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

Faber, Jennifer; Kügler, David; Emad, Bahrami,; Heinz, Lea-Sophie; Timmann, Dagmar; Ernst, Thomas; Deike-Hofmann, Katerina; Klockgether, Thomas; Warrenburg, Bart van de; Gaalen, Judith van; Reetz, Kathrin; Romanzetti, Sandro; Öz, Gülin; Joers, James M.; Diedrichsen, Jörn; Group, ESMMR Study; Reuter, Martin

doi:10.1016/j.neuroimage.2022.119703

Cited by 24 publications

(27 citation statements)

References 62 publications

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“…T1-weighted MRIs were acquired using a magnetization prepared rapid gradient-echo sequence (MPRAGE, TR = 2500 ms, TE = 4.37 ms, TI = 1100 ms, flip angle = 7 deg, FOV 256 mm x 256 mm, 192 slices with a voxel size of 1 mm isotropic) on Siemens 3T scanners (Siemens Medical Systems, Erlangen, Germany). Volumes of the pons 15 , cerebellar white matter (CWM) and cerebellar grey matter (CGM) 12 were measured and normalized by each participants total intracranial volume.…”

Section: Assessmentsmentioning

confidence: 99%

“…These markers reflect key pathological changes of SCA3 and are known to be abnormal before onset of ataxia. [4][5][6][7][10][11][12] To assess the presence and severity of ataxia, we used the Scale for the Assessment and Rating of Ataxia (SARA). 13 Our analysis allowed to propose a staging model of SCA3 based on changes of SARA and the biomarkers under study.…”

Section: Introductionmentioning

confidence: 99%

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Stage-dependent biomarker changes in spinocerebellar ataxia type 3

Faber

Berger

Wilke

et al. 2023

Preprint

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Spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3) is the most common autosomal dominant ataxia. In view of the development of targeted therapies for SCA3, precise knowledge of stage-dependent fluid and MRI biomarker changes is needed. We analyzed cross-sectional data of 292 SCA3 mutation carriers including 57 pre-ataxic individuals, and 108 healthy controls from the European Spinocerebellar ataxia type 3/Machado-Joseph Disease Initiative (ESMI) cohort. Blood concentrations of mutant ATXN3 and neurofilament light (NfL) were determined, and volumes of pons, cerebellar white matter (CWM) and cerebellar grey matter (CGM) were measured on MRI. Mutant ATXN3 concentrations were high before and after ataxia onset, while NfL continuously increased and deviated from normal 11.9 years before onset. Pons and CWM volumes decreased, but the deviation from normal was only 2.0 years (pons) and 0.3 years (CWM) before ataxia onset. We propose a staging model of SCA3 that includes an initial asymptomatic carrier stage followed by the biomarker stage defined by absence of ataxia, but a significant rise of NfL. The biomarker stage leads into the ataxia stage, defined by manifest ataxia. The present analysis provides a robust framework for further studies aiming at elaboration and differentiation of the staging model of SCA3.

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Section: Assessmentsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Stage-dependent biomarker changes in spinocerebellar ataxia type 3

Faber

Berger

Wilke

et al. 2023

Preprint

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“…Volumes of the basal ganglia, namely caudate, putamen and pallidum, thalamus and brainstem volumes midbrain, pons and medulla oblongata as well as the estimated total intracranial volume (eTIV) were assessed in the N4biasfield (ants, version 2.1) 43 corrected T1w MRI using FreeSurfer (version 6.0) 44,45 . Cerebellar subsegmentation was performed using CerebNet resulting in 25 cerebellar cortical and two hemispheric cerebellar white matter labels, which were combined to the total cerebellar gray matter and the total cerebellar white matter (CWM) 46 . All volumes were divided by eTIV, and subsequent statistical analyses were based on these relative values.…”

Section: Methodsmentioning

confidence: 99%

“…44,45 Cerebellar subsegmentation was performed using CerebNet resulting in 25 cerebellar cortical and two hemispheric cerebellar white matter labels, which were combined to the total cerebellar gray matter and the total cerebellar white matter (CWM). 46 All volumes were divided by eTIV, and subsequent statistical analyses were based on these relative values.…”

Section: Mrimentioning

confidence: 99%

Evolution of Clinical Outcome Measures and Biomarkers in Sporadic Adult‐Onset Degenerative Ataxia

et al. 2023

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A BS TRACT: Background: Sporadic adult-onset ataxias without known genetic or acquired cause are subdivided into multiple system atrophy of cerebellar type (MSA-C) and sporadic adult-onset ataxia of unknown etiology (SAOA). Objectives: To study the differential evolution of both conditions including plasma neurofilament light chain (NfL) levels and magnetic resonance imaging (MRI) markers. Methods: SPORTAX is a prospective registry of sporadic ataxia patients with an onset >40 years. Scale for the Assessment and Rating of Ataxia was the primary outcome measure. In subgroups, blood samples were taken and MRIs performed. Plasma NfL was measured via a single molecule assay. Regional brain volumes were automatically measured. To assess signal changes, we defined the pons and middle cerebellar peduncle abnormality score (PMAS). Using mixed-effects models, we analyzed changes on a time scale starting with ataxia onset. Results: Of 404 patients without genetic diagnosis, 130 met criteria of probable MSA-C at baseline and 26 during follow-up suggesting clinical conversion to MSA-C. The remaining 248 were classified as SAOA. At

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“…Technically, more precise segmentation approaches have been applied to cerebellar subfields ( 66 ). However, diverse novel methods ( 95 ) have only been applied in limited studies, which do not have enough quantity to conduct a meta-analysis. Second, we only concentrated on the significant cerebellar changes that have been reported, and we omitted the results with no significance in the VBM studies.…”

Section: Limitationsmentioning

confidence: 99%

Cerebellar gray matter volume changes in patients with schizophrenia: A voxel-based meta-analysis

Liu

Yang

et al. 2022

Front. Psychiatry

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BackgroundIn schizophrenia, the structural changes in the cerebellum are associated with patients’ cognition and motor deficits. However, the findings are inconsistent owing to the heterogeneity in sample size, magnetic resonance imaging (MRI) scanners, and other factors among them. In this study, we conducted a meta-analysis to characterize the anatomical changes in cerebellar subfields in patients with schizophrenia.MethodsSystematic research was conducted to identify studies that compare the gray matter volume (GMV) differences in the cerebellum between patients with schizophrenia and healthy controls with a voxel-based morphometry (VBM) method. A coordinate-based meta-analysis was adopted based on seed-based d mapping (SDM) software. An exploratory meta-regression analysis was conducted to associate clinical and demographic features with cerebellar changes.ResultsOf note, 25 studies comprising 996 patients with schizophrenia and 1,109 healthy controls were included in the present meta-analysis. In patients with schizophrenia, decreased GMVs were demonstrated in the left Crus II, right lobule VI, and right lobule VIII, while no increased GMV was identified. In the meta-regression analysis, the mean age and illness duration were negatively associated with the GMV in the left Crus II in patients with schizophrenia.ConclusionThe most significant structural changes in the cerebellum are mainly located in the posterior cerebellar hemisphere in patients with schizophrenia. The decreased GMVs of these regions might partly explain the cognitive deficits and motor symptoms in patients with schizophrenia.

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

Cited by 24 publications

References 62 publications

Stage-dependent biomarker changes in spinocerebellar ataxia type 3

Stage-dependent biomarker changes in spinocerebellar ataxia type 3

Evolution of Clinical Outcome Measures and Biomarkers in Sporadic Adult‐Onset Degenerative Ataxia

Cerebellar gray matter volume changes in patients with schizophrenia: A voxel-based meta-analysis

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