4.6 Article

Brain Extraction Using Label Propagation and Group Agreement: Pincram

Journal

PLOS ONE
Volume 10, Issue 7, Pages -

Publisher

PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pone.0129211

Keywords

-

Funding

  1. National Institutes of Health [P50 AG05681, P01 AG03991, R01 AG021910, P50 MH071616, U24 RR021382, R01 MH56584]
  2. MRC [MR/K006355/1] Funding Source: UKRI
  3. Medical Research Council [MR/K006355/1] Funding Source: researchfish

Ask authors/readers for more resources

Accurately delineating the brain on magnetic resonance (MR) images of the head is a prerequisite for many neuroimaging methods. Most existing methods exhibit disadvantages in that they are laborious, yield inconsistent results, and/or require training data to closely match the data to be processed. Here, we present pincram, an automatic, versatile method for accurately labelling the adult brain on T1-weighted 3D MR head images. The method uses an iterative refinement approach to propagate labels from multiple atlases to a given target image using image registration. At each refinement level, a consensus label is generated. At the subsequent level, the search for the brain boundary is constrained to the neighbourhood of the boundary of this consensus label. The method achieves high accuracy (Jaccard coefficient > 0.95 on typical data, corresponding to a Dice similarity coefficient of > 0.97) and performs better than many state-of-the-art methods as evidenced by independent evaluation on the Segmentation Validation Engine. Via a novel self-monitoring feature, the program generates the success index, a scalar metadatum indicative of the accuracy of the output label. Pincram is available as open source software.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.6
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

Article Clinical Neurology

Metabolic patterns in brain 18F-fluorodeoxyglucose PET relate to aetiology in paediatric dystonia

Stavros Tsagkaris, Eric K. C. Yau, Verity McClelland, Apostolos Papandreou, Ata Siddiqui, Daniel E. Lumsden, Margaret Kaminska, Eric Guedj, Alexander Hammers, Jean-Pierre Lin

Summary: Tsagkaris et al. found that patients with paediatric dystonia have different patterns of brain glucose metabolism observed through FDG-PET scans. These patterns can be linked to specific clinical signs and may serve as useful biomarkers for differential diagnosis and personalized management. The study sheds light on the pathophysiology of dystonia and supports the network theory for its development.

BRAIN (2023)

Letter Clinical Neurology

Pseudo-CTs from T1-weighted MRI for planning of low-intensity transcranial focused ultrasound neuromodulation: An open-source tool

Siti N. Yaakub, Tristan A. White, Eric Kerfoot, Lennart Verhagen, Alexander Hammers, Elsa F. Fouragnan

BRAIN STIMULATION (2023)

Article Neurosciences

Development of neonatal brain functional centrality and alterations associated with preterm birth

Sunniva Fenn-Moltu, Sean P. Fitzgibbon, Judit Ciarrusta, Michael Eyre, Lucilio Cordero-Grande, Andrew Chew, Shona Falconer, Oliver Gale-Grant, Nicholas Harper, Ralica Dimitrova, Katy Vecchiato, Daphna Fenchel, Ayesha Javed, Megan Earl, Anthony N. Price, Emer Hughes, Eugene P. Duff, Jonathan O'Muircheartaigh, Chiara Nosarti, Tomoki Arichi, Daniel Rueckert, Serena Counsell, Joseph Hajnal, A. David Edwards, Grainne McAlonan, Dafnis Batalle

Summary: The formation of the functional connectome in early life is crucial for future learning and behavior. However, our understanding of how the functional organization of brain regions matures during the early postnatal period, especially in response to adverse neurodevelopmental outcomes like preterm birth, is limited. In this study involving 366 neonates, we found that functional centrality (weighted degree) increased with age in visual regions and decreased in motor and auditory regions in term-born infants. Preterm-born infants scanned at term equivalent age showed higher functional centrality in visual regions and lower measures in motor regions. Functional centrality did not predict neurodevelopmental outcomes at 18 months old.

CEREBRAL CORTEX (2023)

Article Engineering, Electrical & Electronic

A Novel Ultrasound Robot With Force/Torque Measurement and Control for Safe and Efficient Scanning

Xianqiang Bao, Shuangyi Wang, Lingling Zheng, Richard James Housden, Joseph V. Hajnal, Kawal Rhode

Summary: This article proposes an ultrasound robot that integrates force control, force/torque measurement, and online adjustment mechanisms to address the concerns in medical ultrasound. The robot can measure, adjust, and eliminate operating forces, and achieve various scanning depths based on clinical requirements. Simulations and experiments show that the robot performs well in detecting forces and torques, maintaining constant operating force, and achieving different scanning depths.

