title: Framework for integrated MRI average of the spinal cord white and gray matter: the MNI-Poly-AMU template.
abstract: The field of spinal cord MRI is lacking a common template, as existing for the brain, which would allow extraction of multi-parametric data (diffusion-weighted, magnetization transfer, etc.) without user bias, thereby facilitating group analysis and multi-center studies. This paper describes a framework to produce an unbiased average anatomical template of the human spinal cord. The template was created by co-registering T2-weighted images (N = 16 healthy volunteers) using a series of pre-processing steps followed by non-linear registration. A white and gray matter probabilistic template was then merged to the average anatomical template, yielding the MNI-Poly-AMU template, which currently covers vertebral levels C1 to T6. New subjects can be registered to the template using a dedicated image processing pipeline. Validation was conducted on 16 additional subjects by comparing an automatic template-based segmentation and manual segmentation, yielding a median Dice coefficient of 0.89. The registration pipeline is rapid (~15 min), automatic after one C2/C3 landmark manual identification, and robust, thereby reducing subjective variability and bias associated with manual segmentation. The template can notably be used for measurements of spinal cord cross-sectional area, voxel-based morphometry, identification of anatomical features (e.g., vertebral levels, white and gray matter location) and unbiased extraction of multi-parametric data.
authors.affiliation: Montreal Neurological Institute (MNI), McGill University, Montreal, QC, Canada.
authors.forename: V S
authors.initials: VS
authors.lastname: Fonov
authors.affiliation: Centre de Résonance Magnétique Biologique et Médicale (CRMBM), UMR 7339, Aix-Marseille Université (AMU), CNRS, 13385 Marseille, France; Centre d'Exploration Métabolique par Résonance Magnétique (CEMEREM), Hôpital de la Timone, AP-HM, 13005 Marseille, France.
authors.forename: A
authors.initials: A
authors.lastname: Le Troter
authors.affiliation: Centre de Résonance Magnétique Biologique et Médicale (CRMBM), UMR 7339, Aix-Marseille Université (AMU), CNRS, 13385 Marseille, France; Centre d'Exploration Métabolique par Résonance Magnétique (CEMEREM), Hôpital de la Timone, AP-HM, 13005 Marseille, France.
authors.forename: M
authors.initials: M
authors.lastname: Taso
authors.affiliation: Institute of Biomedical Engineering, Polytechnique Montreal (Poly), Montreal, QC, Canada.
authors.forename: B
authors.initials: B
authors.lastname: De Leener
authors.affiliation: Institute of Biomedical Engineering, Polytechnique Montreal (Poly), Montreal, QC, Canada.
authors.forename: G
authors.initials: G
authors.lastname: Lévêque
authors.affiliation: Institute of Biomedical Engineering, Polytechnique Montreal (Poly), Montreal, QC, Canada.
authors.forename: M
authors.initials: M
authors.lastname: Benhamou
authors.affiliation: Université de Lyon, CREATIS, CNRS UMR 5220, Inserm U1044, INSA-Lyon, France.
authors.forename: M
authors.initials: M
authors.lastname: Sdika
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Laboratoire d'Imagerie Biomédicale, F-75005 Paris, France.
authors.forename: H
authors.initials: H
authors.lastname: Benali
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Laboratoire d'Imagerie Biomédicale, F-75005 Paris, France; Département des Maladies du Système Nerveux, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Paris, France.
authors.forename: P-F
authors.initials: PF
authors.lastname: Pradat
authors.affiliation: Montreal Neurological Institute (MNI), McGill University, Montreal, QC, Canada.
authors.forename: D L
authors.initials: DL
authors.lastname: Collins
authors.affiliation: Centre de Résonance Magnétique Biologique et Médicale (CRMBM), UMR 7339, Aix-Marseille Université (AMU), CNRS, 13385 Marseille, France; Centre d'Exploration Métabolique par Résonance Magnétique (CEMEREM), Hôpital de la Timone, AP-HM, 13005 Marseille, France.
authors.forename: V
authors.initials: V
authors.lastname: Callot
authors.affiliation: Institute of Biomedical Engineering, Polytechnique Montreal (Poly), Montreal, QC, Canada; Functional Neuroimaging Unit, CRIUGM, Université de Montréal, Montreal, QC, Canada. Electronic address: jcohen@polymtl.ca.
authors.forename: J
authors.initials: J
authors.lastname: Cohen-Adad
mesh_terms: D000328:Adult; D005260:Female; D066128:Gray Matter / Q000033:anatomy & histology*; D006801:Humans; D008279:Magnetic Resonance Imaging; D008297:Male; D013116:Spinal Cord / Q000033:anatomy & histology; D066127:White Matter / Q000033:anatomy & histology*
keywords: Group analysis; MRI; Registration; Spinal cord; Template