From a0930cb2afa4e5f3dd04109b51aa00b2982577f1 Mon Sep 17 00:00:00 2001 From: namgo Date: Tue, 1 Oct 2024 00:11:34 +0000 Subject: [PATCH] deploy: 54ec596a17aebd919e65047343b80abb37bd14b8 --- _sources/publications/gen-combined.md | 159 +++++++++++++------------- publications/gen-combined.html | 159 +++++++++++++------------- publications/journal_articles.html | 159 +++++++++++++------------- searchindex.js | 2 +- 4 files changed, 247 insertions(+), 232 deletions(-) diff --git a/_sources/publications/gen-combined.md b/_sources/publications/gen-combined.md index cf971969..efd2760d 100644 --- a/_sources/publications/gen-combined.md +++ b/_sources/publications/gen-combined.md @@ -6,15 +6,15 @@

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)

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RF shimming in the cervical spinal cord at 7 T

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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

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

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Spiral volumetric optoacoustic tomography of reduced oxygen saturation in the spinal cord of M83 mouse model of Parkinson’s disease

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European Journal of Nuclear Medicine and Molecular Imaging (2024) Link to paper (Labels: )

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Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox

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Valošek J, Cohen-Adad J

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

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

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

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

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

@@ -41,10 +41,15 @@

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)

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RF shimming in the cervical spinal cord at 7 T

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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

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

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

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

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

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Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox

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Valošek J, Cohen-Adad J

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

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

@@ -59,6 +64,11 @@

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

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

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

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

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

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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

@@ -79,24 +89,9 @@

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)

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

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

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

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## 2022
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Advanced Diffusion MR Imaging for Multiple Sclerosis in the Brain and Spinal Cord

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

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

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

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

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

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

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

@@ -122,26 +117,11 @@

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

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

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

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

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

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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)

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

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Badji A, Cohen-Adad J, Girouard H

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

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The myelin-weighted connectome in Parkinson’s disease

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

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

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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

@@ -167,34 +147,59 @@

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)

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

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

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

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

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

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

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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)

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The myelin-weighted connectome in Parkinson’s disease

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

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

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

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

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

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

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Badji A, Cohen-Adad J, Girouard H

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

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## 2021
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A simple and robust method for automating analysis of naïve and regenerating peripheral nerves

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

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

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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)

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

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

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

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

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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

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

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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)

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

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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

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

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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

@@ -210,6 +215,11 @@

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)

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

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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

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

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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

@@ -230,36 +240,31 @@

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)

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

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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

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

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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)

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

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

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

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+

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

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

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

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)

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

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

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

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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)

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

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

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

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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

@@ -464,16 +469,16 @@

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)

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

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

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

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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)

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

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

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

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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

@@ -519,10 +524,10 @@

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)

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Monitoring for myelopathic progression with multiparametric quantitative MRI

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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

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

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

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

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

Microstructural imaging in the spinal cord and validation strategies

@@ -534,10 +539,10 @@

Perone CS, Calabrese E, Cohen-Adad J

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

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

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

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

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Monitoring for myelopathic progression with multiparametric quantitative MRI

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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

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

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

diff --git a/publications/gen-combined.html b/publications/gen-combined.html index ac7c27f5..f2ada938 100644 --- a/publications/gen-combined.html +++ b/publications/gen-combined.html @@ -363,15 +363,15 @@

SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spi

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)

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-

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

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

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+

Spiral volumetric optoacoustic tomography of reduced oxygen saturation in the spinal cord of M83 mouse model of Parkinson’s disease

+

+

European Journal of Nuclear Medicine and Molecular Imaging (2024) Link to paper (Labels: )

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Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox

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Valošek J, Cohen-Adad J

-

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

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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

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

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

@@ -398,10 +398,15 @@

Myelin basic protein mRNA levels affect myelin sheath dimensions, architectu

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)

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+

RF shimming in the cervical spinal cord at 7 T

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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

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

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-

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

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

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Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox

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Valošek J, Cohen-Adad J

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

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

@@ -417,6 +422,11 @@

Dynamic shimming in the cervical spinal cord for multi-echo gradient-echo im

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

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

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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)

