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Deep Learning for Brain Structures Segmentation in MR Imaging.

Grant number: 16/18332-8
Support Opportunities:Scholarships in Brazil - Master
Start date: January 01, 2017
End date: September 30, 2018
Field of knowledge:Engineering - Electrical Engineering
Principal Investigator:Roberto de Alencar Lotufo
Grantee:Oeslle Alexandre Soares de Lucena
Host Institution: Faculdade de Engenharia Elétrica e de Computação (FEEC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Associated scholarship(s):17/23747-5 - Deep-learning-based tractography for surgical planning in epilepsy treatment, BE.EP.MS

Abstract

The necessity to develop fast, robust and accurate brain MR segmentation tools that require few parametersto adjust is essential since manual segmentation performed by neurologists is a time-consuming task. Among automaticmethods, Deep Learning approaches have outperformed the state-of-the-art in many computer vision problems. DeepLearning techniques major disadvantage is that they usually require large amounts of labeled data for training, which isnot available in medical image segmentation problems.This M.Sc. research project intends to investigate the use of Deep Learning techniques applied to brainstructure segmentation in MR imaging. Two specic applications will be investigated: the brain extraction, also knownas skull-stripping, and corpus callosum (CC) segmentation problems. Our method aims to use the Simultaneous Truth andPerformance Level Estimation (STAPLE) algorithm to generate labeled data and use it as input for a Convolutional NeuralNetwork (CNN). We will compare our methodology with the state-of-the-art techniques for brain and CC segmentation.

News published in Agência FAPESP Newsletter about the scholarship:
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VEICULO: TITULO (DATA)
VEICULO: TITULO (DATA)

Scientific publications (5)
(The scientific publications listed on this page originate from the Web of Science or SciELO databases. Their authors have cited FAPESP grant or fellowship project numbers awarded to Principal Investigators or Fellowship Recipients, whether or not they are among the authors. This information is collected automatically and retrieved directly from those bibliometric databases.)
LUCENA, OESLLE; SOUZA, ROBERTO; RITTNER, LETICIA; FRAYNE, RICHARD; LOTUFO, ROBERTO; IEEE. SILVER STANDARD MASKS FOR DATA AUGMENTATION APPLIED TO DEEP-LEARNING-BASED SKULL-STRIPPING. 2018 IEEE 15TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI 2018), v. N/A, p. 4-pg., . (16/18332-8)
SOUZA, ROBERTO; LUCENA, OESLLE; GARRAFA, JULIA; GOBBI, DAVID; SALUZZI, MARINA; APPENZELLER, SIMONE; RITTNER, LETICIA; FRAYNE, RICHARD; LOTUFO, ROBERTO. An open, multi-vendor, multi-field-strength brain MR dataset and analysis of publicly available skull stripping methods agreement. NeuroImage, v. 170, n. SI, p. 482-494, . (13/23514-0, 13/07559-3, 16/18332-8)
LUCENA, OESLLE; SOUZA, ROBERTO; RITTNER, LETICIA; FRAYNE, RICHARD; LOTUFO, ROBERTO. Convolutional neural networks for skull-stripping in brain MR imaging using silver standard masks. ARTIFICIAL INTELLIGENCE IN MEDICINE, v. 98, p. 48-58, . (13/07559-3, 16/18332-8)
GRANADOS, ALEJANDRO; MANCINI, MATTEO; VOS, SJOERD B.; LUCENA, OESLLE; VAKHARIA, VEJAY; RODIONOV, ROMAN; MISEROCCHI, ANNA; MCEVOY, ANDREW W.; DUNCAN, JOHN S.; SPARKS, RACHEL; et al. A Machine Learning Approach to Predict Instrument Bending in Stereotactic Neurosurgery. MEDICAL IMAGE COMPUTING AND COMPUTER ASSISTED INTERVENTION - MICCAI 2018, PT IV, v. 11073, p. 9-pg., . (17/23747-5, 16/18332-8)
SOUZA, ROBERTO; LUCENA, OESLLE; GARRAFA, JULIA; GOBBI, DAVID; SALUZZI, MARINA; APPENZELLER, SIMONE; RITTNER, LETICIA; FRAYNE, RICHARD; LOTUFO, ROBERTO. An open, multi-vendor, multi-field-strength brain MR dataset and analysis of publicly available skull stripping methods agreement. NeuroImage, v. 170, p. 13-pg., . (13/07559-3, 13/23514-0, 16/18332-8)
Academic Publications
(References retrieved automatically from State of São Paulo Research Institutions)
LUCENA, Oeslle Alexandre Soares de. Aprendizado profundo para análise do cérebro em imagens de ressonância magnética. 2018. Master's Dissertation - Universidade Estadual de Campinas (UNICAMP). Faculdade de Engenharia Elétrica e de Computação Campinas, SP.