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1. Performance of orientation distribution function-fingerprinting with a biophysical multicompartment diffusion model.

Author

Filipiak P, Shepherd T, Lin YC, Placantonakis DG, Boada FE, and Baete SH

Subjects
Brain diagnostic imaging, Corpus Callosum diagnostic imaging, Diffusion Magnetic Resonance Imaging methods, Image Processing, Computer-Assisted methods, Algorithms, White Matter
Abstract

Purpose: Orientation Distribution Function (ODF) peak finding methods typically fail to reconstruct fibers crossing at shallow angles below 40°, leading to errors in tractography. ODF-Fingerprinting (ODF-FP) with the biophysical multicompartment diffusion model allows for breaking this barrier., Methods: A randomized mechanism to generate a multidimensional ODF-dictionary that covers biologically plausible ranges of intra- and extra-axonal diffusivities and fraction volumes is introduced. This enables ODF-FP to address the high variability of brain tissue. The performance of the proposed approach is evaluated on both numerical simulations and a reconstruction of major fascicles from high- and low-resolution in vivo diffusion images., Results: ODF-FP with the suggested modifications correctly identifies fibers crossing at angles as shallow as 10 degrees in the simulated data. In vivo, our approach reaches 56% of true positives in determining fiber directions, resulting in visibly more accurate reconstruction of pyramidal tracts, arcuate fasciculus, and optic radiations than the state-of-the-art techniques. Moreover, the estimated diffusivity values and fraction volumes in corpus callosum conform with the values reported in the literature., Conclusion: The modified ODF-FP outperforms commonly used fiber reconstruction methods at shallow angles, which improves deterministic tractography outcomes of major fascicles. In addition, the proposed approach allows for linearization of the microstructure parameters fitting problem., (© 2022 International Society for Magnetic Resonance in Medicine.)

Published
2022
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2. Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.

Author

Daducci A, Canales-Rodríguez EJ, Descoteaux M, Garyfallidis E, Gur Y, Lin YC, Mani M, Merlet S, Paquette M, Ramirez-Manzanares A, Reisert M, Reis Rodrigues P, Sepehrband F, Caruyer E, Choupan J, Deriche R, Jacob M, Menegaz G, Prčkovska V, Rivera M, Wiaux Y, and Thiran JP

Subjects
Humans, Algorithms, Brain anatomy & histology, Diffusion Magnetic Resonance Imaging methods, Image Processing, Computer-Assisted methods
Abstract

Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies.

Published
2014
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3. The challenge of mapping the human connectome based on diffusion tractography