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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

@@ -437,25 +447,10 @@

Effectiveness of regional diffusion MRI measures in distinguishing multiple

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)

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-

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)

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2022#

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

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

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

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

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

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

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

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

@@ -481,26 +476,11 @@

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

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

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

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-

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

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

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

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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)

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

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Badji A, Cohen-Adad J, Girouard H

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

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-
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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

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

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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

@@ -526,35 +506,60 @@

Reproducibility and Evolution of Diffusion MRI Measurements within the Cervi

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)

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+

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)

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+
+

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)

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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)

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+

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)

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+
+

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)

+
+
+

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)

+

2021#

+
+

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

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

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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)

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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

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

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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

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

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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)

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+

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

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

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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

@@ -570,6 +575,11 @@

Spinal Cord Morphology in Degenerative Myelopathy Patients; Assessing Key Mo

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)

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+

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)

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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

@@ -590,36 +600,31 @@

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)

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-

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

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

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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)

-
-

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)

+
+

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)

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)

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

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

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

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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)

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

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

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

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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

@@ -827,16 +832,16 @@

Changes in structural network are associated with cortical demyelination in

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)

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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

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

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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)

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+

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

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

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

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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

@@ -882,10 +887,10 @@

AxonDeepSeg: automatic axon and myelin segmentation from microscopy data usi

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)

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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

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

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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

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

Microstructural imaging in the spinal cord and validation strategies

@@ -897,10 +902,10 @@

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)

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-

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)

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+

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

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

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

diff --git a/publications/journal_articles.html b/publications/journal_articles.html index 97a1d8c8..6361f5e7 100644 --- a/publications/journal_articles.html +++ b/publications/journal_articles.html @@ -380,15 +380,15 @@

SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spi

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)

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-

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

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

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+

Spiral volumetric optoacoustic tomography of reduced oxygen saturation in the spinal cord of M83 mouse model of Parkinson’s disease

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European Journal of Nuclear Medicine and Molecular Imaging (2024) Link to paper (Labels: )

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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)

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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

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

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

@@ -415,10 +415,15 @@

Myelin basic protein mRNA levels affect myelin sheath dimensions, architectu

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)

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+

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)

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-

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)

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Reproducible Spinal Cord Quantitative MRI Analysis with the Spinal Cord Toolbox

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Valošek J, Cohen-Adad J

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

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

@@ -434,6 +439,11 @@

Dynamic shimming in the cervical spinal cord for multi-echo gradient-echo im

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

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

+
+

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)

+

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

@@ -454,25 +464,10 @@

Effectiveness of regional diffusion MRI measures in distinguishing multiple

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)

-
-

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)

-

2022#

-
-

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)

-

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

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

@@ -498,26 +493,11 @@

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

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

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

-
-

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)

-

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)

-
-

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)

-
-
-

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

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

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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

@@ -543,35 +523,60 @@

Reproducibility and Evolution of Diffusion MRI Measurements within the Cervi

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)

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

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

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

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

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

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

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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)

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The myelin-weighted connectome in Parkinson’s disease

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

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

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

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

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

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

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Badji A, Cohen-Adad J, Girouard H

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

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2021#

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

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

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

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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)

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

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

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

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

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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

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

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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)

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

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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

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

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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

@@ -587,6 +592,11 @@

Spinal Cord Morphology in Degenerative Myelopathy Patients; Assessing Key Mo

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)

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

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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

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

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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

@@ -607,36 +617,31 @@

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)

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-

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

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

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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)

-
-

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)

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+

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)

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)

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

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

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

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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)

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

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

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

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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

@@ -844,16 +849,16 @@

Changes in structural network are associated with cortical demyelination in

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)

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

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

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

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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)

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+

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

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

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

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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

@@ -899,10 +904,10 @@

AxonDeepSeg: automatic axon and myelin segmentation from microscopy data usi

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)

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Monitoring for myelopathic progression with multiparametric quantitative MRI

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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

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

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+

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

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

Microstructural imaging in the spinal cord and validation strategies

@@ -914,10 +919,10 @@

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)

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-

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)

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+

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

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

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

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