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Non linear registration doesn’t matter (much) or how I learned to stop worrying and love the affine
Published:
Kaizen
Published:
During my parent’s generation products from Japan were considered to be of poor quality, similar to how many products from China are viewed today. Japanese cars were cheap and unreliable compared to the stalwart American auto industry. Today, Japanese cars are more popular and reliable than American made (especially in view of the recent massive recalls by GM). Japan is viewed as a gleaming high tech economy.
projects
publications
The role of substrate surface alteration in the fabrication of vertically aligned CdTe nanowires
Published in Nanotechnology, 2008
Neretina, S, Hughes, R A, Devenyi, G A, Sochinskii, N V, Preston, J S, Mascher, P, "The role of substrate surface alteration in the fabrication of vertically aligned CdTe nanowires." Nanotechnology, 2008. http://dx.doi.org/10.1088/0957-4484/19/18/185601
Atypical grain growth for (211) CdTe films deposited on surface reconstructed (100) SrTiO3 substrates
Published in Applied surface science, 2009
Neretina, S, Hughes, R A, Devenyi, G A, Sochinskii, N V, Preston, J S, Mascher, P, "Atypical grain growth for (211) CdTe films deposited on surface reconstructed (100) SrTiO3 substrates." Applied surface science, 2009. http://www.sciencedirect.com/science/article/pii/S0169433208025142
Epitaxially driven formation of intricate supported gold nanostructures on a lattice-matched oxide substrate
Published in Nano letters, 2009
Devenyi, Gabriel A, Li, Jianfeng, Hughes, Robert A, Shi, An-Chang, Mascher, Peter, Preston, John S, "Epitaxially driven formation of intricate supported gold nanostructures on a lattice-matched oxide substrate." Nano letters, 2009. http://dx.doi.org/10.1021/nl902491g
The role of vicinal silicon surfaces in the formation of epitaxial twins during the growth of III-V thin films
Published in Journal of applied physics, 2011
Devenyi, G A, Woo, S Y, Ghanad-Tavakoli, S, Hughes, R A, Kleiman, R N, Botton, G A, Preston, J S, "The role of vicinal silicon surfaces in the formation of epitaxial twins during the growth of III-V thin films." Journal of applied physics, 2011. https://doi.org/10.1063/1.3671022
Manipulating the size distribution of supported gold nanostructures
Published in Applied physics letters, 2012
Sundar, A, Hughes, R A, Farzinpour, P, Gilroy, K D, Devenyi, G A, Preston, J S, Neretina, S, "Manipulating the size distribution of supported gold nanostructures." Applied physics letters, 2012. https://doi.org/10.1063/1.3675569
Photovoltaic properties of M-phthalocyanine/fullerene organic solar cells
Published in Solar Energy, 2012
Yuen, Avery P, Jovanovic, Stephen M, Hor, Ah-Mee, Klenkler, Richard A, Devenyi, Gabriel A, Loutfy, Rafik O, Preston, John S, "Photovoltaic properties of M-phthalocyanine/fullerene organic solar cells." Solar Energy, 2012. http://www.sciencedirect.com/science/article/pii/S0038092X12001259
Tilted epitaxy on (211)-oriented substrates
Published in Applied physics letters, 2013
Woo, S Y, Devenyi, G A, Ghanad-Tavakoli, S, Kleiman, R N, Preston, J S, Botton, G A, "Tilted epitaxy on (211)-oriented substrates." Applied physics letters, 2013. https://doi.org/10.1063/1.4799278
Optimum reactive ion etching of x-cut quartz using SF6 and Ar
Published in Journal of micromechanics and microengineering: structures, devices, and systems, 2013
Minnick, M D, Devenyi, G A, Kleiman, R N, "Optimum reactive ion etching of x-cut quartz using SF6 and Ar." Journal of micromechanics and microengineering: structures, devices, and systems, 2013. https://iopscience.iop.org/article/10.1088/0960-1317/23/11/117002/meta
