49). A total of 31 cerebellar subregions were investigated with the cerebellum segmented into their constituent lobules, in gray matter (GM) and white matter (WM) separately. Additionally, structural correlations with the contralateral cerebrum were analyzed for each cerebellar lobule.

Results

We found significantly larger WM volume in the bilateral lobules VI and Crus I in the ASD group than in other groups. While WM or GM volumes of these right lobules had positive associations with ASD symptoms, there was a negative association between GM volume of the right Crus I and SZ symptoms. We further observed, in the ASD group specifically, significant correlations between WM of the right lobule VI and WM of the left frontal pole (r = 0.67) and between GM of the right lobule VI and the left caudate (r = 0.60).

Conclusions

Our findings support evidence that cerebellar morphology is involved in ASD and SZ with different mechanisms. Furthermore, this study showed that these biological differences require consideration when determining diagnostic criteria and treatment for these disorders.

Ophthalmic changes in a spaceflight analog are associated with brain functional reorganization

Following long-duration spaceflight, some astronauts exhibit ophthalmic structural changes referred to as Spaceflight Associated Neuro-ocular Syndrome (SANS). Optic disc edema is a common sign of SANS. The origin and effects of SANS are not understood as signs of SANS have not manifested in previous spaceflight analog studies. In the current spaceflight analog study, 11 subjects underwent 30 days of strict head down-tilt bed rest in elevated ambient carbon dioxide (HDBR+CO2 ). Using functional magnetic resonance imaging (fMRI), we acquired resting-state fMRI data at 6 time points: before (2), during (2), and after (2) the HDBR+CO2 intervention. Five participants developed optic disc edema during the intervention (SANS subgroup) and 6 did not (NoSANS group). This occurrence allowed us to explore whether development of signs of SANS during the spaceflight analog impacted resting-state functional connectivity during HDBR+CO2 . In light of previous work identifying genetic and biochemical predictors of SANS, we further assessed whether the SANS and NoSANS subgroups exhibited differential patterns of resting-state functional connectivity prior to the HDBR+CO2 intervention. We found that the SANS and NoSANS subgroups exhibited distinct patterns of resting-state functional connectivity changes during HDBR+CO2 within visual and vestibular-related brain networks. The SANS and NoSANS subgroups also exhibited different resting-state functional connectivity prior to HDBR+CO2 within a visual cortical network and within a large-scale network of brain areas involved in multisensory integration. We further present associations between functional connectivity within the identified networks and previously identified genetic and biochemical predictors of SANS. Subgroup differences in resting-state functional connectivity changes may reflect differential patterns of visual and vestibular reweighting as optic disc edema develops during the spaceflight analog. This finding suggests that SANS impacts not only neuro-ocular structures, but also functional brain organization. Future prospective investigations incorporating sensory assessments are required to determine the functional significance of the observed connectivity differences.

Autoencoder based self-supervised test-time adaptation for medical image analysis

Deep neural networks have been successfully applied to medical image analysis tasks like segmentation and synthesis. However, even if a network is trained on a large dataset from the source domain, its performance on unseen test domains is not guaranteed. The performance drop on data obtained differently from the network's training data is a major problem (known as domain shift) in deploying deep learning in clinical practice. Existing work focuses on retraining the model with data from the test domain, or harmonizing the test domain's data to the network training data. A common practice is to distribute a carefully-trained model to multiple users (e.g., clinical centers), and then each user uses the model to process their own data, which may have a domain shift (e.g., varying imaging parameters and machines). However, the lack of availability of the source training data and the cost of training a new model often prevents the use of known methods to solve user-specific domain shifts. Here, we ask whether we can design a model that, once distributed to users, can quickly adapt itself to each new site without expensive retraining or access to the source training data? In this paper, we propose a model that can adapt based on a single test subject during inference. The model consists of three parts, which are all neural networks: a task model (T) which performs the image analysis task like segmentation; a set of autoencoders (AEs); and a set of adaptors (As). The task model and autoencoders are trained on the source dataset and can be computationally expensive. In the deployment stage, the adaptors are trained to transform the test image and its features to minimize the domain shift as measured by the autoencoders' reconstruction loss. Only the adaptors are optimized during the testing stage with a single test subject thus is computationally efficient. The method was validated on both retinal optical coherence tomography (OCT) image segmentation and magnetic resonance imaging (MRI) T1-weighted to T2-weighted image synthesis. Our method, with its short optimization time for the adaptors (10 iterations on a single test subject) and its additional required disk space for the autoencoders (around 15 MB), can achieve significant performance improvement. Our code is publicly available at: https://github.com/YufanHe/self-domain-adapted-network.

