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2. Clinically Meaningful Magnetic Resonance Endpoints Sensitive to Preataxic Spinocerebellar Ataxia Types 1 and 3.

Author

Chandrasekaran, Jayashree, Petit, Emilien, Park, Young, du Montcel, Sophie, Joers, James, Deelchand, Dinesh, Považan, Michal, Banan, Guita, Valabregue, Romain, Ehses, Philipp, Faber, Jennifer, Coupé, Pierrick, Onyike, Chiadi, Barker, Peter, Schmahmann, Jeremy, Ratai, Eva-Maria, Subramony, S, Mareci, Thomas, Bushara, Khalaf, Paulson, Henry, Durr, Alexandra, Klockgether, Thomas, Ashizawa, Tetsuo, Lenglet, Christophe, and Öz, Gülin

Subjects
Humans, Activities of Daily Living, Spinocerebellar Ataxias, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Ataxia, Cerebellar Ataxia
Abstract

OBJECTIVE: This study was undertaken to identify magnetic resonance (MR) metrics that are most sensitive to early changes in the brain in spinocerebellar ataxia type 1 (SCA1) and type 3 (SCA3) using an advanced multimodal MR imaging (MRI) protocol in the multisite trial setting. METHODS: SCA1 or SCA3 mutation carriers and controls (n = 107) underwent MR scanning in the US-European READISCA study to obtain structural, diffusion MRI, and MR spectroscopy data using an advanced protocol at 3T. Morphometric, microstructural, and neurochemical metrics were analyzed blinded to diagnosis and compared between preataxic SCA (n = 11 SCA1, n = 28 SCA3), ataxic SCA (n = 14 SCA1, n = 37 SCA3), and control (n = 17) groups using nonparametric testing accounting for multiple comparisons. MR metrics that were most sensitive to preataxic abnormalities were identified using receiver operating characteristic (ROC) analyses. RESULTS: Atrophy and microstructural damage in the brainstem and cerebellar peduncles and neurochemical abnormalities in the pons were prominent in both preataxic groups, when patients did not differ from controls clinically. MR metrics were strongly associated with ataxia symptoms, activities of daily living, and estimated ataxia duration. A neurochemical measure was the most sensitive metric to preataxic changes in SCA1 (ROC area under the curve [AUC] = 0.95), and a microstructural metric was the most sensitive metric to preataxic changes in SCA3 (AUC = 0.92). INTERPRETATION: Changes in cerebellar afferent and efferent pathways underlie the earliest symptoms of both SCAs. MR metrics collected with a harmonized advanced protocol in the multisite trial setting allow detection of disease effects in individuals before ataxia onset with potential clinical trial utility for subject stratification. ANN NEUROL 2023;93:686-701.

Published
2023

4. Multiway sparse distance weighted discrimination

Author

Guo, Bin, Eberly, Lynn E., Henry, Pierre-Gilles, Lenglet, Christophe, and Lock, Eric F.

Subjects
Statistics - Methodology, Quantitative Biology - Quantitative Methods, Statistics - Machine Learning
Abstract

Modern data often take the form of a multiway array. However, most classification methods are designed for vectors, i.e., 1-way arrays. Distance weighted discrimination (DWD) is a popular high-dimensional classification method that has been extended to the multiway context, with dramatic improvements in performance when data have multiway structure. However, the previous implementation of multiway DWD was restricted to classification of matrices, and did not account for sparsity. In this paper, we develop a general framework for multiway classification which is applicable to any number of dimensions and any degree of sparsity. We conducted extensive simulation studies, showing that our model is robust to the degree of sparsity and improves classification accuracy when the data have multiway structure. For our motivating application, magnetic resonance spectroscopy (MRS) was used to measure the abundance of several metabolites across multiple neurological regions and across multiple time points in a mouse model of Friedreich's ataxia, yielding a four-way data array. Our method reveals a robust and interpretable multi-region metabolomic signal that discriminates the groups of interest. We also successfully apply our method to gene expression time course data for multiple sclerosis treatment. An R implementation is available in the package MultiwayClassification at http://github.com/lockEF/MultiwayClassification ., Comment: 46 pages, 8 figures

Published
2021

5. Artifact-Based Rendering: Harnessing Natural and Traditional Visual Media for More Expressive and Engaging 3D Visualizations

Author

Johnson, Seth, Samsel, Francesca, Abram, Gregory, Olson, Daniel, Solis, Andrew J., Herman, Bridger, Wolfram, Phillip J., Lenglet, Christophe, and Keefe, Daniel F.