Optical characterization of epitaxial single crystal CdTe thin films on Al2O3 (0001) substrates
Published in Thin solid films, 2014
Jovanovic, S M, Devenyi, G A, Jarvis, V M, Meinander, K, Haapamaki, C M, Kuyanov, P, Gerber, M, LaPierre, R R, Preston, J S, "Optical characterization of epitaxial single crystal CdTe thin films on Al2O3 (0001) substrates." Thin solid films, 2014. http://www.sciencedirect.com/science/article/pii/S0040609014009055
Purified water etching of native oxides on heteroepitaxial CdTe thin films
Published in Journal of physics D: Applied physics, 2014
Meinander, Kristoffer, Carvalho, Jessica L, Miki, Carley, Rideout, Joshua, Jovanovic, Stephen M, Devenyi, Gabriel A, Preston, John S, "Purified water etching of native oxides on heteroepitaxial CdTe thin films." Journal of physics D: Applied physics, 2014. https://iopscience.iop.org/article/10.1088/0022-3727/47/49/495304/meta
INTERPRETING DISEASE HETEROGENEITY IN ALZHEIMER'S AND PARKINSON'S DISEASE
Published in Alzheimer's & dementia: the journal of the Alzheimer's Association, 2016
Chakravarty, Mallar, Amaral, Robert S C, Bhagwat, Nikhil, Patel, Raihaan, Garza-Villarreal, Eduardo, Devenyi, Gabriel, Park, Min Tae M, "INTERPRETING DISEASE HETEROGENEITY IN ALZHEIMER'S AND PARKINSON'S DISEASE." Alzheimer's & dementia: the journal of the Alzheimer's Association, 2016.
Advanced processing and simulation of MRS data using the FID appliance (FID-A)-An open source, MATLAB-based toolkit
Published in Magnetic resonance in medicine: official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 2017
Simpson, Robin, Devenyi, Gabriel A, Jezzard, Peter, Hennessy, T Jay, Near, Jamie, "Advanced processing and simulation of MRS data using the FID appliance (FID-A)-An open source, MATLAB-based toolkit." Magnetic resonance in medicine: official journal of the Society of Magnetic Resonance in Medicine / Society of Magnetic Resonance in Medicine, 2017. http://dx.doi.org/10.1002/mrm.26091
BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
Published in PLoS computational biology, 2017
Gorgolewski, Krzysztof J, Alfaro-Almagro, Fidel, Auer, Tibor, Bellec, Pierre, Capotă, Mihai, Chakravarty, M Mallar, Churchill, Nathan W, Cohen, Alexander Li, Craddock, R Cameron, Devenyi, Gabriel A, Eklund, Anders, Esteban, Oscar, Flandin, Guillaume, Ghosh, Satrajit S, Guntupalli, J Swaroop, Jenkinson, Mark, Keshavan, Anisha, Kiar, Gregory, Liem, Franziskus, Raamana, Pradeep Reddy, Raffelt, David, Steele, Christopher J, Quirion, Pierre-Olivier, Smith, Robert E, Strother, Stephen C, Varoquaux, Gaël, Wang, Yida, Yarkoni, Tal, Poldrack, Russell A, "BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods." PLoS computational biology, 2017. http://dx.doi.org/10.1371/journal.pcbi.1005209
The effect of crack cocaine addiction and age on the microstructure and morphology of the human striatum and thalamus using shape analysis and fast diffusion kurtosis imaging
Published in Translational psychiatry, 2017
Garza-Villarreal, E A, Chakravarty, M M, Hansen, B, Eskildsen, S F, Devenyi, G A, Castillo-Padilla, D, Balducci, T, Reyes-Zamorano, E, Jespersen, S N, Perez-Palacios, P, Patel, R, Gonzalez-Olvera, J J, "The effect of crack cocaine addiction and age on the microstructure and morphology of the human striatum and thalamus using shape analysis and fast diffusion kurtosis imaging." Translational psychiatry, 2017. http://dx.doi.org/10.1038/tp.2017.92
ELEVATED CSF LEVELS OF NEUROFILAMENT LIGHT CHAIN IS ASSOCIATED WITH GRAY MATTER NEURODEGENERATION IN BOTH HUMANS AND TRANSGENIC RAT MODEL OF ALZHEIMER's DISEASE