Neuroanatomical norms in the UK Biobank: The impact of allometric scaling, sex, and age

Few neuroimaging studies are sufficiently large to adequately describe population‐wide variations. This study's primary aim was to generate neuroanatomical norms and individual markers that consider age, sex, and brain size, from 629 cerebral measures in the UK Biobank (N = 40,028). The secondary aim was to examine the effects and interactions of sex, age, and brain allometry—the nonlinear scaling relationship between a region and brain size (e.g., total brain volume)—across cerebral measures. Allometry was a common property of brain volumes, thicknesses, and surface areas (83%) and was largely stable across age and sex. Sex differences occurred in 67% of cerebral measures (median |β| = .13): 37% of regions were larger in males and 30% in females. Brain measures (49%) generally decreased with age, although aging effects varied across regions and sexes. While models with an allometric or linear covariate adjustment for brain size yielded similar significant effects, omitting brain allometry influenced reported sex differences in variance. Finally, we contribute to the reproducibility of research on sex differences in the brain by replicating previous studies examining cerebral sex differences. This large‐scale study advances our understanding of age, sex, and brain allometry's impact on brain structure and provides data for future UK Biobank studies to identify the cerebral regions that covary with specific phenotypes, independently of sex, age, and brain size.

A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises

Since its renaissance, deep learning has been widely used in various medical imaging tasks and has achieved remarkable success in many medical imaging applications, thereby propelling us into the so-called artificial intelligence (AI) era. It is known that the success of AI is mostly attributed to the availability of big data with annotations for a single task and the advances in high performance computing. However, medical imaging presents unique challenges that confront deep learning approaches. In this survey paper, we first present traits of medical imaging, highlight both clinical needs and technical challenges in medical imaging, and describe how emerging trends in deep learning are addressing these issues. We cover the topics of network architecture, sparse and noisy labels, federating learning, interpretability, uncertainty quantification, etc. Then, we present several case studies that are commonly found in clinical practice, including digital pathology and chest, brain, cardiovascular, and abdominal imaging. Rather than presenting an exhaustive literature survey, we instead describe some prominent research highlights related to these case study applications. We conclude with a discussion and presentation of promising future directions.

Gender-related neuroanatomical differences in alcohol dependence: findings from the ENIGMA Addiction Working Group

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We tested gender differences in brain volumes of alcohol dependent vs control groups.

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Group differences in brain volumes emerged as gross and widespread.

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Group-by-gender effects emerged in selected brain regions (cerebellum, amygdala)

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In dependent users, greater alcohol use predicted smaller amygdala and larger cerebellum GM volume.

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Our results highlight the need to account for gender differences in MRI studies of alcohol dependence.

Gender-related differences in the susceptibility, progression and clinical outcomes of alcohol dependence are well-known. However, the neurobiological substrates underlying such differences remain unclear. Therefore, this study aimed to investigate gender differences in the neuroanatomy (i.e. regional brain volumes) of alcohol dependence. We examined the volume of a priori regions of interest (i.e., orbitofrontal cortex, hippocampus, amygdala, nucleus accumbens, caudate, putamen, pallidum, thalamus, corpus callosum, cerebellum) and global brain measures (i.e., total grey matter (GM), total white matter (WM) and cerebrospinal fluid). Volumes were compared between 660 people with alcohol dependence (228 women) and 326 controls (99 women) recruited from the ENIGMA Addiction Working Group, accounting for intracranial volume, age and education years. Compared to controls, individuals with alcohol dependence on average had (3–9%) smaller volumes of the hippocampus (bilateral), putamen (left), pallidum (left), thalamus (right), corpus callosum, total GM and WM, and cerebellar GM (bilateral), the latter more prominently in women (right). Alcohol-dependent men showed smaller amygdala volume than control men, but this effect was unclear among women. In people with alcohol dependence, more monthly standard drinks predicted smaller amygdala and larger cerebellum GM volumes. The neuroanatomical differences associated with alcohol dependence emerged as gross and widespread, while those associated with a specific gender may be confined to selected brain regions. These findings warrant future neuroscience research to account for gender differences in alcohol dependence to further understand the neurobiological effects of alcohol dependence.