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Graphics
Abstract

We introduce Artifact-Based Rendering (ABR), a framework of tools, algorithms, and processes that makes it possible to produce real, data-driven 3D scientific visualizations with a visual language derived entirely from colors, lines, textures, and forms created using traditional physical media or found in nature. A theory and process for ABR is presented to address three current needs: (i) designing better visualizations by making it possible for non-programmers to rapidly design and critique many alternative data-to-visual mappings; (ii) expanding the visual vocabulary used in scientific visualizations to depict increasingly complex multivariate data; (iii) bringing a more engaging, natural, and human-relatable handcrafted aesthetic to data visualization. New tools and algorithms to support ABR include front-end applets for constructing artifact-based colormaps, optimizing 3D scanned meshes for use in data visualization, and synthesizing textures from artifacts. These are complemented by an interactive rendering engine with custom algorithms and interfaces that demonstrate multiple new visual styles for depicting point, line, surface, and volume data. A within-the-research-team design study provides early evidence of the shift in visualization design processes that ABR is believed to enable when compared to traditional scientific visualization systems. Qualitative user feedback on applications to climate science and brain imaging support the utility of ABR for scientific discovery and public communication., Comment: Published in IEEE VIS 2019, 9 pages of content with 2 pages of references, 12 figures

Published
2019
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6. Network curvature as a hallmark of brain structural connectivity.

Author

Farooq, Hamza, Chen, Yongxin, Georgiou, Tryphon T, Tannenbaum, Allen, and Lenglet, Christophe

Subjects
Intellectual and Developmental Disabilities (IDD), Neurosciences, Autism, Mental Health, Brain Disorders, Pediatric, Cancer, Biomedical Imaging, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Neurological
Abstract

Although brain functionality is often remarkably robust to lesions and other insults, it may be fragile when these take place in specific locations. Previous attempts to quantify robustness and fragility sought to understand how the functional connectivity of brain networks is affected by structural changes, using either model-based predictions or empirical studies of the effects of lesions. We advance a geometric viewpoint relying on a notion of network curvature, the so-called Ollivier-Ricci curvature. This approach has been proposed to assess financial market robustness and to differentiate biological networks of cancer cells from healthy ones. Here, we apply curvature-based measures to brain structural networks to identify robust and fragile brain regions in healthy subjects. We show that curvature can also be used to track changes in brain connectivity related to age and autism spectrum disorder (ASD), and we obtain results that are in agreement with previous MRI studies.

Published
2019

7. Mapping polarization-sensitive optical coherence tomography and ultra-high-field diffusion MRI in the macaque brain

Author

Pisharady, Pramod K, primary, Yeatts, Marilyn, additional, Farooq, Hamza, additional, Johnson, Matthew, additional, Harel, Noam, additional, Moeller, Steen, additional, Zimmermann, Jan, additional, Yacoub, Essa, additional, Ugurbil, Kamil, additional, Heilbronner, Sarah R., additional, Lenglet, Christophe, additional, and Akkin, Taner, additional

Published
2024
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10. Genotype-specific spinal cord damage in spinocerebellar ataxias: an ENIGMA-Ataxia study.

Author

Ribeiro Rezende, Thiago Junqueira, Adanyaguh, Isaac, Barsottini, Orlando G. P., Bender, Benjamin, Cendes, Fernando, Coutinho, Leo, Deistung, Andreas, Dogan, Imis, Durr, Alexandra, Fernandez-Ruiz, Juan, Göricke, Sophia L., Grisoli, Marina, Hernandez-Castillo, Carlos R., Lenglet, Christophe, Mariotti, Caterina, Martinez, Alberto R. M., Massuyama, Breno K., Mochel, Fanny, Nanetti, Lorenzo, and Nigri, Anna

Subjects
SPINOCEREBELLAR ataxia, SPINAL cord, FRIEDREICH'S ataxia, FAMILIAL spastic paraplegia, PYRAMIDAL tract, DORSAL root ganglia
Published
2024
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11. Generic acquisition protocol for quantitative MRI of the spinal cord

Author

Cohen-Adad, Julien, Alonso-Ortiz, Eva, Abramovic, Mihael, Arneitz, Carina, Atcheson, Nicole, Barlow, Laura, Barry, Robert L., Barth, Markus, Battiston, Marco, Büchel, Christian, Budde, Matthew, Callot, Virginie, Combes, Anna J. E., De Leener, Benjamin, Descoteaux, Maxime, de Sousa, Paulo Loureiro, Dostál, Marek, Doyon, Julien, Dvorak, Adam, Eippert, Falk, Epperson, Karla R., Epperson, Kevin S., Freund, Patrick, Finsterbusch, Jürgen, Foias, Alexandru, Fratini, Michela, Fukunaga, Issei, Wheeler-Kingshott, Claudia A. M. Gandini, Germani, Giancarlo, Gilbert, Guillaume, Giove, Federico, Gros, Charley, Grussu, Francesco, Hagiwara, Akifumi, Henry, Pierre-Gilles, Horák, Tomáš, Hori, Masaaki, Joers, James, Kamiya, Kouhei, Karbasforoushan, Haleh, Keřkovský, Miloš, Khatibi, Ali, Kim, Joo-Won, Kinany, Nawal, Kitzler, Hagen, Kolind, Shannon, Kong, Yazhuo, Kudlička, Petr, Kuntke, Paul, Kurniawan, Nyoman D., Kusmia, Slawomir, Labounek, René, Laganà, Maria Marcella, Laule, Cornelia, Law, Christine S., Lenglet, Christophe, Leutritz, Tobias, Liu, Yaou, Llufriu, Sara, Mackey, Sean, Martinez-Heras, Eloy, Mattera, Loan, Nestrasil, Igor, O’Grady, Kristin P., Papinutto, Nico, Papp, Daniel, Pareto, Deborah, Parrish, Todd B., Pichiecchio, Anna, Prados, Ferran, Rovira, Àlex, Ruitenberg, Marc J., Samson, Rebecca S., Savini, Giovanni, Seif, Maryam, Seifert, Alan C., Smith, Alex K., Smith, Seth A., Smith, Zachary A., Solana, Elisabeth, Suzuki, Yuichi, Tackley, George, Tinnermann, Alexandra, Valošek, Jan, Van De Ville, Dimitri, Yiannakas, Marios C., Weber, II, Kenneth A., Weiskopf, Nikolaus, Wise, Richard G., Wyss, Patrik O., and Xu, Junqian