Author

Maier-Hein, Klaus H., Neher, Peter F., Houde, Jean Christophe, Côté, Marc Alexandre, Garyfallidis, Eleftherios, Zhong, Jidan, Chamberland, Maxime, Yeh, Fang Cheng, Lin, Ying Chia, Ji, Qing, Reddick, Wilburn E., Glass, John O., Chen, David Qixiang, Feng, Yuanjing, Gao, Chengfeng, Wu, Ye, Ma, Jieyan, Renjie, H., Li, Qiang, Westin, Carl Fredrik, Deslauriers-Gauthier, Samuel, González, J. Omar Ocegueda, Paquette, Michael, St-Jean, Samuel, Girard, Gabriel, Rheault, François, Sidhu, Jasmeen, Tax, Chantal M.W., Guo, Fenghua, Mesri, Hamed Y., Dávid, Szabolcs, Froeling, Martijn, Heemskerk, Anneriet M., Leemans, Alexander, Boré, Arnaud, Pinsard, Basile, Bedetti, Christophe, Desrosiers, Matthieu, Brambati, Simona, Doyon, Julien, Sarica, Alessia, Vasta, Roberta, Cerasa, Antonio, Quattrone, Aldo, Yeatman, Jason, Khan, Ali R., Hodges, Wes, Alexander, Simon, Romascano, David, Barakovic, Muhamed, Auría, Anna, Esteban, Oscar, Lemkaddem, Alia, Thiran, Jean Philippe, Cetingul, H. Ertan, Odry, Benjamin L., Mailhe, Boris, Nadar, Mariappan S., Pizzagalli, Fabrizio, Prasad, Gautam, Villalon-Reina, Julio E., Galvis, Justin, Thompson, Paul M., Requejo, Francisco De Santiago, Laguna, Pedro Luque, Lacerda, Luis Miguel, Barrett, Rachel, Dell'Acqua, Flavio, Catani, Marco, Petit, Laurent, Caruyer, Emmanuel, Daducci, Alessandro, Dyrby, Tim B., Holland-Letz, Tim, Hilgetag, Claus C., Stieltjes, Bram, Descoteaux, Maxime, German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Sherbrooke Connectivity Imaging Lab [Sherbrooke] (SCIL), Département d'informatique [Sherbrooke] (UdeS), Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS)-Faculté des sciences [Sherbrooke] (UdeS), Université de Sherbrooke (UdeS)-Université de Sherbrooke (UdeS), Krembil Research Institute, University Health Network, University of Pittsburgh School of Medicine, Pennsylvania Commonwealth System of Higher Education (PCSHE), IMT Institute for Advanced Studies [Lucca], Department of Diagnostic Imaging [Memphis], St Jude Children's Research Hospital, Institute of Medical Science [Toronto], University of Toronto, Zhejiang University of Technology, Shanghai United Imaging Healthcare Co Ltd, Laboratory of Mathematics in Imaging [Boston], Brigham and Women's Hospital [Boston], Centro de Investigación en Matemáticas (CIMAT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Computational Imaging of the Central Nervous System (ATHENA), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Image sciences institute - University of Utrecht (ISI), University Medical Center [Utrecht], Centre de recherche de l'Institut universitaire de gériatrie de Montreal (CRIUGM), Université de Montréal (UdeM), Laboratoire d'Imagerie Biomédicale (LIB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Center for advanced research in sleep medicine, Montreal, Institute of Bioimaging and Molecular Physiology [Germaneto], National Research Council [Italy] (CNR), Department of Speech and Hearing Sciences [Washington], University of Washington [Seattle], Schulich School of Medicine and Dentistry, University of Western Ontario (UWO), Synaptive Medical Inc, Signal Processing Laboratory [Lausanne] (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), Biomedical Image Technologies Lab, ETSI Telecomunicación, Universidad Politécnica de Madrid (UPM), Siemens Healthcare, Keck School of Medicine [Los Angeles], University of Southern California (USC), Institute of Psychiatry, Psychology & Neuroscience, King's College London, King‘s College London, Groupe d'Imagerie Neurofonctionnelle (GIN - UMR 5296), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Service NEUROSPIN (NEUROSPIN), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Vision, Action et Gestion d'informations en Santé (VisAGeS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-SIGNAUX ET IMAGES NUMÉRIQUES, ROBOTIQUE (IRISA-D5), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Danish Research Centre for Magnetic Resonance (DRCMR), Hvidovre Hospital, Department of Applied Mathematics and Computer Science [Lyngby] (DTU Compute), Technical University of Denmark [Lyngby] (DTU), Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), University Hospital Basel [Basel], Université de Montréal. Faculté des arts et des sciences. Département de psychologie, Laboratoire d'Imagerie Biomédicale [Paris] (LIB), Service NEUROSPIN (NEUROSPIN), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université de Sherbrooke [Sherbrooke], Université de Montréal [Montréal], Groupe d'imagerie neurofonctionnelle (GIN), Institut des Maladies Neurodégénératives [Bordeaux] (IMN), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Caruyer, Emmanuel

Subjects
0301 basic medicine, Databases, Factual, Chemistry(all), Computer science, [INFO.INFO-IM] Computer Science [cs]/Medical Imaging, General Physics and Astronomy, computer.software_genre, Biochemistry, 0302 clinical medicine, Image Processing, Computer-Assisted, Diffusion Tractography, lcsh:Science, IN-VIVO, Reliability (statistics), Telecomunicaciones, Ground truth, BRAIN FIBER PATHWAYS, PHANTOMS, Multidisciplinary, Orientation (computer vision), Brain, Human Connectome, Diffusion Tensor Imaging, Mapping, Connectome, Electrónica, WHITE-MATTER, Algorithms, Tractography, Nervous system, GLOBAL TRACTOGRAPHY, Medicina, Science, Physics and Astronomy(all), Machine learning, LINEAR REGISTRATION, VALIDATION, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Medical research, Journal Article, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, Humans, MRI TRACTOGRAPHY, Author Correction, MICROSTRUCTURE INFORMED TRACTOGRAPHY, OCCIPITAL FASCICULUS, human connectome, business.industry, Biochemistry, Genetics and Molecular Biology(all), Reproducibility of Results, General Chemistry, Computational biology and bioinformatics, Data set, 030104 developmental biology, lcsh:Q, Artificial intelligence, business, computer, 030217 neurology & neurosurgery, Genetics and Molecular Biology(all), Neuroscience
Abstract

Tractography based on non-invasive diffusion imaging is central to the study of human brain connectivity. To date, the approach has not been systematically validated in ground truth studies. Based on a simulated human brain data set with ground truth tracts, we organized an open international tractography challenge, which resulted in 96 distinct submissions from 20 research groups. Here, we report the encouraging finding that most state-of-the-art algorithms produce tractograms containing 90% of the ground truth bundles (to at least some extent). However, the same tractograms contain many more invalid than valid bundles, and half of these invalid bundles occur systematically across research groups. Taken together, our results demonstrate and confirm fundamental ambiguities inherent in tract reconstruction based on orientation information alone, which need to be considered when interpreting tractography and connectivity results. Our approach provides a novel framework for estimating reliability of tractography and encourages innovation to address its current limitations., Though tractography is widely used, it has not been systematically validated. Here, authors report results from 20 groups showing that many tractography algorithms produce both valid and invalid bundles.

Published
2017
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