Journal articles

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mri-physics shimming quantitative-mri fmri image-analysis deep-learning microscopy spinal-cord-injury multiple-sclerosis neuroscience

2024

SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spinal Cord Injury

Karthik EN, Valosek J, Farner L, Pfyffer D, Schading-Sassenhausen S, Lebret A, David G, Smith AC, Weber II KA, Seif M, Freund P, Cohen-Adad J, RHSCIR Network Imaging Group

MICCAI Workshop on Applications of Medical AI (AMAI) (2024) Link to paper (Labels: image-analysis, deep-learning)

Contrast-agnostic Spinal Cord Segmentation: A Comparative Study of ConvNets and Vision Transformers

Karthik EN, Bedard S, Valosek J, Chandar S, Cohen-Adad J

MIDL - Medical Imaging with Deep Learning (2024) Link to paper (Labels: image-analysis, deep-learning)

Automatic segmentation of the spinal cord nerve rootlets

Valošek J, Mathieu T, Schlienger R, Kowalczyk OS, Cohen-Adad J

Imaging Neuroscience (2024) Link to paper (Labels: image-analysis, deep-learning)

Calibration-free parallel transmission of the cervical, thoracic, and lumbar spinal cord at 7T

Aigner CS, Sánchez Alarcon MF, D’Astous A, Alonso-Ortiz E, Cohen-Adad J, Schmitter S

Magn Reson Med (2024) Link to paper (Labels: mri-physics, shimming)

Myelin basic protein mRNA levels affect myelin sheath dimensions, architecture, plasticity, and density of resident glial cells

Bagheri H, Friedman H, Hadwen A, Jarweh C, Cooper E, Oprea L, Guerrier C, Khadra A, Collin A, Cohen-Adad J, Young A, Victoriano GM, Swire M, Jarjour A, Bechler ME, Pryce RS, Chaurand P, Cougnaud L, Vuckovic D, Wilion E, Greene O, Nishiyama A, Benmamar-Badel A, Owens T, Grouza V, Tuznik M, Liu H, Rudko DA, Zhang J, Siminovitch KA, Peterson AC

Glia (2024) Link to paper (Labels: neuroscience, image-analysis, deep-learning)

RF shimming in the cervical spinal cord at 7 T

Papp D, Gilbert KM, Cereza G, D’Astous A, Lopez-Rios N, Boudreau M, Couch MJ, Yazdanbakhsh P, Barry RL, Alonso-Ortiz E, Cohen-Adad J

Magn Reson Med (2024) Link to paper (Labels: mri-physics, shimming)

A database of the healthy human spinal cord morphometry in the PAM50 template space

Valošek J, Bédard S, Keřkovský M, Rohan T, Cohen-Adad J

Imaging Neuroscience (2024) Link to paper (Labels: image-analysis, quantitative-mri)

Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox

Valošek J, Cohen-Adad J

Magn Reson Med Sci (2024) Link to paper (Labels: image-analysis, quantitative-mri)

Repeat it without me: Crowdsourcing the T1 mapping common ground via the ISMRM reproducibility challenge

Boudreau M, Karakuzu A, Cohen-Adad J, Bozkurt E, Carr M, Castellaro M, Concha L, Doneva M, Dual SA, Ensworth A, Foias A, Fortier V, Gabr RE, Gilbert G, Glide-Hurst CK, Grech-Sollars M, Hu S, Jalnefjord O, Jovicich J, Keskin K, Koken P, Kolokotronis A, Kukran S, Lee NG, Levesque IR, Li B, Ma D, Mädler B, Maforo NG, Near J, Pasaye E, Ramirez-Manzanares A, Statton B, Stehning C, Tambalo S, Tian Y, Wang C, Weiss K, Zakariaei N, Zhang S, Zhao Z, Stikov N

Magn Reson Med (2024) Link to paper (Labels: mri-physics, image-analysis, quantitative-mri)

Quantifying neurodegeneration of the cervical cord and brain in degenerative cervical myelopathy: A multicentre study using quantitative magnetic resonance imaging

Freund P, Boller V, Emmenegger TM, Akbar M, Hupp M, Pfender N, Wheeler-Kingshott CAMG, Cohen-Adad J, Fehlings MG, Curt A, Seif M

Eur J Neurol (2024) Link to paper (Labels: image-analysis, quantitative-mri)

SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-Weighted MRI Scans

Karthik EN, Valosek J, Smith AC, Pfyffer D, Schading-Sassenhausen S, Farner L, Weber KA II, Freund P, Cohen-Adad J

Radiol Artif Intell (2024) Link to paper (Labels: deep-learning, image-analysis, spinal-cord-injury)

Spinal cord perfusion impairments in the M83 mouse model of Parkinson’s disease

Combes BF, Kalva SK, Benveniste P-L, Tournant A, Law MH, Newton J, Krüger M, Weber RZ, Dias I, Noain D, Dean-Ben XL, Konietzko U, Baumann CR, Gillberg P-G, Hock C, Nitsch RM, Cohen-Adad J, Razansky D, Ni R

Eur J Nucl Med Mol Imaging (2024) Link to paper (Labels: microscopy, deep-learning, image-analysis)

2023

Pontomedullary junction as a reference for spinal cord cross-sectional area: validation across neck positions

Bédard S, Bouthillier M, Cohen-Adad J

Sci Rep (2023) Link to paper (Labels: image-analysis, neuroscience)

HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation

Heidari M, Kazerouni A, Soltany M, Azad R, Aghdam EK, Cohen-Adad J, Merhof D

Winter Conference on Applications of Computer Vision (WACV) (2023) Link to paper (Labels: image-analysis, deep-learning)

Dynamic shimming in the cervical spinal cord for multi-echo gradient-echo imaging at 3 T

Alonso-Ortiz E, Papp D, D’Astous A, Cohen-Adad J

Neuroimage: Reports (2023) Link to paper (Labels: mri-physics, shimming)

Contrast-agnostic deep learning–based registration pipeline: Validation in spinal cord multimodal MRI data

Beal E, Cohen-Adad J

Aperture Neuro (2023) Link to paper (Labels: deep-learning, image-analysis)

An 8-channel Tx dipole and 20-channel Rx loop coil array for MRI of the cervical spinal cord at 7 Tesla

Lopez-Rios N, Gilbert KM, Papp D, Cereza G, Foias A, Rangaprakash D, May MW, Guerin B, Wald LL, Keil B, Stockmann JP, Barry RL, Cohen-Adad J

NMR Biomed (2023) Link to paper (Labels: mri-physics)

Effectiveness of regional diffusion MRI measures in distinguishing multiple sclerosis abnormalities within the cervical spinal cord

Snoussi H, Cohen-Adad J, Combès B, Bannier É, Tounekti S, Kerbrat A, Barillot C, Caruyer E

Brain Behav (2023) Link to paper (Labels: multiple-sclerosis, image-analysis)

2022

Reproducibility and Evolution of Diffusion MRI Measurements within the Cervical Spinal Cord in Multiple Sclerosis

Snoussi H, Caruyer E, Combes B, Commowick O, Bannier E, Kerbrat A, Cohen-Adad J

IEEE International Symposium on Biomedical Imaging (ISBI) (2022) Link to paper (Labels: quantitative-mri, image-analysis)

Intervertebral Disc Labeling with Learning Shape Information, a Look once Approach

Azad R, Heidari M, Cohen-Adad J, Adeli E, Merhof D

Predictive Intelligence in Medicine: 5th International Workshop, PRIME 2022, Held in Conjunction with MICCAI (2022) Link to paper (Labels: image-analysis, deep-learning)

Segmentation of Multiple Sclerosis Lesions across Hospitals: Learn Continually or Train from Scratch?