Published
2021
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12. Genotype-specific spinal cord damage in spinocerebellar ataxias: an ENIGMA-Ataxia study

Author

Rezende, Thiago Junqueira Ribeiro, primary, Adanyaguh, Isaac, additional, Barsottini, Orlando G P, additional, Bender, Benjamin, additional, Cendes, Fernando, additional, Coutinho, Leo, additional, Deistung, Andreas, additional, Dogan, Imis, additional, Durr, Alexandra, additional, Fernandez-Ruiz, Juan, additional, Göricke, Sophia L, additional, Grisoli, Marina, additional, Hernandez-Castillo, Carlos R, additional, Lenglet, Christophe, additional, Mariotti, Caterina, additional, Martinez, Alberto R M, additional, Massuyama, Breno K, additional, Mochel, Fanny, additional, Nanetti, Lorenzo, additional, Nigri, Anna, additional, Ono, Sergio E, additional, Öz, Gülin, additional, Pedroso, José Luiz, additional, Reetz, Kathrin, additional, Synofzik, Matthis, additional, Teive, Helio, additional, Thomopoulos, Sophia I, additional, Thompson, Paul M, additional, Timmann, Dagmar, additional, van de Warrenburg, Bart P C, additional, van Gaalen, Judith, additional, França, Marcondes C, additional, and Harding, Ian H, additional

Published
2024
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13. Tractography dissection variability: What happens when 42 groups dissect 14 white matter bundles on the same dataset?

Author

Schilling, Kurt G., Rheault, François, Petit, Laurent, Hansen, Colin B., Nath, Vishwesh, Yeh, Fang-Cheng, Girard, Gabriel, Barakovic, Muhamed, Rafael-Patino, Jonathan, Yu, Thomas, Fischi-Gomez, Elda, Pizzolato, Marco, Ocampo-Pineda, Mario, Schiavi, Simona, Canales-Rodríguez, Erick J., Daducci, Alessandro, Granziera, Cristina, Innocenti, Giorgio, Thiran, Jean-Philippe, Mancini, Laura, Wastling, Stephen, Cocozza, Sirio, Petracca, Maria, Pontillo, Giuseppe, Mancini, Matteo, Vos, Sjoerd B., Vakharia, Vejay N., Duncan, John S., Melero, Helena, Manzanedo, Lidia, Sanz-Morales, Emilio, Peña-Melián, Ángel, Calamante, Fernando, Attyé, Arnaud, Cabeen, Ryan P., Korobova, Laura, Toga, Arthur W., Vijayakumari, Anupa Ambili, Parker, Drew, Verma, Ragini, Radwan, Ahmed, Sunaert, Stefan, Emsell, Louise, De Luca, Alberto, Leemans, Alexander, Bajada, Claude J., Haroon, Hamied, Azadbakht, Hojjatollah, Chamberland, Maxime, Genc, Sila, Tax, Chantal M.W., Yeh, Ping-Hong, Srikanchana, Rujirutana, Mcknight, Colin D., Yang, Joseph Yuan-Mou, Chen, Jian, Kelly, Claire E., Yeh, Chun-Hung, Cochereau, Jerome, Maller, Jerome J., Welton, Thomas, Almairac, Fabien, Seunarine, Kiran K, Clark, Chris A., Zhang, Fan, Makris, Nikos, Golby, Alexandra, Rathi, Yogesh, O'Donnell, Lauren J., Xia, Yihao, Aydogan, Dogu Baran, Shi, Yonggang, Fernandes, Francisco Guerreiro, Raemaekers, Mathijs, Warrington, Shaun, Michielse, Stijn, Ramírez-Manzanares, Alonso, Concha, Luis, Aranda, Ramón, Meraz, Mariano Rivera, Lerma-Usabiaga, Garikoitz, Roitman, Lucas, Fekonja, Lucius S., Calarco, Navona, Joseph, Michael, Nakua, Hajer, Voineskos, Aristotle N., Karan, Philippe, Grenier, Gabrielle, Legarreta, Jon Haitz, Adluru, Nagesh, Nair, Veena A., Prabhakaran, Vivek, Alexander, Andrew L., Kamagata, Koji, Saito, Yuya, Uchida, Wataru, Andica, Christina, Abe, Masahiro, Bayrak, Roza G., Wheeler-Kingshott, Claudia A.M. Gandini, D'Angelo, Egidio, Palesi, Fulvia, Savini, Giovanni, Rolandi, Nicolò, Guevara, Pamela, Houenou, Josselin, López-López, Narciso, Mangin, Jean-François, Poupon, Cyril, Román, Claudio, Vázquez, Andrea, Maffei, Chiara, Arantes, Mavilde, Andrade, José Paulo, Silva, Susana Maria, Calhoun, Vince D., Caverzasi, Eduardo, Sacco, Simone, Lauricella, Michael, Pestilli, Franco, Bullock, Daniel, Zhan, Yang, Brignoni-Perez, Edith, Lebel, Catherine, Reynolds, Jess E, Nestrasil, Igor, Labounek, René, Lenglet, Christophe, Paulson, Amy, Aulicka, Stefania, Heilbronner, Sarah R., Heuer, Katja, Chandio, Bramsh Qamar, Guaje, Javier, Tang, Wei, Garyfallidis, Eleftherios, Raja, Rajikha, Anderson, Adam W., Landman, Bennett A., and Descoteaux, Maxime