Replicability, Repeatability, and Long-term Reproducibility of Cerebellar Morphometry

To identify robust and reproducible methods of cerebellar morphometry that can be used in future large-scale structural MRI studies, we investigated the replicability, repeatability, and long-term reproducibility of three fully automated software tools: FreeSurfer, CEREbellum Segmentation (CERES), and automatic cerebellum anatomical parcellation using U-Net with locally constrained optimization (ACAPULCO). Replicability was defined as computational replicability, determined by comparing two analyses of the same high-resolution MRI data set performed with identical analysis software and computer hardware. Repeatability was determined by comparing the analyses of two MRI scans of the same participant taken during two independent MRI sessions on the same day for the Kirby-21 study. Long-term reproducibility was assessed by analyzing two MRI scans of the same participant in the longitudinal OASIS-2 study. We determined percent difference, the image intraclass correlation coefficient, the coefficient of variation, and the intraclass correlation coefficient between two analyses. Our results show that CERES and ACAPULCO use stochastic algorithms that result in surprisingly high differences between identical analyses for ACAPULCO and small differences for CERES. Changes between two consecutive scans from the Kirby-21 study were less than ± 5% in most cases for FreeSurfer and CERES (i.e., demonstrating high repeatability). As expected, long-term reproducibility was lower than repeatability for all software tools. In summary, CERES is an accurate, as demonstrated before, and reproducible tool for fully automated segmentation and parcellation of the cerebellum. We conclude with recommendations for the assessment of replicability, repeatability, and long-term reproducibility in future studies on cerebellar structure.

Multi-Scale Self-Guided Attention for Medical Image Segmentation

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at: https://github.com/sinAshish/Multi-Scale-Attention.

Brain connectivity and behavioral changes in a spaceflight analog environment with elevated CO2

Astronauts are exposed to microgravity and elevated CO₂ levels onboard the International Space Station. Little is known about how microgravity and elevated CO₂ combine to affect the brain and sensorimotor performance during and after spaceflight. Here we examined changes in resting-state functional connectivity (FC) and sensorimotor behavior associated with a spaceflight analog environment. Participants underwent 30 days of strict 6^o head-down tilt bed rest with elevated ambient CO₂ (HDBR+CO₂). Resting-state functional magnetic resonance imaging and sensorimotor assessments were collected 13 and 7 days prior to bed rest, on days 7 and 29 of bed rest, and 0, 5, 12, and 13 days following bed rest. We assessed the time course of FC changes from before, during, to after HDBR+CO₂. We then compared the observed connectivity changes with those of a HDBR control group that underwent HDBR in standard ambient air. Moreover, we assessed associations between post-HDBR+CO₂ FC changes and alterations in sensorimotor performance. HDBR+CO₂ was associated with significant changes in functional connectivity between vestibular, visual, somatosensory and motor brain areas. Several of these sensory and motor regions showed post-HDBR+CO₂ FC changes that were significantly associated with alterations in sensorimotor performance. We propose that these FC changes reflect multisensory reweighting associated with adaptation to the HDBR+CO₂ microgravity analog environment. This knowledge will further improve HDBR as a model of microgravity exposure and contribute to our knowledge of brain and performance changes during and after spaceflight.

Longitudinal analysis of regional cerebellum volumes during normal aging

Some cross-sectional studies suggest reduced cerebellar volumes with aging, but there have been few longitudinal studies of age changes in cerebellar subregions in cognitively healthy older adults. In this work, 2,023 magnetic resonance (MR) images of 822 cognitively normal participants from the Baltimore Longitudinal Study of Aging (BLSA) were analyzed. Participants ranged in age from 50 to 95 years (mean 70.7 years) at the baseline assessment. Follow-up intervals were 1-9 years (mean 3.7 years) for participants with two or more visits. We used a recently developed cerebellum parcellation algorithm based on convolutional neural networks to divide the cerebellum into 28 subregions. Linear mixed effects models were applied to the volume of each cerebellar subregion to investigate cross-sectional and longitudinal age effects, as well as effects of sex and their interactions, after adjusting for intracranial volume. Our findings suggest spatially varying atrophy patterns across the cerebellum with respect to age and sex both cross-sectionally and longitudinally.