Karthik EN, Kerbrat A, Labauge P, Granberg T, Talbott J, Reich DS, Filippi M, Bakshi R, Callot V, Chandar S, Cohen-Adad J

Medical Imaging Meets NeurIPS (MedNeurIPS) Workshop (2022) Link to paper (Labels: image-analysis, deep-learning)

NeoRS: A neonatal resting state fMRI data preprocessing pipeline

Enguix V, Kenley J, Luck D, Cohen-Adad J, Lodygensky GA

Front Neuroinform (2022) Link to paper (Labels: mri-physics, image-analysis, quantitative-mri)

Shimming Toolbox: An open-source software toolbox for B0 and B1 shimming in Magnetic Resonance Imaging

D’Astous A, Cereza G, Papp D, Gilbert KM, Stockmann JP, Alonso-Ortiz E, Cohen-Adad J

Magn Reson Med (2022) Link to paper (Labels: mri-physics, shimming)

Automatic measure and normalization of spinal cord cross-sectional area using the pontomedullary junction

Bédard S, Cohen-Adad J

Front Neuroimaging (2022) Link to paper (Labels: image-analysis)

Label fusion and training methods for reliable representation of inter-rater uncertainty

Lemay A, Gros C, Karthik EN, Cohen-Adad J

Machine Learning for Biomedical Imaging (2022) Link to paper (Labels: deep-learning, image-analysis)

Histology-informed automatic parcellation of white matter tracts in the rat spinal cord

Nami H, Perone CS, Cohen-Adad J

Front Neuroanat (2022) Link to paper (Labels: microscopy)

Vendor-neutral sequences and fully transparent workflows improve inter-vendor reproducibility of quantitative MRI

Karakuzu A, Biswas L, Cohen-Adad J, Stikov N

Magn Reson Med (2022) Link to paper (Labels: mri-physics)

Relationship Between Arterial Stiffness Index, Pulse Pressure, and Magnetic Resonance Imaging Markers of White Matter Integrity: A UK Biobank Study

Badji A, Cohen-Adad J, Girouard H

Front Aging Neurosci (2022) Link to paper (Labels: quantitative-mri, image-analysis)

Rapid, automated nerve histomorphometry through open-source artificial intelligence

Daeschler SC, Bourget M-H, Derakhshan D, Sharma V, Asenov SI, Gordon T, Cohen-Adad J, Borschel GH

Sci Rep (2022) Link to paper (Labels: microscopy, deep-learning, image-analysis)

Comparison of multicenter MRI protocols for visualizing the spinal cord gray matter

Cohen-Adad J, Alonso-Ortiz E, Alley S, Lagana MM, Baglio F, Vannesjo SJ, Karbasforoushan H, Seif M, Seifert AC, Xu J, Kim J-W, Labounek R, Vojtíšek L, Dostál M, Valošek J, Samson RS, Grussu F, Battiston M, Gandini Wheeler-Kingshott CAM, Yiannakas MC, Gilbert G, Schneider T, Johnson B, Prados F

Magn Reson Med (2022) Link to paper (Labels: mri-physics)

Quantitative electrophysiological assessments as predictive markers of lower limb motor recovery after spinal cord injury: a pilot study with an adaptive trial design

Huang YN, Meftah EM, Pion CH, Mac-Thiong JM, Cohen-Adad J, Barthélemy D

Spinal Cord Ser Cases (2022) Link to paper (Labels: spinal-cord-injury)

The myelin-weighted connectome in Parkinson’s disease

Boshkovski T, Cohen-Adad J, Misic B, Aranult I, Corvol J-C, Vidailhet M, Lehéricy S, Mancini M, Stikov N

Mov Disord (2022) Link to paper (Labels: quantitative-mri, image-analysis)

Diffusion kurtosis imaging of neonatal spinal cord in clinical routine

Trò R, Roascio M, Tortora D, Severino M, Rossi A, Cohen-Adad J, Fato MM, Arnulfo G

Front Neurol (2022) Link to paper (Labels: quantitative-mri)

Advanced Diffusion MR Imaging for Multiple Sclerosis in the Brain and Spinal Cord

Hori M, Maekawa T, Kamiya K, Hagiwara A, Goto M, Takemura MY, Fujita S, Andica C, Kamagata K, Cohen-Adad J, Aoki S

Magn Reson Med Sci (2022) Link to paper (Labels: multiple-sclerosis, quantitative-mri)

Brain-spinal cord interaction in long-term motor sequence learning in human: An fMRI study

Khatibi A, Vahdat S, Lungu O, Finsterbusch J, Büchel C, Cohen-Adad J, Marchand-Pauvert V, Doyon J

Neuroimage (2022) Link to paper (Labels: neuroscience, fmri, image-analysis)

Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data

Bourget M-H, Kamentsky L, Ghosh SS, Mazzamuto G, Lazari A, Markiewicz CJ, Oostenveld R, Niso G, Halchenko YO, Lipp I, Takerkart S, Toussaint P-J, Khan AR, Nilsonne G, Castelli FM, The BIDS Maintainers, Cohen-Adad J

Front Neurosci (2022) Link to paper (Labels: microscopy)

2021

Benefits of Linear Conditioning with Metadata for Image Segmentation

Lemay A, Gros C, Vincent O, Liu Y, Cohen JP, Cohen-Adad J

MIDL - Medical Imaging with Deep Learning (2021) Link to paper (Labels: image-analysis, deep-learning)

Stacked Hourglass Network with a Multi-level Attention Mechanism: Where to Look for Intervertebral Disc Labeling

Azad R, Rouhier L, Cohen-Adad J

Machine Learning in Medical Imaging (MLMI 2021) (2021) Link to paper (Labels: image-analysis, deep-learning)

A simple and robust method for automating analysis of naïve and regenerating peripheral nerves

Wong A, Hricz N, Malapati H, von Guionneau N, Wong MJ, Harris T, Boudreau M, Cohen-Adad J

PLoS ONE (2021) Link to paper (Labels: microscopy, image-analysis, deep-learning)

ivadomed: A Medical Imaging Deep Learning Toolbox

Gros C, Lemay A, Vincent O, Rouhier L, Bourget M-H, Bucquet A, Cohen J, Cohen-Adad J

J Open Source Softw (2021) Link to paper (Labels: deep-learning, image-analysis)

Quantitative magnetic resonance imaging of spinal cord microstructure in adults with cerebral palsy

Cohen-Adad J

Dev Med Child Neurol (2021) Link to paper (Labels: quantitative-mri)

Atlas-based Quantification of DTI measures in Typically Developing Pediatric Spinal Cord

Shahrampour S, Flanders A, Faro S, Cohen-Adad J, De-leener B, Middleton D, Krisa L, Alizadeh M, Mohamed F

AJNR (2021) Link to paper (Labels: quantitative-mri, image-analysis)

Generic acquisition protocol for quantitative MRI of the spinal cord

Cohen-Adad J, Alonso-Ortiz E, Abramovic M, Arneitz C, Atcheson N, Barlow L, Barry RL, Barth M, Battiston M, Büchel C, Budde M, Callot V, Combes AJE, De Leener B, Descoteaux M, de Sousa PL, Dostál M, Doyon J, Dvorak A, Eippert F, Epperson KR, Epperson KS, Freund P, Finsterbusch J, Foias A, Fratini M, Fukunaga I, Wheeler-Kingshott CAMG, Germani G, Gilbert G, Giove F, Gros C, Grussu F, Hagiwara A, Henry P-G, Horák T, Hori M, Joers J, Kamiya K, Karbasforoushan H, Keřkovský M, Khatibi A, Kim J-W, Kinany N, Kitzler H, Kolind S, Kong Y, Kudlička P, Kuntke P, Kurniawan ND, Kusmia S, Labounek R, Laganà MM, Laule C, Law CS, Lenglet C, Leutritz T, Liu Y, Llufriu S, Mackey S, Martinez-Heras E, Mattera L, Nestrasil I, O’Grady KP, Papinutto N, Papp D, Pareto D, Parrish TB, Pichiecchio A, Prados F, Rovira À, Ruitenberg MJ, Samson RS, Savini G, Seif M, Seifert AC, Smith AK, Smith SA, Smith ZA, Solana E, Suzuki Y, Tackley G, Tinnermann A, Valošek J, Van De Ville D, Yiannakas MC, Weber KA 2nd, Weiskopf N, Wise RG, Wyss PO, Xu J

Nat Protoc (2021) Link to paper (Labels: quantitative-mri)

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

Cohen-Adad J, Alonso-Ortiz E, Abramovic M, Arneitz C, Atcheson N, Barlow L, Barry RL, Barth M, Battiston M, Büchel C, Budde M, Callot V, Combes AJE, De Leener B, Descoteaux M, de Sousa PL, Dostál M, Doyon J, Dvorak A, Eippert F, Epperson KR, Epperson KS, Freund P, Finsterbusch J, Foias A, Fratini M, Fukunaga I, Gandini Wheeler-Kingshott CAM, Germani G, Gilbert G, Giove F, Gros C, Grussu F, Hagiwara A, Henry P-G, Horák T, Hori M, Joers J, Kamiya K, Karbasforoushan H, Keřkovský M, Khatibi A, Kim J-W, Kinany N, Kitzler HH, Kolind S, Kong Y, Kudlička P, Kuntke P, Kurniawan ND, Kusmia S, Labounek R, Laganà MM, Laule C, Law CS, Lenglet C, Leutritz T, Liu Y, Llufriu S, Mackey S, Martinez-Heras E, Mattera L, Nestrasil I, O’Grady KP, Papinutto N, Papp D, Pareto D, Parrish TB, Pichiecchio A, Prados F, Rovira À, Ruitenberg MJ, Samson RS, Savini G, Seif M, Seifert AC, Smith AK, Smith SA, Smith ZA, Solana E, Suzuki Y, Tackley G, Tinnermann A, Valošek J, Van De Ville D, Yiannakas MC, Weber KA Ii, Weiskopf N, Wise RG, Wyss PO, Xu J

Sci Data (2021) Link to paper (Labels: quantitative-mri, image-analysis)