Published
2021
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14. Efficacy and Safety of Leriglitazone in Patients With Friedreich Ataxia: A Phase 2 Double-Blind, Randomized Controlled Trial (FRAMES)

Author

Pandolfo, Massimo, Reetz, Kathrin, Darling, Alejandra, Rodriguez de Rivera, Francisco Javier, Henry, Pierre-Gilles, Joers, James, Lenglet, Christophe, Adanyeguh, Isaac, Deelchand, Dinesh, Mochel, Fanny, Pousset, Françoise, Pascual, Sílvia, Van den Eede, Delphine, Martin-Ugarte, Itziar, Vilà-Brau, Anna, Mantilla, Adriana, Pascual, María, Martinell, Marc, Meya, Uwe, and Durr, Alexandra

Published
2022
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16. Microstructure Imaging of Crossing (MIX) White Matter Fibers from diffusion MRI.

Author

Farooq, Hamza, Xu, Junqian, Nam, Jung Who, Keefe, Daniel F, Yacoub, Essa, Georgiou, Tryphon, and Lenglet, Christophe

Subjects
Corpus Callosum, Axons, Humans, Diffusion Magnetic Resonance Imaging, Models, Neurological, White Matter, Biomedical Imaging, Networking and Information Technology R&D, Neurosciences, Bioengineering, Neurological, Models, Biochemistry and Cell Biology, Other Physical Sciences
Abstract

Diffusion MRI (dMRI) reveals microstructural features of the brain white matter by quantifying the anisotropic diffusion of water molecules within axonal bundles. Yet, identifying features such as axonal orientation dispersion, density, diameter, etc., in complex white matter fiber configurations (e.g. crossings) has proved challenging. Besides optimized data acquisition and advanced biophysical models, computational procedures to fit such models to the data are critical. However, these procedures have been largely overlooked by the dMRI microstructure community and new, more versatile, approaches are needed to solve complex biophysical model fitting problems. Existing methods are limited to models assuming single fiber orientation, relevant to limited brain areas like the corpus callosum, or multiple orientations but without the ability to extract detailed microstructural features. Here, we introduce a new and versatile optimization technique (MIX), which enables microstructure imaging of crossing white matter fibers. We provide a MATLAB implementation of MIX, and demonstrate its applicability to general microstructure models in fiber crossings using synthetic as well as ex-vivo and in-vivo brain data.

Published
2016

17. Fast In Vivo High-Resolution Diffusion MRI of the Human Cervical Spinal Cord Microstructure

Author

Labounek, René, Valošek, Jan, Zimolka, Jakub, Piskořová, Zuzana, Horák, Tomáš, Svátková, Alena, Bednařík, Petr, Hok, Pavel, Vojtíšek, Lubomír, Hluštík, Petr, Bednařík, Josef, Lenglet, Christophe, Magjarevic, Ratko, Editor-in-Chief, Ładyżyński, Piotr, Series Editor, Ibrahim, Fatimah, Series Editor, Lacković, Igor, Series Editor, Rock, Emilio Sacristan, Series Editor, Lhotska, Lenka, editor, Sukupova, Lucie, editor, and Ibbott, Geoffrey S., editor

Published
2019
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18. Author Correction: Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers

