RICCARDO DE FEO

Dottore di ricerca

ciclo: XXXIV


supervisore: Federico Giove

Titolo della tesi: Convolutional neural networks for the segmentation of small rodent brain MRI

Image segmentation is a common step in the analysis of preclinical brain MRI, often performed manually. This is a time-consuming procedure subject to inter- and intra- rater variability. A possible alternative is the use of automated, registration-based segmentation, which suffers from a bias owed to the limited capacity of registration to adapt to pathological conditions such as Traumatic Brain Injury (TBI). In this work a novel method is developed for the segmentation of small rodent brain MRI based on Convolutional Neural Networks (CNNs). The experiments here presented show how CNNs provide a fast, robust and accurate alternative to both manual and registration-based methods. This is demonstrated by accurately segmenting three large datasets of MRI scans of healthy and Huntington disease model mice, as well as TBI rats. MU-Net and MU-Net-R, the CCNs here presented, achieve human-level accuracy while eliminating intra-rater variability, alleviating the biases of registration-based segmentation, and with an inference time of less than one second per scan. Using these segmentation masks I designed a geometric construction to extract 39 parameters describing the position and orientation of the hippocampus, and later used them to classify epileptic vs non-epileptic rats with a balanced accuracy of 0.80, five months after TBI. This clinically transferable geometric approach detects subjects at high-risk of post-traumatic epilepsy, paving the way towards subject stratification for antiepileptogenesis studies.

Produzione scientifica

11573/1670670 - 2023 - Automatic cerebral hemisphere segmentation in rat MRI with ischemic lesions via attention-based convolutional neural networks
Valverde, Juan Miguel; Shatillo, Artem; De Feo, Riccardo; Tohka, Jussi - 01a Articolo in rivista
rivista: NEUROINFORMATICS (Humana Press, Inc.) pp. 57-70 - issn: 1539-2791 - wos: WOS:000862229300001 (5) - scopus: 2-s2.0-85139233757 (6)

11573/1615271 - 2022 - Convolutional neural networks enable robust automatic segmentation of the rat hippocampus in MRI after traumatic brain injury
De Feo, Riccardo; Hämäläinen, Elina; Manninen, Eppu; Immonen, Riikka; Valverde, Juan Miguel; Ndode-Ekane, Xavier Ekolle; Gröhn, Olli; Pitkänen, Asla; Tohka, Jussi - 01a Articolo in rivista
rivista: FRONTIERS IN NEUROLOGY (Lausanne: Frontiers Research Foundation, 2010-) pp. 1-16 - issn: 1664-2295 - wos: WOS:000765066000001 (10) - scopus: 2-s2.0-85125746208 (10)

11573/1670666 - 2022 - Hippocampal position and orientation as prognostic biomarkers for posttraumatic epileptogenesis: an experimental study in a rat lateral fluid percussion model
De Feo, Riccardo; Manninen, Eppu; Chary, Karthik; Hämäläinen, Elina; Immonen, Riikka; Andrade, Pedro; Ekolle Ndode‐Ekane, Xavier; Gröhn, Olli; Pitkänen, Asla; Tohka, Jussi - 01a Articolo in rivista
rivista: EPILEPSIA (Hoboken: John Wiley & Sons Oxford: Blackwell Science Inc.) pp. 1849-1861 - issn: 1528-1167 - wos: WOS:000794055400001 (0) - scopus: 2-s2.0-85129870725 (0)

11573/1670674 - 2022 - Acute hippocampal damage as a prognostic biomarker for cognitive decline but not for epileptogenesis after experimental traumatic brain injury
Manninen, Eppu; Chary, Karthik; De Feo, Riccardo; Hämäläinen, Elina; Andrade, Pedro; Paananen, Tomi; Sierra, Alejandra; Tohka, Jussi; Gröhn, Olli; Pitkänen, Asla - 01a Articolo in rivista
rivista: BIOMEDICINES (Basel: MDPI) pp. 1-21 - issn: 2227-9059 - wos: WOS:000882577400001 (2) - scopus: 2-s2.0-85141845562 (4)

11573/1487121 - 2021 - Automated joint skull-stripping and segmentation with Multi-Task U-Net in large mouse brain MRI databases
De Feo, R.; Shatillo, A.; Sierra, A.; Valverde, J. M.; Grohn, O.; Giove, F.; Tohka, J. - 01a Articolo in rivista
rivista: NEUROIMAGE (Academic Press Incorporated:6277 Sea Harbor Drive:Orlando, FL 32887:(800)543-9534, (407)345-4100, EMAIL: ap@acad.com, INTERNET: http://www.idealibrary.com, Fax: (407)352-3445) pp. 1-12 - issn: 1053-8119 - wos: WOS:000629509400017 (21) - scopus: 2-s2.0-85099447990 (22)