SoftSeg: Advantages of soft versus binary training for image segmentation

Gros C, Lemay A, Cohen-Adad J

Med Image Anal (2021) Link to paper (Labels: deep-learning, image-analysis)

Associations between relative morning blood pressure, cerebral blood flow, and memory in older adults treated and controlled for hypertension

Noriega de la Colina A, Badji A, Robitaille-Grou MC, Gagnon C, Boshkovski T, Lamarre-Cliche M, Joubert S, Gauthier C, Bherer L, Cohen-Adad J, Girouard H

Hypertension (2021) Link to paper (Labels: neuroscience)

Minimum detectable spinal cord atrophy with automatic segmentation: Investigations using an open-access dataset of healthy participants

Bautin P, Cohen-Adad J

NeuroImage Clin (2021) Link to paper (Labels: quantitative-mri, image-analysis, multiple-sclerosis)

Reduced Axon Calibre in the Associative Striatum of the Sapap3 Knockout Mouse

Lousada E, Boudreau M, Cohen-Adad J, Oumesmar BN, Burguiere E, Schreiweis C

Brain Sci (2021) Link to paper (Labels: microscopy)

Quantitative 7-Tesla imaging of cortical myelin changes in early multiple sclerosis

Barletta V, Herranz E, Treaba CA, Mehndiratta A, Ouellette R, Mangeat G, Granberg T, Sloane JA, Klawiter EC, Cohen-Adad J, Mainero C

Front Neurol (2021) Link to paper (Labels: quantitative-mri, multiple-sclerosis)

The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure

Boshkovski T, Kocarev L, Cohen-Adad J, Mišić B, Lehéricy S, Stikov N, Mancini M

Netw Neurosci (2021) Link to paper (Labels: quantitative-mri, image-analysis)

Automatic multiclass intramedullary spinal cord tumor segmentation on MRI with deep learning

Lemay A, Gros C, Zhuo Z, Zhang J, Duan Y, Cohen-Adad J, Liu Y

Neuroimage Clin (2021) Link to paper (Labels: deep-learning, image-analysis)

Rapid simultaneous acquisition of macromolecular tissue volume, susceptibility, and relaxometry maps

Yu FF, Huang SY, Kumar A, Witzel T, Liao C, Duval T, Cohen-Adad J, Bilgic B

Magn Reson Med (2021) Link to paper (Labels: quantitative-mri)

Diffusion MRI reveals tract-specific microstructural correlates of electrophysiological impairments in non-myelopathic and myelopathic spinal cord compression

Valošek J, Labounek R, Horák T, Horáková M, Bednařík P, Keřkovský M, Kočica J, Rohan T, Lenglet C, Cohen-Adad J, Hluštík P, Vlčková E, Kadaňka Z, Bednařík J, Svatkova A

Eur J Neurol (2021) Link to paper (Labels: spinal-cord-injury, quantitative-mri, image-analysis)

Tracking White and Gray Matter Degeneration along the Spinal Cord Axis in Degenerative Cervical Myelopathy

Vallotton K, David G, Hupp M, Pfender N, Cohen-Adad J, Fehlings MG, Samson RS, Wheeler-Kingshott CAMG, Curt A, Freund P, Seif M

J Neurotrauma (2021) Link to paper (Labels: spinal-cord-injury, quantitative-mri, image-analysis)

Spinal Cord Morphology in Degenerative Myelopathy Patients; Assessing Key Morphological Characteristics Using Machine Vision Tools

Ost K, Jacobs WB, Evaniew N, Cohen-Adad J, Anderson D, Cadotte D

Journal of Clinical Medicine (2021) Link to paper (Labels: spinal-cord-injury, quantitative-mri, image-analysis)

Spatial correspondence of spinal cord white matter tracts using diffusion tensor imaging, fibre tractography, and atlas-based segmentation

McLachlin S, Leung J, Sivan V, Quirion P-O, Wilkie P, Cohen-Adad J, Whyne C M, Hardisty M R

Neuroradiology (2021) Link to paper (Labels: quantitative-mri, image-analysis)

2020

Injury Volume Extracted from MRI Predicts Neurologic Outcome in Acute Spinal Cord Injury: A Prospective TRACK-SCI Pilot Study

Mummaneni N, Burke JF, DiGiorgio AM, Thomas LH, Duong-Fernandez X, Harris M, Pascual LU, Ferguson AR, Russell Huie J, Pan JZ, Hemmerle DD, Singh V, Torres-Espin A, Omondi C, Kyritsis N, Weinstein PR, Whetstone WD, Manley GT, Bresnahan JC, Beattie MS, Cohen-Adad J, Dhall SS, Talbott JF

J Clin Neurosci (2020) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

HARDI-ZOOMit protocol improves specificity to microstructural changes in presymptomatic myelopathy

Labounek R, Valošek J, Horák T, Svátková A, Bednařík P, Vojtíšek L, Horáková M, Nestrašil I, Lenglet C, Cohen-Adad J, Bednařík J, Hluštík P

Sci Rep (2020) Link to paper (Labels: quantitative-mri)

An interactive meta-analysis of MRI biomarkers of myelin

Mancini M, Karakuzu A, Cohen-Adad J, Cercignani M, Nichols T, Stikov N

eLife (2020) Link to paper (Labels: quantitative-mri)

Cortico-spinal imaging to study pain

Tinnermann A, Büchel C, Cohen-Adad J

NeuroImage (2020) Link to paper (Labels: neuroscience)

qMRLab: Quantitative MRI analysis, under one umbrella

Karakuzu A, Boudreau M, Duval T, Boshkovski T, Leppert IL, Cabana J-F, Gagnon I, Beliveau P, Pike GB, Cohen-Adad J, Stikov N

Journal of Open Source Software (2020) Link to paper (Labels: quantitative-mri, image-analysis)

Resting-state brain and spinal cord networks in humans are functionally integrated

Vahdat S, Khatibi A, Lungu O, Finsterbusch J, Büchel C, Cohen-Adad J, Marchand-Pauvert V, Doyon J

PLoS Biol (2020) Link to paper (Labels: neuroscience, fmri)

Machine learning and multi-parametric brain MRI to differentiate hereditary diffuse leukodystrophy with spheroids from multiple sclerosis

Mangeat G, Ouellette R, Wabartha M, De Leener B, Plattén M, Danylaité Karrenbauer V, Warntjes M, Stikov N, Mainero C, Cohen-Adad J, Granberg T

J Neuroimaging (2020) Link to paper (Labels: multiple-sclerosis, deep-learning, quantitative-mri, image-analysis)

Validation of Rapid Magnetic Resonance Myelin Imaging in Multiple Sclerosis

Ouellette R, Mangeat G, Polyak I, Warntjes M, Forslin Y, Bergendal Å, Plattén M, Uppman M, Treaba CA, Cohen-Adad J, Piehl F, Wiberg MK, Fredrikson S, Mainero C, Granberg T

Ann Neurol (2020) Link to paper (Labels: multiple-sclerosis, quantitative-mri)

Multi-parametric quantitative in vivo spinal cord MRI with unified signal readout and image denoising

Grussu F, Battiston M, Veraart J, Schneider T, Cohen-Adad J, Shepherd TM, Alexander DC, Fieremans E, Novikov DS, Gandini Wheeler-Kingshott CAM

Neuroimage (2020) Link to paper (Labels: quantitative-mri)

Imaging mechanisms of disease progression in multiple sclerosis: beyond brain atrophy

Bagnato F, Gauthier SA, Laule C, Moore GRW, Bove R, Cai Z, Cohen-Adad J, Harrison DM, Klawiter EC, Morrow SA, Öz G, Rooney WD, Smith SA, Calabresi PA, Henry RG, Oh J, Ontaneda D, Pelletier D, Reich DS, Shinohara RT, Sicotte NL; NAIMS Cooperative

J Neuroimaging (2020) Link to paper (Labels: quantitative-mri, multiple-sclerosis)

7 T imaging reveals a gradient in spinal cord lesion distribution in multiple sclerosis

Ouellette R, Treaba CA, Granberg T, Herranz E, Barletta V, Mehndiratta A, De Leener B, Tauhid S, Yousuf F, Dupont SM, Klawiter EC, Sloane JA, Bakshi R, Cohen-Adad J, Mainero C

Brain (2020) Link to paper (Labels: multiple-sclerosis, quantitative-mri)

Multiple sclerosis lesions in motor tracts from the brain to the cervical cord: spatial distribution and correlation with disability

Kerbrat A, Gros C, Badji A, Bannier E, Galassi F, Combès B, Chouteau R, Labauge P, Ayrignac X, Carra Dallière C, Maranzano J, Zhuoquiong R, Granberg T, Ouellette R, Stawiarz L, Hillert J, Talbott J, Tachibana Y, Hori M, Kamiya K, Chougar L, Lefeuvre J, Reich DS, Nair G, Valsasina P, Rocca MA, Filippi M, Chu R, Bakshi R, Callot V, Pelletier J, Audoin B, Maarouf A, Collongues N, De Seze J, Edan G, Cohen-Adad J