IEEE TRANSACTIONS ON INSTRUMENTATION AND MEASUREMENT (2023)

Article Acoustics

3-D Coherent Multitransducer Ultrasound Imaging With Sparse Spiral Arrays

Laura Peralta, Daniele Mazierli, Alberto Gomez, Joseph Hajnal, Piero Tortoli, Alessandro Ramalli

Summary: Coherent multitransducer ultrasound (CoMTUS) utilizes the coherent combination of multiple arrays to create an extended effective aperture, resulting in improved resolution, field-of-view, and sensitivity in images. This study demonstrates the feasibility of implementing CoMTUS in 3-D imaging using a pair of 256-element 2-D sparse spiral arrays, which reduces channel count and data processing. The imaging performance of CoMTUS is investigated using simulations, phantom tests, and experimental free-hand operation, showing significant improvements in spatial resolution, contrast-to-noise ratio, and generalized CNR compared to a single dense array system.

IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL (2023)

Article Radiology, Nuclear Medicine & Medical Imaging

Simultaneous Optimization of MP2RAGE T1-weighted (UNI) and FLuid And White matter Suppression (FLAWS) brain images at 7T using Extended Phase Graph (EPG) Simulations

Ayse Sila Dokumaci, Fraser R. Aitken, Jan Sedlacik, Pip Bridgen, Raphael Tomi-Tricot, Ronald Mooiweer, Katy Vecchiato, Tom Wilkinson, Chiara Casella, Sharon Giles, Joseph Hajnal, Shaihan J. Malik, Jonathan O'Muircheartaigh, David W. Carmichael

Summary: In this study, an optimized MP2RAGE protocol at 7 Tesla was developed to provide T1-weighted uniform image and gray matter-dominant fluid and white matter suppression contrast images simultaneously in a clinically applicable acquisition time. The results showed that high-contrast images with excellent anatomical detail could be obtained using the optimized parameter set.

MAGNETIC RESONANCE IN MEDICINE (2023)

Letter Anesthesiology

Reliability and safety of anaesthetic equipment around an high-field 7-Tesla MRI scanner

Philippa Bridgen, Shaihan Malik, Thomas Wilkinson, John N. Cronin, Tahzeeb Bhagat, Nicholas Hart, Stuart Mc Corkell, Joanne Perkins, Shane Tibby, Sara Hanna, Richard Kirwan, Thomas Pauly, Arthur Weeks, Geoff Charles-Edwards, Francesco Padormo, David Stell, Kariem El-Boghdadly, Sebastien Ourselin, Sharon L. Giles, Anthony D. Edwards, Joseph V. Hajnal, Benjamin J. Blaise

BRITISH JOURNAL OF ANAESTHESIA (2023)

Article Neurosciences

Comprehensive volumetric phenotyping of the neonatal brain in Down syndrome

Abi Fukami-Gartner, Ana A. Baburamani, Ralica Dimitrova, Prachi A. Patkee, Olatz Ojinaga-Alfageme, Alexandra F. Bonthrone, Daniel Cromb, Alena U. Uus, Serena J. Counsell, Joseph Hajnal, Jonathan O'Muircheartaigh, Mary A. Rutherford

Summary: Down syndrome (DS) is a common genetic cause of intellectual disability. In this study, researchers analyzed the brain volumes of neonates with DS using neuroimaging techniques. They found that the DS brain showed significant reductions in overall volume, cerebral white matter, and cerebellar volumes, as well as differences in relative lobar volumes. Furthermore, certain features such as enlarged deep gray matter volume and lateral ventricle enlargement were observed. Assessing phenotypic severity at the neonatal stage may help guide early interventions and improve neurodevelopmental outcomes in children with DS.

CEREBRAL CORTEX (2023)

Article Neurosciences

Automatic and manual segmentation of the piriform cortex: Method development and validation in patients with temporal lobe epilepsy and Alzheimer's disease

David Steinbart, Siti N. Yaakub, Mirja Steinbrenner, Lynn S. Guldin, Martin Holtkamp, Simon S. Keller, Bernd Weber, Theodor Rueber, Rolf Heckemann, Maria Ilyas-Feldmann, Alexander Hammers

Summary: This study proposes a manual segmentation protocol and an automatic segmentation method to investigate the relationship between the piriform cortex and memory as well as epilepsy. The results show differences in the volumes of the piriform cortex in healthy individuals, temporal lobe epilepsy patients, and Alzheimer's disease patients, providing a new biomarker for early diagnosis.

HUMAN BRAIN MAPPING (2023)

Article Computer Science, Interdisciplinary Applications

Fetal MRI by Robust Deep Generative Prior Reconstruction and Diffeomorphic Registration

Lucilio Cordero-Grande, Juan Enrique Ortuno-Fisac, Alejandra Aguado del Hoyo, Alena Uus, Maria Deprez, Andres Santos, Joseph V. Hajnal, Maria J. Ledesma-Carbayo

Summary: In this paper, a deep generative prior and a diffeomorphic volume to slice registration method are proposed for robust volumetric reconstructions. Experiments on 72 fetal datasets show that our method outperforms existing techniques in improving image quality and accurately predicting gestational age.