11573/1550042 - 2021 - Comparing methods of detecting and segmenting unruptured intracranial aneurysms on TOF-MRAS: the ADAM challenge
Timmins, Kimberley M; Van Der Schaaf, Irene C; Bennink, Edwin; Ruigrok, Ynte M; An, Xingle; Baumgartner, Michael; Bourdon, Pascal; De Feo, Riccardo; Noto, Tommaso Di; Dubost, Florian; Fava-Sanches, Augusto; Feng, Xue; Giroud, Corentin; Group, Inteneural; Hu, Minghui; Jaeger, Paul F; Kaiponen, Juhana; Klimont, Michał; Li, Yuexiang; Li, Hongwei; Lin, Yi; Loehr, Timo; Ma, Jun; Maier-Hein, Klaus H; Marie, Guillaume; Menze, Bjoern; Richiardi, Jonas; Rjiba, Saifeddine; Shah, Dhaval; Shit, Suprosanna; Tohka, Jussi; Urruty, Thierry; Walińska, Urszula; Yang, Xiaoping; Yang, Yunqiao; Yin, Yin; Velthuis, Birgitta K; Kuijf, Hugo J - 01a Articolo in rivista
rivista: NEUROIMAGE (Academic Press Incorporated:6277 Sea Harbor Drive:Orlando, FL 32887:(800)543-9534, (407)345-4100, EMAIL: ap@acad.com, INTERNET: http://www.idealibrary.com, Fax: (407)352-3445) pp. 1-21 - issn: 1053-8119 - wos: WOS:000677954600004 (32) - scopus: 2-s2.0-85108723810 (41)

11573/1487123 - 2020 - RatLesNetv2: a fully convolutional network for rodent brain lesion segmentation
Miguel Valverde, Juan; Shatillo, Artem; De Feo, Riccardo; Gröhn, Olli; Sierra, Alejandra; Tohka, Jussi - 01a Articolo in rivista
rivista: FRONTIERS IN NEUROSCIENCE (Lausanne : EPFL : Frontiers Research Foundation, 2007-) pp. 1-11 - issn: 1662-453X - wos: WOS:000604598400001 (14) - scopus: 2-s2.0-85099071044 (15)

11573/1336536 - 2019 - Apparent diffusion coefficient assessment of brain development in normal fetuses and ventriculomegaly
Di Trani, M. G.; Manganaro, L.; Antonelli, A.; Guerreri, M.; De Feo, R.; Catalano, C.; Capuani, S. - 01a Articolo in rivista
rivista: FRONTIERS IN PHYSICS (Lausanne : Frontiers Editorial Office, 2013-) pp. 1-9 - issn: 2296-424X - wos: WOS:000498164400001 (9) - scopus: 2-s2.0-85075150336 (8)

11573/1338621 - 2019 - Towards an efficient segmentation of small rodents brain: a short critical review
Feo, R.; Giove, F. - 01g Articolo di rassegna (Review)
rivista: JOURNAL OF NEUROSCIENCE METHODS (Elsevier BV:PO Box 211, 1000 AE Amsterdam Netherlands:011 31 20 4853757, 011 31 20 4853642, 011 31 20 4853641, EMAIL: nlinfo-f@elsevier.nl, INTERNET: http://www.elsevier.nl, Fax: 011 31 20 4853598 primo editore:Elsevier/North-Holland Biomedical Press, Amsterdam) pp. 82-89 - issn: 0165-0270 - wos: WOS:000472590200010 (27) - scopus: 2-s2.0-85066147720 (28)

11573/1338657 - 2019 - Automatic Rodent Brain MRI Lesion Segmentation with Fully Convolutional Networks
Valverde, J. M.; Shatillo, A.; De Feo, R.; Grohn, O.; Sierra, A.; Tohka, J. - 02a Capitolo o Articolo
libro: International Workshop on Machine Learning in Medical Imaging - (978-3-030-32691-3; 978-3-030-32692-0)

11573/1173662 - 2018 - Apparent diffusion coefficient values of the normal foetal brain developing
Di Trani, M. G.; Manganaro, L.; Antonelli, A.; Guerreri, M.; De Feo, R.; Bernardo, S.; Catalano, C.; Capuani, S. - 04f Poster
congresso: Proceedings of the International School on Magnetic Resonance and Brain Function – XII Workshop. (Erice)
libro: Proceedings of the International School on Magnetic Resonance and Brain Function – XII Workshop. Frontiers in Physics. - ()

11573/1216519 - 2018 - Performance of diffusion kurtosis imaging versus diffusion tensor imaging in discriminating between benign tissue, low and high Gleason grade prostate cancer
Di Trani, Maria Giovanna; Nezzo, Marco; Caporale, Alessandra S.; De Feo, Riccardo; Miano, Roberto; Mauriello, Alessandro; Bove, Pierluigi; Manenti, Guglielmo; Capuani, Silvia - 01a Articolo in rivista
rivista: ACADEMIC RADIOLOGY (Radiological Society of North America:820 Jorie Boulevard:Oak Brook, IL 60523:(630)571-7873, EMAIL: subscrib@rsna.org, INTERNET: http://www.rsna.org, Fax: (630)571-7837) pp. 1328-1337 - issn: 1076-6332 - wos: WOS:000488147800008 (14) - scopus: 2-s2.0-85057983821 (16)

© Università degli Studi di Roma "La Sapienza" - Piazzale Aldo Moro 5, 00185 Roma