Brain (2020) Link to paper (Labels: multiple-sclerosis, image-analysis)

Deep Semantic Segmentation of Natural and Medical Images: A Review

Taghanaki SA, Abhishek K, Cohen JP, Cohen-Adad J, Hamarneh G

Artificial Intelligence Review (2020) Link to paper (Labels: deep-learning, image-analysis)

2019

Geometric evaluation of distortion correction methods in diffusion MRI of the spinal cord

Snoussi H, Caruyer E, Cohen-Adad J, Commowick O, Combès B, Bannier E, Anne K, Barillot C

IEEE International Symposium on Biomedical Imaging (ISBI) (2019) Link to paper (Labels: quantitative-mri, image-analysis)

Open-source pipeline for multi-class segmentation of the spinal cord with deep learning

Paugam F, Lefeuvre J, Perone CS, Gros C, Reich DS, Sati P, Cohen-Adad J

Magn Reson Imaging (2019) Link to paper (Labels: deep-learning, image-analysis)

Signal Intensity within Cerebral Venous Sinuses on Synthetic MRI

Chougar L, Hagiwara A, Takano N, Andica C, Cohen-Adad J, Warntjes M, Maekawa T, Hori M, Koshino S, Nakazawa M, Abe O, Aoki S

Magn Reson Med Sci (2019) Link to paper (Labels: image-analysis, mri-physics, quantitative-mri)

Convolutional Neural Network-Based Automated Segmentation of the Spinal Cord and Contusion Injury: Deep Learning Biomarker Correlates of Motor Impairment in Acute Spinal Cord Injury

McCoy DB, Dupont SM, Gros C, Cohen-Adad J, Huie RJ, Ferguson A, Duong-Fernandez X, Thomas LH, Singh V, Narvid J, Pascual L, Kyritsis N, Beattie MS, Bresnahan JC, Dhall S, Whetstone W, Talbott JF, Investigators T-S

AJNR Am J Neuroradiol (2019) Link to paper (Labels: deep-learning, image-analysis, spinal-cord-injury)

Promises and limitations of deep learning for medical image segmentation

Perone CS, Cohen-Adad J

Journal of Medical Artificial Intelligence (2019) Link to paper (Labels: deep-learning, image-analysis)

Unsupervised domain adaptation for medical imaging segmentation with self-ensembling

Perone CS, Ballester P, Barros RC, Cohen-Adad J

Neuroimage (2019) Link to paper (Labels: deep-learning, image-analysis)

Arterial stiffness and white matter integrity in the elderly: A diffusion tensor and magnetization transfer imaging study

Badji A, Noriega de la Colina A, Karakuzu A, Duval T, Desjardins-Crepeau L, Joubert S, Bherer L, Lamarre-Cliche M, Stikov N, Girouard H, Cohen-Adad J

Neuroimage (2019) Link to paper (Labels: neuroscience, quantitative-mri)

Fixed-Point U-Net Quantization for Medical Image Segmentation

Hemmat M, Honari S, Rouhier L, Perone CS, Cohen-Adad J, Savaria Y, David J-P

MICCAI Workshop on Hardware Aware Learning for Medical Imaging and Computer Assisted Intervention (2019) Link to paper (Labels: image-analysis)

Arterial stiffness cut-off value and white matter integrity in the elderly

Badji A, Noriega de la Colina A, Karakuzu A, Duval T, Desjardins-Crépeau L, Parizet M, Joubert S, Bherer L, Lamarre-Cliche M, Stikov N, Cohen-Adad J, Girouard H

Neuroimage Clin (2019) Link to paper (Labels: neuroscience, quantitative-mri)

Construction of a rat spinal cord atlas of axon morphometry

Saliani A, Zaimi A, Nami H, Duval T, Stikov N, Cohen-Adad J

Neuroimage (2019) Link to paper (Labels: microscopy, image-analysis)

Traumatic and nontraumatic spinal cord injury: pathological insights from neuroimaging

Gergely D, Mohammadi S, Martin A, Cohen-Adad J, Weiskopf N, Thompson A, Freund P

Nat Rev Neurol (2019) Link to paper (Labels: spinal-cord-injury, image-analysis)

Profiles of cortical inflammation in multiple sclerosis by 11C-PBR28 MR-PET and 7 Tesla imaging

Herranz E, Louapre C, Treaba CA, Govindarajan ST, Ouellette R, Mangeat G, Loggia ML, Cohen-Adad J, Klawiter EC, Sloane JA, Mainero C

Mult Scler (2019) Link to paper (Labels: multiple-sclerosis, neuroscience, quantitative-mri)

Brainstem and spinal cord MRI identifies altered sensorimotor pathways post-stroke

Karbasforoushan H, Cohen-Adad J, Dewald JPA

Nat Commun (2019) Link to paper (Labels: quantitative-mri, neuroscience)

Presymptomatic spinal cord pathology in c9orf72 mutation carriers: A longitudinal neuroimaging study

Querin G, Bede P, El Mendili MM, Li M, Pélégrini-Issac M, Rinaldi D, Catala M, Saracino D, Salachas F, Camuzat A, Marchand-Pauvert V, Cohen-Adad J, Colliot O, Le Ber I, Pradat P-F

Ann Neurol (2019) Link to paper (Labels: neuroscience, image-analysis)

Gray Matter Alterations in Early and Late Relapsing-Remitting Multiple Sclerosis Evaluated with Synthetic Quantitative Magnetic Resonance Imaging

Andica C, Hagiwara A, Kamagata K, Yokoyama K, Shimoji K, Saito A, Takenaka Y, Nakazawa M, Hori M, Cohen-Adad J, Takemura MY, Hattori N, Aoki S

Sci Rep (2019) Link to paper (Labels: multiple-sclerosis, quantitative-mri)

Guidelines for the conduct of clinical trials in spinal cord injury: Neuroimaging biomarkers

Seif M, Gandini Wheeler-Kingshott CA, Cohen-Adad J, Flanders AE, Freund P

Spinal Cord (2019) Link to paper (Labels: spinal-cord-injury, image-analysis)

Arterial stiffness and brain integrity: A review of MRI findings

Badji A, Sabra D, Bherer L, Cohen-Adad J, Girouard H, Gauthier C

Ageing Res Rev (2019) Link to paper (Labels: neuroscience, quantitative-mri)

Automatic segmentation of the spinal cord and intramedullary multiple sclerosis lesions with convolutional neural networks

Gros C, De Leener B, Badji A, Maranzano J, Eden D, Dupont SM, Talbott J, Zhuoquiong R, Liu Y, Granberg T, Ouellette R, Tachibana Y, Hori M, Kamiya K, Chougar L, Stawiarz L, Hillert J, Bannier E, Kerbrat A, Edan G, Labauge P, Callot V, Pelletier J, Audoin B, Rasoanandrianina H, Brisset JC, Valsasina P, Rocca MA, Filippi M, Bakshi R, Tauhid S, Prados F, Yiannakas M, Kearney H, Ciccarelli O, Smith S, Treaba CA, Mainero C, Lefeuvre J, Reich DS, Nair G, Auclair V, McLaren DG, Martin AR, Fehlings MG, Vahdat S, Khatibi A, Doyon J, Shepherd T, Charlson E, Narayanan S, Cohen-Adad J

Neuroimage (2019) Link to paper (Labels: deep-learning, image-analysis, multiple-sclerosis)

Linearity, Bias, Intrascanner Repeatability, and Interscanner Reproducibility of Quantitative Multidynamic Multiecho Sequence for Rapid Simultaneous Relaxometry at 3 T: A Validation Study With a Standardized Phantom and Healthy Controls

Hagiwara A, Hori M, Cohen-Adad J, Nakazawa M, Suzuki Y, Kasahara A, Horita M, Haruyama T, Andica C, Maekawa T, Kamagata K, Kumamaru KK, Abe O, Aoki S

Invest Radiol (2019) Link to paper (Labels: quantitative-mri, image-analysis)

The spinal and cerebral profile of adult spinal-muscular atrophy: A multimodal imaging study

Querin G, El Mendili MM, Lenglet T, Behin A, Stojkovic T, Salachas F, Devos D, Le Forestier N, Del Mar Amador M, Debs R, Lacomblez L, Meninger V, Bruneteau G, Cohen-Adad J, Lehéricy S, Laforêt P, Blancho S, Benali H, Catala M, Li M, Marchand-Pauvert V, Hogrel JY, Bede P, Pradat PF

Neuroimage Clin (2019) Link to paper (Labels: neuroscience, image-analysis)

Axons morphometry in the human spinal cord

Duval T, Saliani A, Nami H, Nanci A, Stikov N, Leblond H, Cohen-Adad J

Neuroimage (2019) Link to paper (Labels: microscopy)