IEEE TRANSACTIONS ON MEDICAL IMAGING (2023)

Article Psychology, Developmental

Longitudinal neonatal brain development and socio-demographic correlates of infant outcomes following preterm birth

Lucy Vanes, Sunniva Fenn-Moltu, Laila Hadaya, Sean Fitzgibbon, Lucilio Cordero-Grande, Anthony Price, Andrew Chew, Shona Falconer, Tomoki Arichi, Serena J. Counsell, Joseph V. Hajnal, Dafnis Batalle, David Edwards, Chiara Nosarti

Summary: Preterm birth increases the risk of adverse behavioural outcomes in later life. Our study examines the longitudinal development of neonatal brain volume and functional connectivity after preterm birth and their relationship to psychomotor outcomes and psychopathology in toddlerhood. We found that better psychomotor functioning is associated with specific brain volume and connectivity changes in the neonatal period, while increased psychopathology is related to alterations in regional subcortical volume. Additionally, socio-economic deprivation and cognitively stimulating parenting play different roles in predicting psychopathology and psychomotor outcomes. Our findings highlight the importance of longitudinal imaging and environmental influences in understanding behavioural development in preterm infants.

DEVELOPMENTAL COGNITIVE NEUROSCIENCE (2023)

Article Biology

Spatiotemporal tissue maturation of thalamocortical pathways in the human fetal brain

Sian Wilson, Maximilian Pietsch, Lucilio Cordero-Grande, Daan Christiaens, Alena Uus, Vyacheslav R. Karolis, Vanessa Kyriakopoulou, Kathleen Colford, Anthony N. Price, Jana Hutter, Mary A. Rutherford, Emer J. Hughes, Serena J. Counsell, Jacques-Donald Tournier, Joseph Hajnal, A. David Edwards, Jonathan O'Muicheartaigh, Tomoki Arichi, Finnegan J. Calabro

Summary: In this study, high-resolution in utero diffusion magnetic resonance imaging was used to examine the development of thalamocortical white matter in 140 fetuses. The researchers delineated the thalamocortical pathways and parcellated the fetal thalamus based on its cortical connectivity. They quantified microstructural tissue components along the tracts in fetal compartments and identified changes in diffusion metrics reflecting critical neurobiological transitions. These findings provide a normative reference for further studies on developmental disruptions and their contributions to pathophysiology.

ELIFE (2023)

Article Automation & Control Systems

SAPM: Self-Adaptive Parallel Manipulator With Pose and Force Adjustment for Robotic Ultrasonography

Xianqiang Bao, Shuangyi Wang, Lingling Zheng, Richard James Housden, Joseph Hajnal, Kawal Rhode

Summary: This article proposes a novel self-adaptive parallel manipulator (SAPM) for robotic ultrasonography. The SAPM can automatically adjust the ultrasound probe pose, provide approximate constant operating forces/torques, achieve mechanical measurement, and cushion undesired produced forces. Experimental results show that the SAPM can provide 3 DOFs motion, operating force/torque measurement, and automatically adjust the US probe pose to capture high-quality ultrasound images.

IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS (2023)

Article Infectious Diseases

SARS-CoV-2 infection following booster vaccination: Illness and symptom profile in a prospective, observational community-based case-control study

Michela Antonelli, Rose S. Penfold, Liane Dos Santos Canas, Carole Sudre, Khaled Rjoob, Ben Murray, Erika Molteni, Eric Kerfoot, Nathan Cheetham, Juan Capdevila Pujol, Lorenzo Polidori, Anna May, Jonathan Wolf, Marc Modat, Tim Spector, Alexander Hammers, Sebastien Ourselin, Claire Steves

Summary: This study describes the characteristics of SARS-CoV-2 illness following a third vaccination and assesses the risk of progression to symptomatic disease in SARS-CoV-2 infected individuals with time since vaccination. The results suggest that a third dose of monovalent vaccine may reduce symptoms, severity, and duration of SARS-CoV-2 infection following vaccination.

JOURNAL OF INFECTION (2023)

Article Radiology, Nuclear Medicine & Medical Imaging

Characterisation of a novel [18F]FDG brain PET database and combination with a second database for optimising detection of focal abnormalities, using focal cortical dysplasia as an example

Sameer Omer Jin, Ines Merida, Ioannis Stavropoulos, Robert D. C. Elwes, Tanya Lam, Eric Guedj, Nadine Girard, Nicolas Costes, Alexander Hammers

Summary: This study compared two different databases of [F-18]FDG PET data and achieved a higher abnormality detection rate by adjusting spatial resolution and global values. The results demonstrate the importance of increasing database size and overcoming database differences, which can be applicable to traditional statistical analysis or machine learning, as well as clinical implementation.

EJNMMI RESEARCH (2023)

No Data Available