Non-linear realignment improves hippocampus subfield segmentation reliability

Shaw, Thomas; Bollmann, Steffen; Atcheson, Nicole; Strike, Lachlan T.; Guo, Christine; McMahon, Katie L.; Fripp, Jürgen; Wright, Margaret J.; Salvado, Olivier; Barth, Markus

doi:10.1016/j.neuroimage.2019.116206

Cited by 13 publications

(8 citation statements)

References 35 publications

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“…A single-subject template (SST) was then created using the ANTs template construction pipeline ( 66 ). This template represented the average morphology of the time series, which ensured an equally biased registration to each time point ( 65 ), which was also shown to increase segmentation consistency ( 67 ). Second, manual annotated labels based on 20 individual expert labels ( 68 ) were transformed into the SST image space ( 69 ).…”

Section: Methodsmentioning

confidence: 99%

Iron Rims in Patients With Multiple Sclerosis as Neurodegenerative Marker? A 7-Tesla Magnetic Resonance Study

Dal‐Bianco¹,

Schranzer

Gräβner

et al. 2021

Front. Neurol.

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Introduction: Multiple sclerosis (MS) is a demyelinating and neurodegenerative disease of the central nervous system, characterized by inflammatory-driven demyelination. Symptoms in MS manifest as both physical and neuropsychological deficits. With time, inflammation is accompanied by neurodegeneration, indicated by brain volume loss on an MRI. Here, we combined clinical, imaging, and serum biomarkers in patients with iron rim lesions (IRLs), which lead to severe tissue destruction and thus contribute to the accumulation of clinical disability.Objectives: Subcortical atrophy and ventricular enlargement using an automatic segmentation pipeline for 7 Tesla (T) MRI, serum neurofilament light chain (sNfL) levels, and neuropsychological performance in patients with MS with IRLs and non-IRLs were assessed.Methods: In total 29 patients with MS [15 women, 24 relapsing-remitting multiple sclerosis (RRMS), and five secondary-progressive multiple sclerosis (SPMS)] aged 38 (22–69) years with an Expanded Disability Status Score of 2 (0–8) and a disease duration of 11 (5–40) years underwent neurological and neuropsychological examinations. Volumes of lesions, subcortical structures, and lateral ventricles on 7-T MRI (SWI, FLAIR, and MP2RAGE, 3D Segmentation Software) and sNfL concentrations using the Simoa SR-X Analyzer in IRL and non-IRL patients were assessed.Results: (1) Iron rim lesions patients had a higher FLAIR lesion count (p = 0.047). Patients with higher MP2Rage lesion volume exhibited more IRLs (p <0.014) and showed poorer performance in the information processing speed tested within 1 year using the Symbol Digit Modalities Test (SDMT) (p <0.047). (2) Within 3 years, patients showed atrophy of the thalamus (p = 0.021) and putamen (p = 0.043) and enlargement of the lateral ventricles (p = 0.012). At baseline and after 3 years, thalamic volumes were lower in IRLs than in non-IRL patients (p = 0.045). (3) At baseline, IRL patients had higher sNfL concentrations (p = 0.028). Higher sNfL concentrations were associated with poorer SDMT (p = 0.004), regardless of IRL presence. (4) IRL and non-IRL patients showed no significant difference in the neuropsychological performance within 1 year.Conclusions: Compared with non-IRL patients, IRL patients had higher FLAIR lesion counts, smaller thalamic volumes, and higher sNfL concentrations. Our pilot study combines IRL and sNfL, two biomarkers considered indicative for neurodegenerative processes. Our preliminary data underscore the reported destructive nature of IRLs.

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Section: Methodsmentioning

confidence: 99%

Iron Rims in Patients With Multiple Sclerosis as Neurodegenerative Marker? A 7-Tesla Magnetic Resonance Study

Dal‐Bianco¹,

Schranzer

Gräβner

et al. 2021

Front. Neurol.

