Topologically preserving straightening of spinal cord MRI

To propose a robust and accurate method for straightening magnetic resonance (MR) images of the spinal cord, based on spinal cord segmentation, that preserves spinal cord topology and that works for any MRI contrast, in a context of spinal cord template‐based analysis.

[1]  Julien Cohen-Adad,et al.  Robust, accurate and fast automatic segmentation of the spinal cord , 2014, NeuroImage.

[2]  C. Pozzilli,et al.  MRI of spinal cord in MS. , 2000, Journal of neurovirology.

[3]  C. R. Deboor,et al.  A practical guide to splines , 1978 .

[4]  A. Thompson,et al.  Voxel-based analysis of grey and white matter degeneration in cervical spondylotic myelopathy , 2016, Scientific Reports.

[5]  R. Henry,et al.  Quantitative MRI of the spinal cord and brain in adrenomyeloneuropathy: in vivo assessment of structural changes. , 2016, Brain : a journal of neurology.

[6]  Habib Benali,et al.  Fast and Accurate Semi-Automated Segmentation Method of Spinal Cord MR Images at 3T Applied to the Construction of a Cervical Spinal Cord Template , 2015, PloS one.

[7]  John L. Ulmer,et al.  Morphology and Morphometry of Human Chronic Spinal Cord Injury Using Diffusion Tensor Imaging and Fuzzy Logic , 2008, Annals of Biomedical Engineering.

[8]  Julien Cohen-Adad,et al.  Automatic Labeling of Vertebral Levels Using a Robust Template-Based Approach , 2014, Int. J. Biomed. Imaging.

[9]  J. Cohen-Adad,et al.  Demyelination and degeneration in the injured human spinal cord detected with diffusion and magnetization transfer MRI , 2011, NeuroImage.

[10]  David H. Miller,et al.  Feasibility of grey matter and white matter segmentation of the upper cervical cord in vivo: A pilot study with application to magnetisation transfer measurements , 2012, NeuroImage.

[11]  Mark W. Woolrich,et al.  Bayesian analysis of neuroimaging data in FSL , 2009, NeuroImage.

[12]  Jared Narvid,et al.  An Imaging-Based Approach to Spinal Cord Infection. , 2016, Seminars in ultrasound, CT, and MR.

[13]  Andrea Bergmann,et al.  Statistical Parametric Mapping The Analysis Of Functional Brain Images , 2016 .

[14]  J. Cohen‐Adad,et al.  Segmentation of the human spinal cord , 2016, Magnetic Resonance Materials in Physics, Biology and Medicine.

[15]  Patrick W. Stroman,et al.  Spatial normalization, bulk motion correction and coregistration for functional magnetic resonance imaging of the human cervical spinal cord and brainstem. , 2008, Magnetic resonance imaging.

[16]  Mark W. Woolrich,et al.  FSL , 2012, NeuroImage.

[17]  D. L. Collins,et al.  Framework for integrated MRI average of the spinal cord white and gray matter: The MNI–Poly–AMU template , 2014, NeuroImage.

[18]  J. Ranjeva,et al.  Tract‐specific and age‐related variations of the spinal cord microstructure: a multi‐parametric MRI study using diffusion tensor imaging (DTI) and inhomogeneous magnetization transfer (ihMT) , 2016, NMR in biomedicine.

[19]  P. W. Stroman,et al.  The current state-of-the-art of spinal cord imaging: Applications , 2014, NeuroImage.

[20]  M. Nakamura M. D.,et al.  Preferential spinal central gray matter involvement in neuromyelitis optica , 2008, Journal of Neurology.

[21]  Julien Cohen-Adad,et al.  The current state-of-the-art of spinal cord imaging: Methods , 2014, NeuroImage.

[22]  M. Fehlings,et al.  Degenerative Cervical Myelopathy: Epidemiology, Genetics, and Pathogenesis , 2015, Spine.

[23]  P. Morgan,et al.  Measurement of cervical spinal cord cross‐sectional area by MRI using edge detection and partial volume correction , 2005, Journal of magnetic resonance imaging : JMRI.

[24]  A. Thompson,et al.  Spinal cord atrophy and disability in multiple sclerosis. A new reproducible and sensitive MRI method with potential to monitor disease progression. , 1996, Brain : a journal of neurology.

[25]  H. Benali,et al.  Validation of a semiautomated spinal cord segmentation method , 2015, Journal of magnetic resonance imaging : JMRI.

[26]  Yasuto Itoyama,et al.  Preferential spinal central gray matter involvement in neuromyelitis optica , 2008, Journal of neurology.

[27]  Seth A. Smith,et al.  Groupwise multi-atlas segmentation of the spinal cord's internal structure , 2014, Medical Image Anal..

[28]  M. A. Horsfield,et al.  Rapid semi-automatic segmentation of the spinal cord from magnetic resonance images: Application in multiple sclerosis , 2010, NeuroImage.

[29]  Julien Cohen-Adad,et al.  A reliable spatially normalized template of the human spinal cord — Applications to automated white matter/gray matter segmentation and tensor-based morphometry (TBM) mapping of gray matter alterations occurring with age , 2015, NeuroImage.

[30]  Julien Cohen-Adad,et al.  Quantitative MRI of the Spinal Cord , 2014 .

[31]  Julien Cohen-Adad,et al.  SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data , 2017, NeuroImage.

[32]  P. Valsasina,et al.  Spatial Normalization and Regional Assessment of Cord Atrophy: Voxel-Based Analysis of Cervical Cord 3D T1-Weighted Images , 2012, American Journal of Neuroradiology.

[33]  R. Henry,et al.  Age, Gender and Normalization Covariates for Spinal Cord Gray Matter and Total Cross-Sectional Areas at Cervical and Thoracic Levels: A 2D Phase Sensitive Inversion Recovery Imaging Study , 2015, PloS one.

[34]  F. Pernus,et al.  Automated curved planar reformation of 3D spine images , 2005, Physics in medicine and biology.

[35]  Yvan Petit,et al.  Morphometrics of the Entire Human Spinal Cord and Spinal Canal Measured From In Vivo High-Resolution Anatomical Magnetic Resonance Imaging , 2014, Spine.

[36]  David M. Mount,et al.  It's okay to be skinny, if your friends are fat , 1999 .

[37]  Julien Cohen-Adad,et al.  Automatic Segmentation of the Spinal Cord and Spinal Canal Coupled With Vertebral Labeling , 2015, IEEE Transactions on Medical Imaging.

[38]  André J. W. van der Kouwe,et al.  Brain morphometry with multiecho MPRAGE , 2008, NeuroImage.

[39]  S. Rossignol,et al.  Involvement of spinal sensory pathway in ALS and specificity of cord atrophy to lower motor neuron degeneration , 2013, Amyotrophic lateral sclerosis & frontotemporal degeneration.

[40]  Karl J. Friston,et al.  Statistical parametric maps in functional imaging: A general linear approach , 1994 .

[41]  David H. Miller,et al.  Fully automated segmentation of the cervical cord from T1-weighted MRI using PropSeg: Application to multiple sclerosis☆ , 2015, NeuroImage: Clinical.

[42]  Satrajit S. Ghosh,et al.  Nipype: A Flexible, Lightweight and Extensible Neuroimaging Data Processing Framework in Python , 2011, Front. Neuroinform..

[43]  R W Cox,et al.  AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. , 1996, Computers and biomedical research, an international journal.

[44]  Les A. Piegl,et al.  The NURBS Book , 1995, Monographs in Visual Communication.