Spatial distribution of multiple sclerosis lesions in the cervical spinal cord

Eden D, Gros C, Badji A, Dupont SM, De Leener B, Maranzano J, Zhuoquiong R, Liu Y, Granberg T, Ouellette R, Stawiarz L, Hillert J, Talbott J, Bannier E, Kerbrat A, Edan G, Labauge P, Callot V, Pelletier J, Audoin B, Rasoanandrianina H, Brisset JC, Valsasina P, Rocca MA, Filippi M, Bakshi R, Tauhid S, Prados F, Yiannakas M, Kearney H, Ciccarelli O, Smith S, Treaba CA, Mainero C, Lefeuvre J, Reich DS, Nair G, Shepherd T, Charlson E, Tachibana Y, Hori M, Kamiya K, Chougar L, Narayanan S, Cohen-Adad J

Brain (2019) Link to paper (Labels: quantitative-mri, image-analysis, multiple-sclerosis)

2018

Deep semi-supervised segmentation with weight-averaged consistency targets

Perone CS, Cohen-Adad J

4th Deep Learning in Medical Image Analysis (DLMIA) Workshop (2018) Link to paper (Labels: image-analysis, deep-learning)

AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks

Zaimi A, Wabartha M, Herman V, Antonsanti P-L, Perone CS, Cohen-Adad J

Sci Rep (2018) Link to paper (Labels: microscopy, deep-learning, image-analysis)

Effect of cardiac-related translational motion in diffusion MRI of the spinal cord

Morozov D, Lopez Rios N, Duval T, Foias A, Cohen-Adad J

Magn Reson Imaging (2018) Link to paper (Labels: mri-physics)

Spinal cord gray matter segmentation using deep dilated convolutions

Perone CS, Calabrese E, Cohen-Adad J

Sci Rep (2018) Link to paper (Labels: deep-learning, image-analysis)

Can microstructural MRI detect subclinical tissue injury in subjects with asymptomatic cervical spinal cord compression? A prospective cohort study

Martin AR, De Leener B, Cohen-Adad J, Cadotte DW, Nouri A, Wilson JR, Tetreault L, Crawley AP, Mikulis DJ, Ginsberg H, Fehlings MG

BMJ Open (2018) Link to paper (Labels: quantitative-mri, spinal-cord-injury)

Microstructural imaging in the spinal cord and validation strategies

Cohen-Adad J

Neuroimage (2018) Link to paper (Labels: quantitative-mri, microscopy)

Inter-Vendor Reproducibility of Myelin Water Imaging Using a 3D Gradient and Spin Echo Sequence

Lee L, Ljungberg E, Shin D, Figley C, Vavasour I, Rauscher A, Cohen-Adad J, Li D, Traboulsee A, MacKay A, Lee J, Kolind S

Front Neurosci (2018) Link to paper (Labels: quantitative-mri, image-analysis)

What Has Been Learned from Magnetic Resonance Imaging Examination of the Injured Human Spinal Cord: A Canadian Perspective

Cadotte DW, Akbar MA, Fehlings MG, Stroman PW, Cohen-Adad J

J Neurotrauma (2018) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

Size-adaptable 13-channel receive array for brain MRI in human neonates at 3 T

Lopez Rios N, Foias A, Lodygensky G, Dehaes M, Cohen-Adad J

NMR Biomed (2018) Link to paper (Labels: mri-physics)

Postmortem diffusion MRI of the entire human spinal cord at microscopic resolution

Calabrese E, Adil SM, Cofer G, Perone CS, Cohen-Adad J, Lad SP, Johnson GA

Neuroimage Clin (2018) Link to paper (Labels: quantitative-mri, image-analysis)

Monitoring for myelopathic progression with multiparametric quantitative MRI

Martin AR, De Leener B, Cohen-Adad J, Kalsi-Ryan S, Cadotte DW, Wilson JR, Tetreault L, Nouri A, Crawley A, Mikulis DJ, Ginsberg H, Massicotte EM, Fehlings MG

PLoS ONE (2018) Link to paper (Labels: quantitative-mri, spinal-cord-injury)

Design and construction of an optimized transmit/receive hybrid birdcage resonator to improve full body images of medium-sized animals in 7T scanner

Lopez Rios N, Pouliot P, Papoutsis K, Foias A, Stikov N, Lesage F, Dehaes M, Cohen-Adad J

PLoS ONE (2018) Link to paper (Labels: mri-physics)

Test-retest reliability of myelin imaging in the human spinal cord: Measurement errors versus region- and aging-induced variations

Levy S, Guertin MC, Khatibi A, Mezer A, Martinu K, Chen JI, Stikov N, Rainville P, Cohen-Adad J

PLoS ONE (2018) Link to paper (Labels: quantitative-mri)

Automatic spinal cord localization, robust to MRI contrasts using global curve optimization

Gros C, De Leener B, Dupont SM, Martin AR, Fehlings MG, Bakshi R, Tummala S, Auclair V, McLaren DG, Callot V, Cohen-Adad J, Sdika M

Med Image Anal (2018) Link to paper (Labels: image-analysis)

Scan-rescan of axcaliber, macromolecular tissue volume, and g-ratio in the spinal cord

Duval T, Smith V, Stikov N, Klawiter EC, Cohen-Adad J

Magn Reson Med (2018) Link to paper (Labels: quantitative-mri)

Spinal Cord Gray Matter Atrophy in Amyotrophic Lateral Sclerosis

Paquin ME, El Mendili MM, Gros C, Dupont SM, Cohen-Adad J, Pradat PF

AJNR Am J Neuroradiol (2018) Link to paper (Labels: image-analysis, neuroscience)

Changes in structural network are associated with cortical demyelination in early multiple sclerosis

Mangeat G, Badji A, Ouellette R, Treaba CA, Herranz E, Granberg T, Louapre C, Stikov N, Sloane JA, Bellec P, Mainero C, Cohen-Adad J

Hum Brain Mapp (2018) Link to paper (Labels: quantitative-mri, image-analysis, multiple-sclerosis)

Neuroinflammation of the spinal cord and nerve roots in chronic radicular pain patients

Albrecht DS, Ahmed SU, Kettner NW, Borra RJH, Cohen-Adad J, Deng H, Houle TT, Opalacz A, Roth SA, Melo MFV, Chen L, Mao J, Hooker JM, Loggia ML, Zhang Y

Pain (2018) Link to paper (Labels: spinal-cord-injury, neuroscience)

Real-time correction of respiration-induced distortions in the human spinal cord using a 24-channel shim array

Topfer R, Foias A, Stikov N, Cohen-Adad J

Magn Reson Med (2018) Link to paper (Labels: mri-physics, shimming)

PAM50: Unbiased multimodal template of the brainstem and spinal cord aligned with the ICBM152 space

De Leener B, Fonov VS, Collins DL, Callot V, Stikov N, Cohen-Adad J

Neuroimage (2018) Link to paper (Labels: image-analysis)

Promise and pitfalls of g-ratio estimation with MRI

Campbell JSW, Leppert IR, Narayanan S, Boudreau M, Duval T, Cohen-Adad J, Pike GB, Stikov N

Neuroimage (2018) Link to paper (Labels: quantitative-mri)

A pneumatic phantom for mimicking respiration-induced artifacts in spinal MRI

De Tillieux P, Topfer R, Foias A, Leroux I, El Maachi I, Leblond H, Stikov N, Cohen-Adad J

Magn Reson Med (2018) Link to paper (Labels: mri-physics, shimming)

2017

Axon and Myelin Morphology in Animal and Human Spinal Cord

Saliani A, Perraud B, Duval T, Stikov N, Rossignol S, Cohen-Adad J

Front Neuroanat (2017) Link to paper (Labels: microscopy)

Spinal cord grey matter segmentation challenge

Prados F, Ashburner J, Blaiotta C, Brosch T, Carballido-Gamio J, Cardoso MJ, Conrad BN, Datta E, Dávid G, De Leener B, Dupont SM, Freund P, Wheeler-Kingshott CAMG, Grussu F, Henry R, Landman BA, Ljungberg E, Lyttle B, Ourselin S, Papinutto N, Saporito S, Schlaeger R, Smith SA, Summers P, Tam R, Yiannakas MC, Zhu A, Cohen-Adad J

Neuroimage (2017) Link to paper (Labels: image-analysis)

AxonPacking: An Open-Source Software to Simulate Arrangements of Axons in White Matter

Mingasson T, Duval T, Stikov N, Cohen-Adad J

Front Neuroinform (2017) Link to paper (Labels: microscopy, image-analysis)

In vivo characterization of cortical and white matter neuroaxonal pathology in early multiple sclerosis

Granberg T, Fan Q, Treaba CA, Ouellette R, Herranz E, Mangeat G, Louapre C, Cohen-Adad J, Klawiter EC, Sloane JA, Mainero C