Automatic cerebellum anatomical parcellation using U-Net with locally constrained optimization

The cerebellum plays a central role in sensory input, voluntary motor action, and many neuropsychological functions and is involved in many brain diseases and neurological disorders. Cerebellar parcellation from magnetic resonance images provides a way to study regional cerebellar atrophy and also provides an anatomical map for functional imaging. In a recent comparison, a multi-atlas approach proved to be superior to other parcellation methods including some based on convolutional neural networks (CNNs) which have a considerable speed advantage. In this work, we developed an alternative CNN design for cerebellar parcellation, yielding a method that achieves the leading performance to date. The proposed method was evaluated on multiple data sets to show its broad applicability, and a Singularity container has been made publicly available.

A Comprehensive Approach to Disentangle the Effect of Cerebellar Damage on Physical Disability in Multiple Sclerosis

Cerebellar damage occurs frequently in multiple sclerosis (MS) patients, with a wide exhibition of symptoms particularly as impairments of balance and gait. Recent studies implementing new postprocessing magnetic resonance imaging (MRI) techniques showed how cerebellar subregional atrophy provides an explanation of disability in MS. The aim of this work was to evaluate the relationship between quantitative measures of physical disability, cerebellar subregional atrophy, and cerebellar peduncle disruption. Forty-nine MS patients and 32 healthy subjects as controls (HS) underwent a 3-Tesla MRI including 3D T1-weighted and diffusion tensor imaging. Patients underwent static posturography to calculate the body's center of pressure (COP) displacement, Expanded Disability Status Scale (EDSS), and 25-ft walking test (25-FWT). Cerebellar lobular volumes were automatically calculated using the Spatially Unbiased Infratentorial Toolbox. Tract-based spatial statistics (TBSS) in FSL was used to process diffusion tensor imaging (DTI) Fit-generated fractional anisotropy (FA) maps to assess structural connectivity of cerebellar peduncles. Stepwise multivariate linear regression analyses were used to explore relationships between variables. Cerebellar volumes (anterior and posterior, as well as lobular volumes from I to X) were significantly lower in patients with MS than HS (p < 0.05). FA in all cerebellar peduncles was lower in MS patients than in HS (p < 0.05). EDSS and 25-FWT showed an association with atrophy of lobule VIIIb (β = −0.37, p < 0.01, and β = −0.45, p < 0.001, respectively) COP measures inversely correlated with volume of lobules I–IV (β = −0.37, p < 0.01, and β = −0.36, p < 0.01). Lower FA in the three cerebellar peduncles of MS patients positively correlated with cerebellar lobular volumes. Our findings show how sensorimotor cerebellum atrophy and disruption of both afferent and efferent cerebellar connections contribute to physical disability in MS patients.

Deep Cerebellar Nuclei Segmentation via Semi-Supervised Deep Context-Aware Learning from 7T Diffusion MRI

Deep cerebellar nuclei are a key structure of the cerebellum that are involved in processing motor and sensory information. It is thus a crucial step to accurately segment deep cerebellar nuclei for the understanding of the cerebellum system and its utility in deep brain stimulation treatment. However, it is challenging to clearly visualize such small nuclei under standard clinical magnetic resonance imaging (MRI) protocols and therefore precise segmentation is not feasible. Recent advances in 7 Tesla (T) MRI technology and great potential of deep neural networks facilitate automatic patient-specific segmentation. In this paper, we propose a novel deep learning framework (referred to as DCN-Net) for fast, accurate, and robust patient-specific segmentation of deep cerebellar dentate and interposed nuclei on 7T diffusion MRI. DCN-Net effectively encodes contextual information on the patch images without consecutive pooling operations and adding complexity via proposed dilated dense blocks. During the end-to-end training, label probabilities of dentate and interposed nuclei are independently learned with a hybrid loss, handling highly imbalanced data. Finally, we utilize self-training strategies to cope with the problem of limited labeled data. To this end, auxiliary dentate and interposed nuclei labels are created on unlabeled data by using DCN-Net trained on manual labels. We validate the proposed framework using 7T B0 MRIs from 60 subjects. Experimental results demonstrate that DCN-Net provides better segmentation than atlas-based deep cerebellar nuclei segmentation tools and other state-of-the-art deep neural networks in terms of accuracy and consistency. We further prove the effectiveness of the proposed components within DCN-Net in dentate and interposed nuclei segmentation.