Published in Alzheimer's & dementia: the journal of the Alzheimer's Association, 2017
Kang, Min Su, Shin, Monica, Zimmer, Eduardo R, Mathotaarachchi, Sulantha S, Pascoal, Tharick A, Ng, Kok Pin, Therriault, Joseph, Devenyi, Gabriel, Chakravarty, Mallar, Blennow, Kaj, Zetterberg, Henrik, Soucy, Jean-Paul, Poirier, Judes, Gauthier, Serge, Cuello, A Claudio, Rosa-Neto, Pedro, "ELEVATED CSF LEVELS OF NEUROFILAMENT LIGHT CHAIN IS ASSOCIATED WITH GRAY MATTER NEURODEGENERATION IN BOTH HUMANS AND TRANSGENIC RAT MODEL OF ALZHEIMER's DISEASE." Alzheimer's & dementia: the journal of the Alzheimer's Association, 2017. http://doi.wiley.com/10.1016/j.jalz.2017.06.2320
Cerebellar anatomical alterations and attention to eyes in autism
Published in Scientific reports, 2017
Laidi, Charles, Boisgontier, Jennifer, Chakravarty, M Mallar, Hotier, Sevan, d'Albis, Marc-Antoine, Mangin, Jean-François, Devenyi, Gabriel A, Delorme, Richard, Bolognani, Federico, Czech, Christian, Bouquet, Céline, Toledano, Elie, Bouvard, Manuel, Gras, Doriane, Petit, Julie, Mishchenko, Marina, Gaman, Alexandru, Scheid, Isabelle, Leboyer, Marion, Zalla, Tiziana, Houenou, Josselin, "Cerebellar anatomical alterations and attention to eyes in autism." Scientific reports, 2017. http://dx.doi.org/10.1038/s41598-017-11883-w
Heritability of hippocampal subfield volumes using a twin and non-twin siblings design
Published in Human brain mapping, 2017
Patel, Sejal, Park, Min Tae M, Devenyi, Gabriel A, Patel, Raihaan, Masellis, Mario, Knight, Jo, Chakravarty, M Mallar, "Heritability of hippocampal subfield volumes using a twin and non-twin siblings design." Human brain mapping, 2017. http://dx.doi.org/10.1002/hbm.23654
Cerebellum and attention to the eyes in autism
Published in European neuropsychopharmacology: the journal of the European College of Neuropsychopharmacology, 2017
Laidi, C, Boisgontier, J, Chakravarty, M, Hotier, S, D'Albis, M, Mangin, J, Devenyi, G, Delorme, R, Bolognani, F, Czech, C, Bouvard, M, Gras, D, Petit, J, Mishchenko, M, Gaman, A, Scheid, I, Leboyer, M, Zalla, T, Houenou, J, "Cerebellum and attention to the eyes in autism." European neuropsychopharmacology: the journal of the European College of Neuropsychopharmacology, 2017. https://linkinghub.elsevier.com/retrieve/pii/S0924977X17311525
Neuroanatomical and Symptomatic Sex Differences in Individuals at Clinical High Risk for Psychosis
Published in Frontiers in psychiatry / Frontiers Research Foundation, 2017
Guma, Elisa, Devenyi, Gabriel A, Malla, Ashok, Shah, Jai, Chakravarty, M Mallar, Pruessner, Marita, "Neuroanatomical and Symptomatic Sex Differences in Individuals at Clinical High Risk for Psychosis." Frontiers in psychiatry / Frontiers Research Foundation, 2017. http://dx.doi.org/10.3389/fpsyt.2017.00291
Regionally specific changes in the hippocampal circuitry accompany progression of cerebrospinal fluid biomarkers in preclinical Alzheimer's disease
Published in Human brain mapping, 2018
Tardif, Christine L, Devenyi, Gabriel A, Amaral, Robert S C, Pelleieux, Sandra, Poirier, Judes, Rosa-Neto, Pedro, Breitner, John, Chakravarty, M Mallar, {PREVENT-AD Research Group}, "Regionally specific changes in the hippocampal circuitry accompany progression of cerebrospinal fluid biomarkers in preclinical Alzheimer's disease." Human brain mapping, 2018. http://dx.doi.org/10.1002/hbm.23897
Ten simple rules for collaborative lesson development
Published in PLoS computational biology, 2018
