title: Robust thalamic nuclei segmentation method based on local diffusion magnetic resonance properties.
abstract: The thalamus is an essential relay station in the cortical-subcortical connections. It is characterized by a complex anatomical architecture composed of numerous small nuclei, which mediate the involvement of the thalamus in a wide range of neurological functions. We present a novel framework for segmenting the thalamic nuclei, which explores the orientation distribution functions (ODFs) from diffusion magnetic resonance images at 3 T. The differentiation of the complex intra-thalamic microstructure is improved by using the spherical harmonic (SH) representation of the ODFs, which provides full angular characterization of the diffusion process in each voxel. The clustering was performed using the k-means algorithm initialized in a data-driven manner. The method was tested on 35 healthy volunteers and our results show a robust, reproducible and accurate segmentation of the thalamus in seven nuclei groups. Six of them closely matched the anatomy and were labeled as anterior, ventral anterior, medio-dorsal, ventral latero-ventral, ventral latero-dorsal and pulvinar, while the seventh cluster included the centro-lateral and the latero-posterior nuclei. Results were evaluated both qualitatively, by comparing the segmented nuclei to the histological atlas of Morel, and quantitatively, by measuring the clusters' extent and the clusters' spatial distribution across subjects and hemispheres. We also showed the robustness of our approach across different sequences and scanners, as well as intra-subject reproducibility of the segmented clusters using additional two scan-rescan datasets. We also observed an overlap between the path of the main long-connection tracts passing through the thalamus and the spatial distribution of the nuclei identified with our clustering algorithm. Our approach, based on SH representations of the ODFs, outperforms the one based on angular differences between the principle diffusion directions, which is considered so far as state-of-the-art method. Our findings show an anatomically reliable segmentation of the main groups of thalamic nuclei that could be of potential use in many clinical applications.
authors.affiliation: Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland. giovanni.battistella@mssm.edu.|Department of Neurology, Icahn School of Medicine at Mount Sinai, One Gustave L Levy Pl, Annenberg Building, Floor 20, Room 81, New York, NY, 10029, USA. giovanni.battistella@mssm.edu.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Battistella
authors.affiliation: Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland. elena.najdenovska@unil.ch.|Centre d'Imagerie BioMédicale (CIBM), Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland. elena.najdenovska@unil.ch.|Department of Clinical Neuroscience, Neurosurgery Service and Gamma Knife Center, Lausanne University Hospital (CHUV), 1011, Lausanne, Switzerland. elena.najdenovska@unil.ch.
authors.forename: Elena
authors.initials: E
authors.lastname: Najdenovska
authors.affiliation: Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.
authors.forename: Philippe
authors.initials: P
authors.lastname: Maeder
authors.affiliation: Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.|Medical Image Processing Lab (MIPLab), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
authors.forename: Naghmeh
authors.initials: N
authors.lastname: Ghazaleh
authors.affiliation: Centre d'Imagerie BioMédicale (CIBM), Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.|Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Daducci
authors.affiliation: Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.|Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Thiran
authors.affiliation: Department of Pediatrics, University Hospital Center Sainte-Justine, Montreal, H3T 1C5, Canada.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Jacquemont
authors.affiliation: Department of Clinical Neuroscience, Neurosurgery Service and Gamma Knife Center, Lausanne University Hospital (CHUV), 1011, Lausanne, Switzerland.|Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.|Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne, Switzerland.
authors.forename: Constantin
authors.initials: C
authors.lastname: Tuleasca
authors.affiliation: Department of Clinical Neuroscience, Neurosurgery Service and Gamma Knife Center, Lausanne University Hospital (CHUV), 1011, Lausanne, Switzerland.|Faculty of Biology and Medicine, University of Lausanne (UNIL), Lausanne, Switzerland.
authors.forename: Marc
authors.initials: M
authors.lastname: Levivier
authors.affiliation: Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.|Centre d'Imagerie BioMédicale (CIBM), Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.|Signal Processing Laboratory (LTS5), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
authors.forename: Meritxell
authors.initials: M
authors.lastname: Bach Cuadra
authors.affiliation: Department of Radiology, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.|Centre d'Imagerie BioMédicale (CIBM), Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), 1011, Lausanne, Switzerland.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Fornari
mesh_terms: D000328:Adult; D000369:Aged, 80 and over; D000465:Algorithms; D001931:Brain Mapping / Q000379:methods; D038524:Diffusion Magnetic Resonance Imaging / Q000379:methods; D005260:Female; D006801:Humans; D008297:Male; D008875:Middle Aged; D009434:Neural Pathways / Q000033:anatomy & histology*; D015203:Reproducibility of Results; D013787:Thalamic Nuclei / Q000033:anatomy & histology*
keywords: Orientation distribution function; Segmentation; Spherical harmonics; Thalamic nuclei