Brain (2017) Link to paper (Labels: quantitative-mri, multiple-sclerosis)

Brain processing of the temporal dimension of acute pain in short-term memory

Khoshnejad M, Roy M, Martinu K, Chen JI, Cohen-Adad J, Grondin S, Rainville P

Pain (2017) Link to paper (Labels: neuroscience)

MRI Atlas-Based Measurement of Spinal Cord Injury Predicts Outcome in Acute Flaccid Myelitis

McCoy DB, Talbott JF, Wilson M, Mamlouk M, Cohen-Adad J, Wilson M, Narvid J

AJNR Am J Neuroradiol (2017) Link to paper (Labels: spinal-cord-injury, quantitative-mri, image-analysis)

SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data

De Leener B, Lévy S, Dupont SM, Fonov VS, Stikov N, Louis Collins D, Callot V, Cohen-Adad J

Neuroimage (2017) Link to paper (Labels: image-analysis)

Functional Magnetic Resonance Imaging of the Spinal Cord: Current Status and Future Developments

Cohen-Adad J

Semin Ultrasound CT MR (2017) Link to paper (Labels: fmri)

g-Ratio weighted imaging of the human spinal cord in vivo

Duval T, Lévy S, Stikov N, Campbell J, Mezer A, Witzel T, Keil B, Smith V, Wald LL, Klawiter E, Cohen-Adad J

Neuroimage (2017) Link to paper (Labels: quantitative-mri)

Fully-integrated framework for the segmentation and registration of the spinal cord white and gray matter

Dupont SM, De Leener B, Taso M, Le Troter A, Nadeau S, Stikov N, Callot V, Cohen-Adad J

Neuroimage (2017) Link to paper (Labels: image-analysis)

A Novel MRI Biomarker of Spinal Cord White Matter Injury: T2*-Weighted White Matter to Gray Matter Signal Intensity Ratio

Martin AR, De Leener B, Cohen-Adad J, Cadotte DW, Kalsi-Ryan S, Lange SF, Tetreault L, Nouri A, Crawley A, Mikulis DJ, Ginsberg H, Fehlings MG

AJNR Am J Neuroradiol (2017) Link to paper (Labels: quantitative-mri, spinal-cord-injury)

Clinically Feasible Microstructural MRI to Quantify Cervical Spinal Cord Tissue Injury Using DTI, MT, and T2*-Weighted Imaging: Assessment of Normative Data and Reliability

Martin AR, De Leener B, Cohen-Adad J, Cadotte DW, Kalsi-Ryan S, Lange SF, Tetreault L, Nouri A, Crawley A, Mikulis DJ, Ginsberg H, Fehlings MG

AJNR Am J Neuroradiol (2017) Link to paper (Labels: quantitative-mri, spinal-cord-injury)

Topologically preserving straightening of spinal cord MRI

De Leener B, Mangeat G, Dupont S, Martin AR, Callot V, Stikov N, Fehlings MG, Cohen-Adad J

J Magn Reson Imaging (2017) Link to paper (Labels: image-analysis)

2016

Brainhack: a collaborative workshop for the open neuroscience community

Craddock CR, S Margulies D, Bellec P, Nolan Nichols B, Alcauter S, A Barrios F, Burnod Y, J Cannistraci C, Cohen-Adad J, De Leener B, Dery S, Downar J, Dunlop K, R Franco A, Seligman Froehlich C, J Gerber A, S Ghosh S, J Grabowski T, Hill S, Sólon Heinsfeld A, Matthew Hutchison R, Kundu P, R Laird A, Liew SL, J Lurie D, G McLaren D, Meneguzzi F, Mennes M, Mesmoudi S, O'Connor D, H Pasaye E, Peltier S, Poline JB, Prasad G, Fraga Pereira R, Quirion PO, Rokem A, S Saad Z, Shi Y, C Strother S, Toro R, Q Uddin L, D Van Horn J, W Van Meter J, C Welsh R, Xu T

Gigascience (2016) Link to paper (Labels: neuroscience, image-analysis)

ZOOM or Non-ZOOM? Assessing Spinal Cord Diffusion Tensor Imaging Protocols for Multi-Centre Studies

Samson RS, Levy S, Schneider T, Smith AK, Smith SA, Cohen-Adad J, Gandini Wheeler-Kingshott CA

PLoS ONE (2016) Link to paper (Labels: quantitative-mri, mri-physics)

Segmentation of the human spinal cord

De Leener B, Taso M, Cohen-Adad J, Callot V

MAGMA (2016) Link to paper (Labels: image-analysis)

Is the Relationship between Cortical and White Matter Pathologic Changes in Multiple Sclerosis Spatially Specific? A Multimodal 7-T and 3-T MR Imaging Study with Surface and Tract-based Analysis

Louapre C, Govindarajan ST, Gianni C, Cohen-Adad J, Gregory MD, Nielsen AS, Madigan N, Sloane JA, Kinkel RP, Mainero C

Radiology (2016) Link to paper (Labels: quantitative-mri, image-analysis, multiple-sclerosis)

Quantitative magnetization transfer imaging made easy with qMTLab: Software for data simulation, analysis, and visualization

Cabana J-F, Gu Y, Boudreau M, Levesque IR, Atchia Y, Sled JG, Narayanan S, Arnold DL, Pike GB, Cohen-Adad J, Duval T, Vuong M-T, Stikov N

Concepts in Magnetic Resonance Part A (2016) Link to paper (Labels: quantitative-mri, image-analysis)

Modeling white matter microstructure

Duval T, Stikov N, Cohen-Adad J

Funct Neurol (2016) Link to paper (Labels: quantitative-mri)

AxonSeg: open source software for axon and myelin segmentation and morphometric analysis

Zaimi A, Duval T, Gasecka A, Côté D, Stikov N, Cohen-Adad J

Front Neuroinform (2016) Link to paper (Labels: microscopy, image-analysis)

A 24-channel shim array for the human spinal cord: Design, evaluation, and application

Topfer R, Starewicz P, Lo KM, Metzemaekers K, Jette D, Hetherington HP, Stikov N, Cohen-Adad J

Magn Reson Med (2016) Link to paper (Labels: mri-physics, shimming)

2015

Simultaneous Brain-Cervical Cord FMRI Reveals Intrinsic Spinal Cord Plasticity during Motor Sequence Learning

Vahdat S, Lungu O, Cohen-Adad J, Marchand-Pauvert V, Benali H, Doyon J

PLoS Biol (2015) Link to paper (Labels: neuroscience, fmri)

Quantifying the microvascular origin of BOLD-fMRI from first principles with two-photon microscopy and an oxygen-sensitive nanoprobe

Gagnon L, Sakadzic S, Lesage F, Musacchia JJ, Lefebvre J, Fang Q, Yucel MA, Evans KC, Mandeville ET, Cohen-Adad J, Polimeni JR, Yaseen MA, Lo EH, Greve DN, Buxton RB, Dale AM, Devor A, Boas DA

J Neurosci (2015) Link to paper (Labels: neuroscience, fmri, microscopy)

High resolution imaging of the central nervous system: how novel imaging methods combined with navigation strategies will advance patient care

Farooq H, Genis H, Alarcon J, Vuong B, Jivraj J, Yang VXD, Cohen-Adad J, Fehlings MG, Cadotte A

Prog Brain Res (2015) Link to paper (Labels: quantitative-mri, spinal-cord-injury, neuroscience)

A gradient in cortical pathology in multiple sclerosis by in vivo quantitative 7 T imaging

Mainero C, Louapre C, Govindarajan ST, Gianni C, Nielsen AS, Cohen-Adad J, Sloane J, Kinkel RP

Brain (2015) Link to paper (Labels: multiple-sclerosis, quantitative-mri)

A Temperature Phantom to Probe the Ensemble Average Propagator Asymmetry: an In-Silico Study

Piazzolato M, Wassermann D, Duval T, Campbell JSW, Boutelier T, Cohen-Adad J, Deriche R

MICCAI Workshop on Computational Diffusion MRI (2015) Link to paper (Labels: mri-physics, quantitative-mri)

Translating state-of-the-art spinal cord MRI techniques to clinical use: A systematic review of clinical studies utilizing DTI, MT, MWF, MRS, and fMRI

Martin AR, Aleksanderek I, Cohen-Adad J, Tarmohamed Z, Tetreault L, Smith N, Cadotte DW, Crawley AP, Ginsberg H, Mikulis D, Fehlings MG

Neuroimage Clin (2015) Link to paper (Labels: quantitative-mri, image-analysis, spinal-cord-injury, multiple-sclerosis, fmri)

Fully automated segmentation of the cervical cord from T1-weighted MRI using PropSeg: Application to multiple sclerosis

Yiannakas MC, Mustafa A, De Leener B, Kearney H, Tur C, Altmann DR, De Angelis F, Plantone D, Ciccarelli O, Miller DH, Cohen-Adad J, Wheeler-Kingshott C