Cerebellar degeneration in adult spinal muscular atrophy patients

BACKGROUND

Spinal muscular atrophy (SMA) is a genetic motor neuron disease related to deletions in the SMN1 gene. There is mounting evidence that the disease is not restricted to motor neurons. In this neuroimaging study, we aimed to investigate the presence of in-vivo cerebellar damage in adult SMA patients not treated with disease-modifying treatment.

METHODS

Twenty-five molecularly confirmed patients with SMA type III or IV and 25 healthy controls underwent MRI with cerebellar focused structural analysis by the CERES automated pipeline. Volumetry (total and gray matter-GM) as well as cortical thickness of the cerebellar lobules were compared in both groups. Full clinical and demographic data were then assessed for correlations with cerebellar imaging findings.

RESULTS

Volumes of cerebellar lobules VIIIB (right), IX and X were significantly smaller in patients with SMA. Lobule IX also had GM atrophy in comparison to controls. We found no significant correlation between clinical findings and cerebellar damage.

CONCLUSIONS

Neuroimaging detects cerebellar structural changes in adult SMA patients, suggesting that neurodegeneration is not confined to the lower motor neurons in the disease.

Structural Correlates of the Sensorimotor Cerebellum in Parkinson's Disease and Essential Tremor

BACKGROUND

Parkinson's disease (PD) and essential tremor (ET) are commonly encountered movement disorders. Pathophysiologic processes that localize to the cerebellum are described in both. There are limited studies investigating cerebellar structural changes in these conditions, largely because of inherent challenges in the efficiency of segmentation.

METHODS

We applied a novel multiatlas cerebellar segmentation method to T1-weighted images in 282 PD and 111 essential tremor patients to define 26 cerebellar lobule volumes. The severity of postural and resting tremor in both populations and gait and postural instability in PD patients were defined using subscores of the UPDRS and Washington Heights-Inwood Genetic Study motor scales. These clinical measurements were related to lobule volume size. Multiple comparisons were controlled using a false discovery rate method.

RESULTS

Group differences were identified between ET and PD patients, with reductions in deep cerebellar nucleus volume in ET versus reduced lobule VI volume in PD. In ET patients, lobule VIII was negatively correlated with the severity of postural tremor. In PD patients, lobule IV was positively correlated with resting tremor and total tremor severity. We observed differences in cerebellar structure that localized to sensorimotor lobules of the cerebellum. Lobule volumes appeared to differentially relate to clinical symptoms, suggesting important clinicopathologic distinctions between these conditions. These results emphasize the role of the cerebellum in tremor symptoms and should foster future clinical and pathologic investigations of the sensorimotor lobules of the cerebellum. © 2020 International Parkinson and Movement Disorder Society.

Graded Cerebellar Lobular Volume Deficits in Adolescents and Young Adults with Fetal Alcohol Spectrum Disorders (FASD)

The extensive prenatal developmental growth period of the cerebellum renders it vulnerable to unhealthy environmental agents, especially alcohol. Fetal alcohol spectrum disorders (FASD) is marked by neurodysmorphology including cerebral and cerebellar volume deficits, but the cerebellar lobular deficit profile has not been delineated. Legacy MRI data of 115 affected and 59 unaffected adolescents and young adults were analyzed for lobular gray matter volume and revealed graded deficits supporting a spectrum of severity. Graded deficits were salient in intracranial volume (ICV), where the fetal alcohol syndrome (FAS) group was smaller than the fetal alcohol effects (FAE) group, which was smaller than the controls. Adjusting for ICV, volume deficits were present in VIIB and VIIIA of the FAE group and were more widespread in FAS and included lobules I, II, IV, V, VI, Crus II, VIIB, and VIIIA. Graded deficits (FAS < FAE) were consistently present in lobules VI; neither group showed volume deficits in Crus I or IX. Neuroradiological readings blind to diagnosis identified 20 anomalies, 8 involving the cerebellum, 5 of which were in the FAS group. We speculate that the regional cerebellar FASD-related volume deficits may contribute to diagnostically characteristic functional impairment involving emotional control, visuomotor coordination, and postural stability.