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“…By averaging multiple low SNR images, we obtained virtually noise free sharp images (Shaw et al, 2019), without the need for additional in scanner hardware. The key lies in sophisticated post-processing, the increased availability of powerful computation hardware and image analysis software, notably the ANTs, FSL and MRtrix packages.…”

Section: Discussionmentioning

confidence: 99%

HumanBrainAtlas: an in vivo MRI dataset for detailed segmentations

Schira

Isherwood

Kassem

et al. 2022

Preprint

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We introduce HumanBrainAtlas, an initiative to construct a highly detailed, open-access atlas of the living human brain that combines high-resolution in vivo MR imaging and detailed segmentations previously possible only in histological preparations. Here, we present and evaluate the first step of this initiative: a comprehensive dataset of two healthy male volunteers reconstructed to a 0.25 mm3 isotropic resolution for T1w, T2w and DWI contrasts. Multiple high-resolution acquisitions were collected for each contrast and each participant, followed by averaging using symmetric group-wise normalisation (Advanced Normalisation Tools). The resulting image quality permits structural parcellations rivalling histology-based atlases, while maintaining the advantages of in vivo MRI. For example, components of the thalamus, hypothalamus, and hippocampus - difficult or often impossible to identify using standard MRI protocols, can be identified within the present data. Our data are virtually distortion free, fully 3D, and compatible with existing in vivo Neuroimaging analysis tools. The dataset is suitable for teaching and is publicly available via our website (www.hba.neura.edu.au), which also provides data processing scripts. Instead of focusing on coordinates in an averaged brain space, our approach focuses on providing an example segmentation at great detail in the high quality individual brain, this serves as an illustration on what features contrasts and relations can be used to interpret MRI datasets, in research, clinical and education settings.

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“…Another approach is to remove background noise from the MP2RAGE uniform image using the inversion time images (https://github.com/JosePMarques/MP2RAGE-related-scripts). Multiple TSE scans were collected to average the TSE runs to improve image quality; see Shaw et al 122 for implementation of TSE alignment and averaging using the QTAB dataset.…”

Section: Usage Notesmentioning

confidence: 99%

“…Multiple TSE scans were collected to average the TSE runs to improve image quality; see Shaw et al 130 for implementation of TSE alignment and averaging using the QTAB dataset. Two participants (twin pair sub-0109 and sub-0113) required an increased number of slices for their session 1 structural scans (T1w, T2w, FLAIR) for adequate brain coverage.…”

Section: Miscellaneous Imagingmentioning

confidence: 99%

The Queensland Twin Adolescent Brain Project, a longitudinal study of adolescent brain development

Strike

Hansell

Chuang

et al. 2022

Preprint

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We describe the Queensland Twin Adolescent Brain (QTAB) dataset and provide a detailed methodology and technical validation to facilitate data usage. The QTAB dataset comprises multimodal neuroimaging, as well as cognitive and mental health data collected in adolescent twins over two sessions (session 1: N = 422, age 9-14 years; session 2: N = 304, 10-16 years). The MRI protocol consisted of T1-weighted (MP2RAGE), T2-weighted, FLAIR, high-resolution TSE, SWI, resting-state fMRI, DWI, and ASL scans. Two fMRI tasks were added in session 2 to probe emotion-relevant neural processes (emotional conflict task) and evoke activity in the Theory of Mind network (passive movie watching task). Outside of the scanner, we assessed cognitive function using standardised tests. We also obtained self-reports of symptoms for anxiety and depression, perceived stress, sleepiness, pubertal development measures, and risk and protective factors. We additionally collected several biological samples for genomic and metagenomic analysis. The QTAB project was established to promote health-related research in adolescence.

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Non-linear realignment improves hippocampus subfield segmentation reliability

Cited by 13 publications

References 35 publications

Iron Rims in Patients With Multiple Sclerosis as Neurodegenerative Marker? A 7-Tesla Magnetic Resonance Study

Iron Rims in Patients With Multiple Sclerosis as Neurodegenerative Marker? A 7-Tesla Magnetic Resonance Study

HumanBrainAtlas: an in vivo MRI dataset for detailed segmentations

The Queensland Twin Adolescent Brain Project, a longitudinal study of adolescent brain development

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