Neuroimage Clin (2015) Link to paper (Labels: image-analysis)

Spinal Cord Segmentation by One Dimensional Normalized Template Matching: A Novel, Quantitative Technique to Analyze Advanced Magnetic Resonance Imaging Data

Cadotte A, Cadotte DW, Livne M, Cohen-Adad J, Fleet D, Mikulis D, Fehlings MG

PLoS ONE (2015) Link to paper (Labels: quantitative-mri, image-analysis)

Quantitative analysis of the myelin g-ratio from electron microscopy images of the macaque corpus callosum

Stikov N, Campbell JS, Stroh T, Lavelee M, Frey S, Novek J, Nuara S, Ho MK, Bedell BJ, Dougherty RF, Leppert IR, Boudreau M, Narayanan S, Duval T, Cohen-Adad J, Picard PA, Gasecka A, Cote D, Pike GB

Data Brief (2015) Link to paper (Labels: quantitative-mri, microscopy, neuroscience)

In vivo histology of the myelin g-ratio with magnetic resonance imaging

Stikov N, Campbell JS, Stroh T, Lavelee M, Frey S, Novek J, Nuara S, Ho MK, Bedell BJ, Dougherty RF, Leppert IR, Boudreau M, Narayanan S, Duval T, Cohen-Adad J, Picard PA, Gasecka A, Cote D, Pike GB

Neuroimage (2015) Link to paper (Labels: quantitative-mri, neuroscience)

Real diffusion-weighted MRI enabling true signal averaging and increased diffusion contrast

Eichner C, Cauley SF, Cohen-Adad J, Moller HE, Turner R, Setsompop K, Wald LL

Neuroimage (2015) Link to paper (Labels: quantitative-mri, image-analysis)

White matter atlas of the human spinal cord with estimation of partial volume effect

Levy S, Benhamou M, Naaman C, Rainville P, Callot V, Cohen-Adad J

Neuroimage (2015) Link to paper (Labels: quantitative-mri, image-analysis)

In vivo mapping of human spinal cord microstructure at 300mT/m

Duval T, McNab JA, Setsompop K, Witzel T, Schneider T, Huang SY, Keil B, Klawiter EC, Wald LL, Cohen-Adad J

Neuroimage (2015) Link to paper (Labels: quantitative-mri)

Multivariate combination of magnetization transfer, T2* and B0 orientation to study the myelo-architecture of the in vivo human cortex

Mangeat G, Govindarajan ST, Mainero C, Cohen-Adad J

Neuroimage (2015) Link to paper (Labels: quantitative-mri, image-analysis)

Automatic segmentation of the spinal cord and spinal canal coupled with vertebral labeling

De Leener B, Cohen-Adad J, Kadoury S

IEEE Trans Med Imaging (2015) Link to paper (Labels: image-analysis)

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

Taso M, Le Troter A, Sdika M, Cohen-Adad J, Arnoux PJ, Guye M, Ranjeva JP, Callot V

Neuroimage (2015) Link to paper (Labels: quantitative-mri, image-analysis)

Validation of a semiautomated spinal cord segmentation method

El Mendili MM, Chen R, Tiret B, Pelegrini-Issac M, Cohen-Adad J, Lehericy S, Pradat PF, Benali H

J Magn Reson Imaging (2015) Link to paper (Labels: image-analysis)

Reproducibility of T2* mapping in the human cerebral cortex in vivo at 7 Tesla MRI

Govindarajan ST, Cohen-Adad J, Sormani MP, Fan AP, Louapre C, Mainero C

J Magn Reson Imaging (2015) Link to paper (Labels: quantitative-mri, neuroscience)

Characterizing the location of spinal and vertebral levels in the human cervical spinal cord

Cadotte DW, Cadotte A, Cohen-Adad J, Fleet D, Livne M, Wilson JR, Mikulis D, Nugaeva N, Fehlings MG

AJNR Am J Neuroradiol (2015) Link to paper (Labels: neuroscience)

Spinal diffusion tensor imaging: A comprehensive review with emphasis on spinal cord anatomy and clinical applications

Hendrix P, Griessenauer CJ, Cohen-Adad J, Rajasekaran S, Cauley KA, Shoja MM, Pezeshk P, Shane Tubbs R

Clin Anat (2015) Link to paper (Labels: quantitative-mri)

The impact of gradient strength on in vivo diffusion MRI estimates of axon diameter

Huang SY, Nummenmaa A, Witzel T, Duval T, Cohen-Adad J, Wald LL, McNab JA

Neuroimage (2015) Link to paper (Labels: mri-physics, quantitative-mri)

2014

The current state-of-the-art of spinal cord imaging: methods

Stroman PW, Wheeler-Kingshott C, Bacon M, Schwab JM, Bosma R, Brooks J, Cadotte D, Carlstedt T, Ciccarelli O, Cohen-Adad J, Curt A, Evangelou N, Fehlings MG, Filippi M, Kelley BJ, Kollias S, Mackay A, Porro CA, Smith S, Strittmatter SM, Summers P, Tracey I

Neuroimage (2014) Link to paper (Labels: quantitative-mri)

What can we learn from T2* maps of the cortex?

Cohen-Adad J

Neuroimage (2014) Link to paper (Labels: quantitative-mri, neuroscience)

Automatic 3D segmentation of spinal cord MRI using propagated deformable models

De Leener B, Cohen-Adad J, Kadoury S

Proceedings of the SPIE (2014) Link to paper (Labels: image-analysis)

The current state-of-the-art of spinal cord imaging: applications

Wheeler-Kingshott CA, Stroman PW, Schwab JM, Bacon M, Bosma R, Brooks J, Cadotte DW, Carlstedt T, Ciccarelli O, Cohen-Adad J, Curt A, Evangelou N, Fehlings MG, Filippi M, Kelley BJ, Kollias S, Mackay A, Porro CA, Smith S, Strittmatter SM, Summers P, Thompson AJ, Tracey I

Neuroimage (2014) Link to paper (Labels: quantitative-mri, spinal-cord-injury, multiple-sclerosis, neuroscience)

Framework for integrated MRI average of the spinal cord white and gray matter: the MNI-Poly-AMU template

Fonov VS, Le Troter A, Taso M, De Leener B, Leveque G, Benhamou M, Sdika M, Benali H, Pradat PF, Collins DL, Callot V, Cohen-Adad J

Neuroimage (2014) Link to paper (Labels: image-analysis)

Recovery of locomotion after partial spinal cord lesions in cats: assessment using behavioral, electrophysiological and imaging techniques

Cohen-Adad J, Martinez M, Delivet-Mongrain H, Rossignol S

Acta Neurobiol Exp (Wars) (2014) Link to paper (Labels: spinal-cord-injury, neuroscience)

Automatic labeling of vertebral levels using a robust template-based approach

Ullmann E, Thong W, Pelletier Paquette JP, Cohen-Adad J

Int J Biomed Imaging (2014) Link to paper (Labels: image-analysis)

Multi-parametric spinal cord MRI as potential progression marker in amyotrophic lateral sclerosis

El Mendili MM, Cohen-Adad J, Pelegrini-Issac M, Rossignol S, Morizot-Koutlidis R, Marchand-Pauvert V, Iglesias C, Sangari S, Katz R, Lehericy S, Benali H, Pradat PF

PLoS ONE (2014) Link to paper (Labels: quantitative-mri, neuroscience)

Robust, accurate and fast automatic segmentation of the spinal cord

De Leener B, Kadoury S, Cohen-Adad J

Neuroimage (2014) Link to paper (Labels: image-analysis)

Effect of respiration on the B0 field in the human spinal cord at 3T

Verma T, Cohen-Adad J

Magn Reson Med (2014) Link to paper (Labels: mri-physics, shimming)

Nineteen-channel receive array and four-channel transmit array coil for cervical spinal cord imaging at 7T

Zhao W, Cohen-Adad J, Polimeni JR, Keil B, Guerin B, Setsompop K, Serano P, Mareyam A, Hoecht P, Wald LL

Magn Reson Med (2014) Link to paper (Labels: mri-physics)

2013

Fast diffusion tensor imaging and tractography of the whole cervical spinal cord using point spread function corrected echo planar imaging

Lundell H, Barthelemy D, Biering-Sorensen F, Cohen-Adad J, Nielsen JB, Dyrby TB

Magn Reson Med (2013) Link to paper (Labels: image-analysis, quantitative-mri)

7-T MRI of the spinal cord can detect lateral corticospinal tract abnormality in amyotrophic lateral sclerosis

Cohen-Adad J, Zhao W, Keil B, Ratai E-M, Triantafyllou C, Lawson R, Dheel C, Wald LL, Rosen BR, Cudkowicz M, Atassi N

Muscle Nerve (2013) Link to paper (Labels: neuroscience, quantitative-mri)