Author

Cohen-Adad, Julien, Alonso-Ortiz, Eva, Abramovic, Mihael, Arneitz, Carina, Atcheson, Nicole, Barlow, Laura, Barry, Robert L., Barth, Markus, Battiston, Marco, Büchel, Christian, Budde, Matthew, Callot, Virginie, Combes, Anna J. E., De Leener, Benjamin, Descoteaux, Maxime, de Sousa, Paulo Loureiro, Dostál, Marek, Doyon, Julien, Dvorak, Adam, Eippert, Falk, Epperson, Karla R., Epperson, Kevin S., Freund, Patrick, Finsterbusch, Jürgen, Foias, Alexandru, Fratini, Michela, Fukunaga, Issei, Gandini Wheeler-Kingshott, Claudia A. M., Germani, Giancarlo, Gilbert, Guillaume, Giove, Federico, Gros, Charley, Grussu, Francesco, Hagiwara, Akifumi, Henry, Pierre-Gilles, Horák, Tomáš, Hori, Masaaki, Joers, James, Kamiya, Kouhei, Karbasforoushan, Haleh, Keřkovský, Miloš, Khatibi, Ali, Kim, Joo-Won, Kinany, Nawal, Kitzler, Hagen H., Kolind, Shannon, Kong, Yazhuo, Kudlička, Petr, Kuntke, Paul, Kurniawan, Nyoman D., Kusmia, Slawomir, Labounek, René, Laganà, Maria Marcella, Laule, Cornelia, Law, Christine S., Lenglet, Christophe, Leutritz, Tobias, Liu, Yaou, Llufriu, Sara, Mackey, Sean, Martinez-Heras, Eloy, Mattera, Loan, Nestrasil, Igor, O’Grady, Kristin P., Papinutto, Nico, Papp, Daniel, Pareto, Deborah, Parrish, Todd B., Pichiecchio, Anna, Prados, Ferran, Rovira, Àlex, Ruitenberg, Marc J., Samson, Rebecca S., Savini, Giovanni, Seif, Maryam, Seifert, Alan C., Smith, Alex K., Smith, Seth A., Smith, Zachary A., Solana, Elisabeth, Suzuki, Y., Tackley, George, Tinnermann, Alexandra, Valošek, Jan, Van De Ville, Dimitri, Yiannakas, Marios C., Weber II, Kenneth A., Weiskopf, Nikolaus, Wise, Richard G., Wyss, Patrik O., and Xu, Junqian

Published
2021
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19. Open-access quantitative MRI data of the spinal cord and reproducibility across participants, sites and manufacturers

Author

Cohen-Adad, Julien, Alonso-Ortiz, Eva, Abramovic, Mihael, Arneitz, Carina, Atcheson, Nicole, Barlow, Laura, Barry, Robert L., Barth, Markus, Battiston, Marco, Büchel, Christian, Budde, Matthew, Callot, Virginie, Combes, Anna J. E., De Leener, Benjamin, Descoteaux, Maxime, de Sousa, Paulo Loureiro, Dostál, Marek, Doyon, Julien, Dvorak, Adam, Eippert, Falk, Epperson, Karla R., Epperson, Kevin S., Freund, Patrick, Finsterbusch, Jürgen, Foias, Alexandru, Fratini, Michela, Fukunaga, Issei, Gandini Wheeler-Kingshott, Claudia A. M., Germani, Giancarlo, Gilbert, Guillaume, Giove, Federico, Gros, Charley, Grussu, Francesco, Hagiwara, Akifumi, Henry, Pierre-Gilles, Horák, Tomáš, Hori, Masaaki, Joers, James, Kamiya, Kouhei, Karbasforoushan, Haleh, Keřkovský, Miloš, Khatibi, Ali, Kim, Joo-Won, Kinany, Nawal, Kitzler, Hagen H., Kolind, Shannon, Kong, Yazhuo, Kudlička, Petr, Kuntke, Paul, Kurniawan, Nyoman D., Kusmia, Slawomir, Labounek, René, Laganà, Maria Marcella, Laule, Cornelia, Law, Christine S., Lenglet, Christophe, Leutritz, Tobias, Liu, Yaou, Llufriu, Sara, Mackey, Sean, Martinez-Heras, Eloy, Mattera, Loan, Nestrasil, Igor, O’Grady, Kristin P., Papinutto, Nico, Papp, Daniel, Pareto, Deborah, Parrish, Todd B., Pichiecchio, Anna, Prados, Ferran, Rovira, Àlex, Ruitenberg, Marc J., Samson, Rebecca S., Savini, Giovanni, Seif, Maryam, Seifert, Alan C., Smith, Alex K., Smith, Seth A., Smith, Zachary A., Solana, Elisabeth, Suzuki, Y., Tackley, George, Tinnermann, Alexandra, Valošek, Jan, Van De Ville, Dimitri, Yiannakas, Marios C., Weber II, Kenneth A., Weiskopf, Nikolaus, Wise, Richard G., Wyss, Patrik O., and Xu, Junqian

Published
2021
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20. Brain Parcellation and Connectivity Mapping Using Wasserstein Geometry

Author

Farooq, Hamza, Chen, Yongxin, Georgiou, Tryphon, Lenglet, Christophe, Hege, Hans-Christian, Series Editor, Hoffman, David, Series Editor, Johnson, Christopher R., Series Editor, Polthier, Konrad, Series Editor, Rumpf, Martin, Series Editor, Kaden, Enrico, editor, Grussu, Francesco, editor, Ning, Lipeng, editor, Tax, Chantal M. W., editor, and Veraart, Jelle, editor