Volumetric reduction of cerebellar lobules associated with memory decline across the adult lifespan

Background

The human cerebellum plays an essential role in motor control, is involved in cognitive function and helps to regulate emotional responses. However, little is known about the relationship between cerebellar lobules and age-related memory decline. We aimed to investigate volume alterations in cerebellar lobules at different ages and assess their correlations with reduced memory recall abilities.

Methods

A sample of 275 individuals were divided into the following four groups: 20-35 years (young), 36-50 years (early-middle age), 51-65 years (late-middle age), and 66-89 years (old). Volumes of the cerebellar lobules were obtained using volBrain software. Analysis of covariance and post hoc analysis were used to analyze group differences in cerebellar lobular volumes, and multiple comparisons were performed using the Bonferroni method. Spearman correlation was used to investigate the relationship between lobular volumes and memory recall scores.

Results

In this study, we found that older adults had smaller cerebellar volumes than the other subjects. Volumetric decreases in size were noted in bilateral lobule VI and lobule crus I. Moreover, the volumes of bilateral lobule crus I, lobule VI, and right lobule IV were significantly associated with memory recall scores.

Conclusions

In the present study, we found that some lobules of the cerebellum appear more predisposed to age-related changes than other lobules. These findings provide further evidence that specific regions of the cerebellum could be used to assess the risk of memory decline across the adult lifespan.

Deep CNN ensembles and suggestive annotations for infant brain MRI segmentation

Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive volumetric studies and quantitative analysis of early brain development. However, computing such segmentations is very challenging, especially for 6-month infant brain, due to the poor image quality, among other difficulties inherent to infant brain MRI, e.g., the isointense contrast between white and gray matter and the severe partial volume effect due to small brain sizes. This study investigates the problem with an ensemble of semi-dense fully convolutional neural networks (CNNs), which employs T1-weighted and T2-weighted MR images as input. We demonstrate that the ensemble agreement is highly correlated with the segmentation errors. Therefore, our method provides measures that can guide local user corrections. To the best of our knowledge, this work is the first ensemble of 3D CNNs for suggesting annotations within images. Our quasi-dense architecture allows the efficient propagation of gradients during training, while limiting the number of parameters, requiring one order of magnitude less parameters than popular medical image segmentation networks such as 3D U-Net (Çiçek, et al.). We also investigated the impact that early or late fusions of multiple image modalities might have on the performances of deep architectures. We report evaluations of our method on the public data of the MICCAI iSEG-2017 Challenge on 6-month infant brain MRI segmentation, and show very competitive results among 21 teams, ranking first or second in most metrics.

SUITer: An Automated Method for Improving Segmentation of Infratentorial Structures at Ultra-High-Field MRI

BACKGROUND AND PURPOSE

The advent of high and ultra-high-field MRI has significantly improved the investigation of infratentorial structures by providing high-resolution images. However, none of the publicly available methods for cerebellar image analysis has been optimized for high-resolution images yet.

METHODS

We present the implementation of an automated algorithm-SUITer (spatially unbiased infratentorial for enhanced resolution) method for cerebellar lobules parcellation on high-resolution MR images acquired at both 3 and 7T MRI. SUITer was validated on five manually segmented data and compared with SUIT, FreeSurfer, and convolutional neural networks (CNN). SUITer was then applied to 3 and 7T MR images from 10 multiple sclerosis (MS) patients and 10 healthy controls (HCs).

RESULTS

The difference in volumes estimation for the cerebellar grey matter (GM), between the manual segmentation (ground truth), SUIT, CNN, and SUITer was reduced when computed by SUITer compared to SUIT (5.56 vs. 29.23 mL) and CNN (5.56 vs. 9.43 mL). FreeSurfer showed low volumes difference (3.56 mL). SUITer segmentations showed a high correlation (R² = .91) and a high overlap with manual segmentations for cerebellar GM (83.46%). SUITer also showed low volumes difference (7.29 mL), high correlation (R² = .99), and a high overlap (87.44%) for cerebellar GM segmentations across magnetic fields. SUITer showed similar cerebellar GM volume differences between MS patients and HC at both 3T and 7T (7.69 and 7.76 mL, respectively).

CONCLUSIONS

SUITer provides accurate segmentations of infratentorial structures across different resolutions and MR fields.