Visualizing integrative functioning in the human brainstem and spinal cord with spinal functional magnetic resonance imaging

Cadotte DW, Cohen-Adad J, Fehlings MG

Clinical Neurosurgery (2013) Link to paper (Labels: neuroscience, fmri)

Identification of discrete functional subregions of the human periaqueductal gray

Satpute A, Wager T, Cohen-Adad J, Bianciardi M, Choi J-K, Buhle J, Wald LL, Fedman Barret L

Proc Natl Acad Sci U S A (2013) Link to paper (Labels: quantitative-mri, neuroscience)

Pushing the limits of in vivo diffusion MRI for the Human Connectome Project

Setsompop K, Kimmlingen R, Eberlein E, Witzel T, Cohen-Adad J, McNab JA, Keil B, Tisdall MD, Hoecht P, Dietz P, Cauley SF, Tountcheva V, Matschl V, Lenz H, Bhat H, Heberlein K, Potthast A, Thein H, Van Horn JD, Toga AW, Schmitt F, Lehne D, Rosen BR, Wedeen VJ, Wald LL

NeuroImage (2013) Link to paper (Labels: mri-physics, quantitative-mri)

The Human Connectome Project and beyond: initial applications of 300 mT/m gradients

McNab JA, Edlow BL, Witzel T, Huang SY, Bhat H, Heberlein K, Feiweier T, Liu K, Keil B, Cohen-Adad J, Tisdall MD, Folkerth RD, Kinney HC, Wald LL

NeuroImage (2013) Link to paper (Labels: mri-physics, quantitative-mri)

Involvement of spinal sensory pathway in ALS and specificity of cord atrophy to lower motor neuron degeneration

Cohen-Adad J, El Mendili MM, Morizot-Koutlidis R, Lehericy S, Meininger V, Blancho S, Rossignol S, Benali H, Pradat P-F

Amyotroph Lateral Scler Frontotemporal Degener (2013) Link to paper (Labels: quantitative-mri, neuroscience)

2012

Accelerated Diffusion Spectrum Imaging with Compressed Sensing using Adaptive Dictionaries

Bilgic B, Setsompop K, Cohen-Adad J, Wedeen VJ, Wald LL, Adalsteinsson E

Med Image Comput Comput Assist Interv (2012) Link to paper (Labels: mri-physics, image-analysis)

Focal cortical lesion detection in multiple sclerosis: 3 Tesla DIR versus 7 Tesla FLASH-T2

Nielsen AS, Kinkel RP, Tinelli E, Benner T, Cohen-Adad J, Mainero C

J Magn Reson Imaging (2012) Link to paper (Labels: multiple-sclerosis, quantitative-mri)

Reduction of physiological noise with independent component analysis improves the detection of nociceptive responses with fMRI of the human spinal cord

Xie G, Piche M, Khoshejad M, Perlbarg V, Chen J-I, Hoge RD, Benali H, Rossignol S, Rainville P, Cohen-Adad J

NeuroImage (2012) Link to paper (Labels: fmri, image-analysis)

Accelerated diffusion spectrum imaging with compressed sensing using adaptive dictionaries

Bilgic B, Setsompop K, Cohen-Adad J, Yendiki A, Wald LL, Adalsteinsson E

Magn Reson Med (2012) Link to paper (Labels: quantitative-mri, mri-physics, image-analysis)

7T MRI of spinal cord injury

Cohen-Adad J, Zhao W, Wald LL, Oaklander AL

Neurology (2012) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

Cervical spinal cord injection of epidural corticosteroids: comprehensive longitudinal study including multiparametric magnetic resonance imaging

Cohen-Adad J, Buchbinder B, Oaklander AL

Pain (2012) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

T2* mapping and B0 orientation-dependence at 7T reveal cyto- and myeloarchitecture organization of the human cortex

Cohen-Adad J, Polimeni JR, Helmer KG, Benner T, McNab JA, Wald LL, Rosen B, Mainero C

Neuroimage (2012) Link to paper (Labels: quantitative-mri, neuroscience)

Improving diffusion MRI using simultaneous multi-slice echo planar imaging

Setsompop K, Cohen-Adad J, Gagoski BA, Raij T, Yendiki A, Keil B, Wedeen VJ, Wald LL

Neuroimage (2012) Link to paper (Labels: mri-physics)

2011

Impact of outliers on diffusion tensor and Q-ball imaging: clinical implications and correction strategies

Sharman M, Cohen-Adad J, Descoteaux M, Messé A, Benali H, Lehericy S

J Magn Reson Imaging (2011) Link to paper (Labels: quantitative-mri, image-analysis)

32-channel RF coil optimized for brain and cervical spinal cord at 3 T

Cohen-Adad J, Mareyam A, Keil B, Polimeni JR, Wald LL

Magn Reson Med (2011) Link to paper (Labels: mri-physics)

Quality assessment of high angular resolution diffusion imaging data using bootstrap on Q-ball reconstruction

Cohen-Adad J, Descoteaux M, Wald LL

J Magn Reson Imaging (2011) Link to paper (Labels: quantitative-mri, image-analysis)

Wallerian degeneration after spinal cord lesions in cats detected with diffusion tensor imaging

Cohen-Adad J, Leblond H, Delivet-Mongrain H, Martinez M, Benali H, Rossignol S

Neuroimage (2011) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

Demyelination and degeneration in the injured human spinal cord detected with diffusion and magnetization transfer MRI

Cohen-Adad J, El Mendili M-M, Lehéricy S, Pradat P-F, Blancho S, Rossignol S, Benali H

Neuroimage (2011) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

In vivo evidence of disseminated subpial T2* signal changes in multiple sclerosis at 7 T: a surface-based analysis

Cohen-Adad J, Benner T, Greve DN, Kinkel RP, Radding A, Fischl B, Rosen BR, Mainero C

Neuroimage (2011) Link to paper (Labels: multiple-sclerosis, quantitative-mri)

2010

BOLD signal responses to controlled hypercapnia in human spinal cord

Cohen-Adad J, Gauthier CJ, Brooks JCW, Slessarev M, Han J, Fisher JA, Rossignol S, Hoge RD

Neuroimage (2010) Link to paper (Labels: fmri, neuroscience)

Characterization of the hemodynamic response in the vivo rat lumbar spinal cord by intrinsic optical imaging and laser speckle microscopy

Brieu N, Beaumont E, Dubeau S, Cohen-Adad J, Lesage F

J Neurosci Methods (2010) Link to paper (Labels: fmri, microscopy, neuroscience)

Human cervical spinal cord funiculi: investigation with magnetic resonance diffusion tensor imaging

Onu M, Gervai P, Cohen-Adad J, Lawrence J, Kornelsen J, Tomanek B, Sboto-Frankenstein UN

J Magn Reson Imaging (2010) Link to paper (Labels: quantitative-mri, image-analysis, neuroscience)

2009

Characterization of cardiac-related noise in fMRI of the cervical spinal cord

Piché M, Cohen-Adad J, Nejad MK, Perlbarg V, Xie G, Beaudoin G, Benali H, Rainville P

Magn Reson Imaging (2009) Link to paper (Labels: fmri)

Investigations on spinal cord fMRI of cats under ketamine

Cohen-Adad J, Hoge RD, Leblond H, Xie G, Beaudoin G, Song AW, Krueger G, Doyon J, Benali H, Rossignol S

Neuroimage (2009) Link to paper (Labels: fmri, neuroscience)

2008

Detection of multiple pathways in the spinal cord using q-ball imaging

Cohen-Adad J, Descoteaux M, Rossignol S, Hoge RD, Deriche R, Benali H

Neuroimage (2008) Link to paper (Labels: quantitative-mri)

In vivo DTI of the healthy and injured cat spinal cord at high spatial and angular resolution

Cohen-Adad J, Benali H, Hoge RD, Rossignol S

Neuroimage (2008) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

Development of clinical diffusion tensor MRI of the spinal cord in a context of spinal cord injury

Cohen-Adad J, Benali H, Barrière G, Leblond H, Hoge RD, Rossignol S

IRBM (2008) Link to paper (Labels: spinal-cord-injury, quantitative-mri)

2007

Application of the general linear model to hemodynamic response estimation in diffuse optical imaging

Chapuisat S, Cohen-Adad J, Grova C, Lina JM, Rossignol S, Doyon J, Benali H, Lesage F

SPIE Photonics North (2007) Link to paper (Labels: fmri, neuroscience)

Activation detection in diffuse optical imaging by means of the general linear model

Cohen-Adad J, Chapuisat S, Doyon J, Rossignol S, Lina JM, Benali H, Lesage F

Med Image Anal (2007) Link to paper (Labels: fmri)

2006

Knowledge modeling in image guided neurosurgery: application in understanding intra-operative brain shift

Cohen-Adad J, Paul P, Morandi X, Jannin P

SPIE Medical Imaging (2006) Link to paper (Labels: image-analysis, neuroscience)