Published
2018
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21. Automatic clustering and population analysis of white matter tracts using maximum density paths

Author

Prasad, Gautam, Joshi, Shantanu H, Jahanshad, Neda, Villalon-Reina, Julio, Aganj, Iman, Lenglet, Christophe, Sapiro, Guillermo, McMahon, Katie L, de Zubicaray, Greig I, Martin, Nicholas G, Wright, Margaret J, Toga, Arthur W, and Thompson, Paul M

Subjects
Biomedical and Clinical Sciences, Health Sciences, Bioengineering, Algorithms, Anisotropy, Cluster Analysis, Diffusion Tensor Imaging, Female, Humans, Image Processing, Computer-Assisted, Male, Nerve Fibers, Neural Pathways, Reproducibility of Results, White Matter, Young Adult, HARDI, Tractography, MRI, Brain, Clustering, Atlas, Dijkstra, Shortest path, Geodesic distance, Hough, Connectivity, Maximum density path, Curve registration, Longest path, Medical and Health Sciences, Psychology and Cognitive Sciences, Neurology & Neurosurgery, Biomedical and clinical sciences, Health sciences
Abstract

We introduce a framework for population analysis of white matter tracts based on diffusion-weighted images of the brain. The framework enables extraction of fibers from high angular resolution diffusion images (HARDI); clustering of the fibers based partly on prior knowledge from an atlas; representation of the fiber bundles compactly using a path following points of highest density (maximum density path; MDP); and registration of these paths together using geodesic curve matching to find local correspondences across a population. We demonstrate our method on 4-Tesla HARDI scans from 565 young adults to compute localized statistics across 50 white matter tracts based on fractional anisotropy (FA). Experimental results show increased sensitivity in the determination of genetic influences on principal fiber tracts compared to the tract-based spatial statistics (TBSS) method. Our results show that the MDP representation reveals important parts of the white matter structure and considerably reduces the dimensionality over comparable fiber matching approaches.

Published
2014

22. A Sparse Bayesian Learning Algorithm for White Matter Parameter Estimation from Compressed Multi-shell Diffusion MRI

Author

Pisharady, Pramod Kumar, Sotiropoulos, Stamatios N., Sapiro, Guillermo, Lenglet, Christophe, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Descoteaux, Maxime, editor, Maier-Hein, Lena, editor, Franz, Alfred, editor, Jannin, Pierre, editor, Collins, D. Louis, editor, and Duchesne, Simon, editor

Published
2017
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30. Brain Tissue Micro-Structure Imaging from Diffusion MRI Using Least Squares Variable Separation

Author

Farooq, Hamza, Xu, Junqian, Yacoub, Essa, Georgiou, Tryphon, Lenglet, Christophe, Hege, Hans-Christian, Series editor, Hoffman, David, Series editor, Johnson, Christopher R., Series editor, Polthier, Konrad, Series editor, Rumpf, Martin, Series editor, Fuster, Andrea, editor, Ghosh, Aurobrata, editor, Kaden, Enrico, editor, Rathi, Yogesh, editor, and Reisert, Marco, editor

Published
2016
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31. List of Contributors

Author

Albott, Cristina S., primary, Aravalli, Rajagopal N., additional, Bardot, Dawn, additional, Bateman, Michael G., additional, Camchong, Jazmin, additional, Chen, Mo, additional, Chen, Wei, additional, Cline, Christopher C., additional, Crane, Andrew, additional, Danczyk, Georgette, additional, De Martino, Federico, additional, Durfee, William K., additional, Eggen, Michael D., additional, Erdman, Arthur G., additional, Frost, Kate L., additional, Gaasedelen, Erik N., additional, Gillick, Bernadette T., additional, Harel, Noam, additional, He, Bin, additional, Holm, Mikayle A., additional, Hortensius, Rebecca A., additional, Howard, Brian T., additional, Huddleston, Stephen J., additional, Iaizzo, Paul A., additional, Iles, Tinen L., additional, John, Ranjit, additional, Kelly, Rosemary F., additional, Kerns, Natalie, additional, Kimberley, Teresa J., additional, Kulkarni, Kanchan, additional, Lee, Steven W., additional, Lenglet, Christophe, additional, Liao, Kenneth K., additional, Lim, Kelvin O., additional, Lin, Wei-Han, additional, Low, Walter C., additional, Lu, Ming, additional, Lu, Wei-Cheng, additional, Mattison, Lars M., additional, Mattson, Alexander R., additional, Miller, Zachary D., additional, Nantsupawat, Teerapat, additional, Nemanich, Samuel T., additional, Netoff, Theoden I., additional, Nguyen, Anh Tuan, additional, Ogle, Brenda M., additional, Olson, Matthew, additional, Patriat, Remi, additional, Pearce, Clairice, additional, Prudente, Cecilia N., additional, Roukoz, Henri, additional, Roy, Abhrajeet V., additional, Sanchez, Jorge D. Zhingre, additional, Sathnur, Neeraj, additional, Schiestl, Randy, additional, Shaffer, Andrew W., additional, Shiao, Maple, additional, Sipe, Christopher, additional, Spratt, John R., additional, Steer, Clifford J., additional, Tolkacheva, Elena G., additional, Toman, Nikolas G., additional, Ugurbil, Kamil, additional, Vitek, Jerrold L., additional, Voth, Joseph, additional, Xie, Hui, additional, Xu, Jian, additional, Yacoub, Essa, additional, Yang, Zhi, additional, and Zhu, Xiao-Hong, additional

Published
2019
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33. Sparse Bayesian Inference of White Matter Fiber Orientations from Compressed Multi-resolution Diffusion MRI

Author

Pisharady, Pramod Kumar, Duarte-Carvajalino, Julio M., Sotiropoulos, Stamatios N., Sapiro, Guillermo, Lenglet, Christophe, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Navab, Nassir, editor, Hornegger, Joachim, editor, Wells, William M., editor, and Frangi, Alejandro, editor

Published
2015
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35. MR Imaging in Ataxias : Consensus Recommendations by the Ataxia Global Initiative Working Group on MRI Biomarkers

Author

Öz, Gülin, Cocozza, Sirio, Henry, Pierre-Gilles, Lenglet, Christophe, Deistung, Andreas, Faber, Jennifer, Schwarz, Adam J., Timmann-Braun, Dagmar, Van Dijk, Koene R. A., and Harding, Ian H.

Subjects
Medizin
Abstract

With many viable strategies in the therapeutic pipeline, upcoming clinical trials in hereditary and sporadic degenerative ataxias will benefit from non-invasive MRI biomarkers for patient stratification and the evaluation of therapies. The MRI Biomarkers Working Group of the Ataxia Global Initiative therefore devised guidelines to facilitate harmonized MRI data acquisition in clinical research and trials in ataxias. Recommendations are provided for a basic structural MRI protocol that can be used for clinical care and for an advanced multi-modal MRI protocol relevant for research and trial settings. The advanced protocol consists of modalities with demonstrated utility for tracking brain changes in degenerative ataxias and includes structural MRI, magnetic resonance spectroscopy, diffusion MRI, quantitative susceptibility mapping, and resting-state functional MRI. Acceptable ranges of acquisition parameters are provided to accommodate diverse scanner hardware in research and clinical contexts while maintaining a minimum standard of data quality. Important technical considerations in setting up an advanced multi-modal protocol are outlined, including the order of pulse sequences, and example software packages commonly used for data analysis are provided. Outcome measures most relevant for ataxias are highlighted with use cases from recent ataxia literature. Finally, to facilitate access to the recommendations by the ataxia clinical and research community, examples of datasets collected with the recommended parameters are provided and platform-specific protocols are shared via the Open Science Framework. in press

Published
2023

36. Rich Club Analysis of Structural Brain Connectivity at 7 Tesla Versus 3 Tesla

Author

Dennis, Emily L., Zhan, Liang, Jahanshad, Neda, Mueller, Bryon A., Jin, Yan, Lenglet, Christophe, Yacoub, Essa, Sapiro, Guillermo, Ugurbil, Kamil, Harel, Noam, Toga, Arthur W., Lim, Kelvin O., Thompson, Paul M., Farin, Gerald, Series editor, Hege, Hans-Christian, Series editor, Hoffman, David, Series editor, Johnson, Christopher R., Series editor, Polthier, Konrad, Series editor, Rumpf, Martin, Series editor, Schultz, Thomas, editor, Nedjati-Gilani, Gemma, editor, Venkataraman, Archana, editor, O'Donnell, Lauren, editor, and Panagiotaki, Eleftheria, editor

Published
2014
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37. Fast In Vivo High-Resolution Diffusion MRI of the Human Cervical Spinal Cord Microstructure

Author

Labounek, René, primary, Valošek, Jan, additional, Zimolka, Jakub, additional, Piskořová, Zuzana, additional, Horák, Tomáš, additional, Svátková, Alena, additional, Bednařík, Petr, additional, Hok, Pavel, additional, Vojtíšek, Lubomír, additional, Hluštík, Petr, additional, Bednařík, Josef, additional, and Lenglet, Christophe, additional

Published
2018
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39. Axon fiber orientation as the source of T1 relaxation anisotropy in white matter: A study on corpus callosum in vivo and ex vivo.

Author

Kauppinen, Risto A., Thothard, Jeromy, Leskinen, Henri P. P., Pisharady, Pramod K., Manninen, Eppu, Kettunen, Mikko, Lenglet, Christophe, Gröhn, Olli H. J., Garwood, Michael, and Nissi, Mikko J.

Subjects
FIBER orientation, CORPUS callosum, WHITE matter (Nerve tissue), AXONS, DIFFUSION magnetic resonance imaging
Abstract

Purpose: Recent studies indicate that T1 in white matter (WM) is influenced by fiber orientation in B0. The purpose of the study was to investigate the interrelationships between axon fiber orientation in corpus callosum (CC) and T1 relaxation time in humans in vivo as well as in rat brain ex vivo. Methods: Volunteers were scanned for relaxometric and diffusion MRI at 3 T and 7 T. Angular T1 plots from WM were computed using fractional anisotropy and fiber‐to‐field‐angle maps. T1 and fiber‐to‐field angle were measured in five sections of CC to estimate the effects of inherently varying fiber orientations on T1 within the same tracts in vivo. Ex vivo rat‐brain preparation encompassing posterior CC was rotated in B0 and T1, and diffusion MRI images acquired at 9.4 T. T1 angular plots were determined at several rotation angles in B0. Results: Angular T1 plots from global WM provided reference for estimated fiber orientation–linked T1 changes within CC. In anterior midbody of CC in vivo, where small axons are dominantly present, a shift in axon orientation is accompanied by a change in T1, matching that estimated from WM T1 data. In CC, where large and giant axons are numerous, the measured T1 change is about 2‐fold greater than the estimated one. Ex vivo rotation of the same midsagittal CC region of interest produced angular T1 plots at 9.4 T, matching those observed at 7 T in vivo. Conclusion: These data causally link axon fiber orientation in B0 to the T1 relaxation anisotropy in WM. [ABSTRACT FROM AUTHOR]

Published
2023
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40. A natural history study to track brain and spinal cord changes in individuals with Friedreich’s ataxia: TRACK-FA study protocol

Author

Georgiou-Karistianis, Nellie, primary, Corben, Louise A., additional, Reetz, Kathrin, additional, Adanyeguh, Isaac M., additional, Corti, Manuela, additional, Deelchand, Dinesh K., additional, Delatycki, Martin B., additional, Dogan, Imis, additional, Evans, Rebecca, additional, Farmer, Jennifer, additional, França, Marcondes C., additional, Gaetz, William, additional, Harding, Ian H., additional, Harris, Karen S., additional, Hersch, Steven, additional, Joules, Richard, additional, Joers, James J., additional, Krishnan, Michelle L., additional, Lax, Michelle, additional, Lock, Eric F., additional, Lynch, David, additional, Mareci, Thomas, additional, Muthuhetti Gamage, Sahan, additional, Pandolfo, Massimo, additional, Papoutsi, Marina, additional, Rezende, Thiago J. R., additional, Roberts, Timothy P. L., additional, Rosenberg, Jens T., additional, Romanzetti, Sandro, additional, Schulz, Jörg B., additional, Schilling, Traci, additional, Schwarz, Adam J., additional, Subramony, Sub, additional, Yao, Bert, additional, Zicha, Stephen, additional, Lenglet, Christophe, additional, and Henry, Pierre-Gilles, additional

Published
2022
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41. Progressive Spinal Cord Degeneration in Friedreich's Ataxia: Results from ENIGMA‐Ataxia

Author

Rezende, Thiago J.R., primary, Adanyeguh, Isaac M., additional, Arrigoni, Filippo, additional, Bender, Benjamin, additional, Cendes, Fernando, additional, Corben, Louise A., additional, Deistung, Andreas, additional, Delatycki, Martin, additional, Dogan, Imis, additional, Egan, Gary F., additional, Göricke, Sophia L., additional, Georgiou‐Karistianis, Nellie, additional, Henry, Pierre‐Gilles, additional, Hutter, Diane, additional, Jahanshad, Neda, additional, Joers, James M., additional, Lenglet, Christophe, additional, Lindig, Tobias, additional, Martinez, Alberto R.M., additional, Martinuzzi, Andrea, additional, Paparella, Gabriella, additional, Peruzzo, Denis, additional, Reetz, Kathrin, additional, Romanzetti, Sandro, additional, Schöls, Ludger, additional, Schulz, Jörg B., additional, Synofzik, Matthis, additional, Thomopoulos, Sophia I., additional, Thompson, Paul M., additional, Timmann, Dagmar, additional, Harding, Ian H., additional, and França, Marcondes C., additional

Published
2022
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48. ODF Maxima Extraction in Spherical Harmonic Representation via Analytical Search Space Reduction

Author

Aganj, Iman, Lenglet, Christophe, Sapiro, Guillermo, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Jiang, Tianzi, editor, Navab, Nassir, editor, Pluim, Josien P. W., editor, and Viergever, Max A., editor

Published
2010
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49. Multiple Q-Shell ODF Reconstruction in Q-Ball Imaging

Author

Aganj, Iman, Lenglet, Christophe, Sapiro, Guillermo, Yacoub, Essa, Ugurbil, Kamil, Harel, Noam, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Yang, Guang-Zhong, editor, Hawkes, David, editor, Rueckert, Daniel, editor, Noble, Alison, editor, and Taylor, Chris, editor

Published
2009
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50. Estimating Orientation Distribution Functions with Probability Density Constraints and Spatial Regularity

Author

Goh, Alvina, Lenglet, Christophe, Thompson, Paul M., Vidal, René, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Yang, Guang-Zhong, editor, Hawkes, David, editor, Rueckert, Daniel, editor, Noble, Alison, editor, and Taylor, Chris, editor

Published
2009
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