Devenyi, Gabriel A, Emonet, Rémi, Harris, Rayna M, Hertweck, Kate L, Irving, Damien, Milligan, Ian, Wilson, Greg, "Ten simple rules for collaborative lesson development." PLoS computational biology, 2018. http://dx.doi.org/10.1371/journal.pcbi.1005963
Evaluating accuracy of striatal, pallidal, and thalamic segmentation methods: Comparing automated approaches to manual delineation
Published in NeuroImage, 2018
Makowski, Carolina, Béland, Sophie, Kostopoulos, Penelope, Bhagwat, Nikhil, Devenyi, Gabriel A, Malla, Ashok K, Joober, Ridha, Lepage, Martin, Chakravarty, M Mallar, "Evaluating accuracy of striatal, pallidal, and thalamic segmentation methods: Comparing automated approaches to manual delineation." NeuroImage, 2018. http://dx.doi.org/10.1016/j.neuroimage.2017.02.069
Manual segmentation of the fornix, fimbria, and alveus on high-resolution 3T MRI: Application via fully-automated mapping of the human memory circuit white and grey matter in healthy and pathological aging
Published in NeuroImage, 2018
Amaral, Robert S C, Park, Min Tae M, Devenyi, Gabriel A, Lynn, Vivian, Pipitone, Jon, Winterburn, Julie, Chavez, Sofia, Schira, Mark, Lobaugh, Nancy J, Voineskos, Aristotle N, Pruessner, Jens C, Chakravarty, M Mallar, {Alzheimer's Disease Neuroimaging Initiative}, "Manual segmentation of the fornix, fimbria, and alveus on high-resolution 3T MRI: Application via fully-automated mapping of the human memory circuit white and grey matter in healthy and pathological aging." NeuroImage, 2018. http://dx.doi.org/10.1016/j.neuroimage.2016.10.027
Patterns of reduced cortical thickness and striatum pathological morphology in cocaine addiction
Published in bioRxiv, 2018
Garza-Villarreal, Eduardo A, Alcala, Ruth, Balducci, Thania, Angeles-Valdez, Diego, Chakravarty, Mallar, Devenyi, Gabriel A, Gonzalez-Olvera, Jorge J, "Patterns of reduced cortical thickness and striatum pathological morphology in cocaine addiction." bioRxiv, 2018. https://www.biorxiv.org/content/early/2018/04/22/306068.abstract
Warping an atlas derived from serial histology to 5 high-resolution MRIs
Published in Scientific data, 2018
Tullo, Stephanie, Devenyi, Gabriel A, Patel, Raihaan, Park, Min Tae M, Collins, D Louis, Chakravarty, M Mallar, "Warping an atlas derived from serial histology to 5 high-resolution MRIs." Scientific data, 2018. http://dx.doi.org/10.1038/sdata.2018.107
Regional brain volume changes following chronic antipsychotic administration are mediated by the dopamine D2 receptor
Published in NeuroImage, 2018
Guma, Elisa, Rocchetti, Jill, Devenyi, Gabriel A, Tanti, Arnaud, Mathieu, Axel, Lerch, Jason P, Elgbeili, Guillaume, Courcot, Blandine, Mechawar, Naguib, Chakravarty, M Mallar, Giros, Bruno, "Regional brain volume changes following chronic antipsychotic administration are mediated by the dopamine D2 receptor." NeuroImage, 2018. http://dx.doi.org/10.1016/j.neuroimage.2018.04.054
Early-in-life neuroanatomical and behavioural trajectories in a triple transgenic model of Alzheimer's disease
Published in Brain structure & function, 2018
Kong, Vincent, Devenyi, Gabriel A, Gallino, Daniel, Ayranci, Gülebru, Germann, Jürgen, Rollins, Colleen, Chakravarty, M Mallar, "Early-in-life neuroanatomical and behavioural trajectories in a triple transgenic model of Alzheimer's disease." Brain structure & function, 2018. http://dx.doi.org/10.1007/s00429-018-1691-4
A multicohort, longitudinal study of cerebellar development in attention deficit hyperactivity disorder
Published in Journal of child psychology and psychiatry, and allied disciplines, 2018
in press
Shaw, Philip, Ishii-Takahashi, Ayaka, Park, Min Tae, Devenyi, Gabriel A, Zibman, Chava, Kasparek, Steven, Sudre, Gustavo, Mangalmurti, Aman, Hoogman, Martine, Tiemeier, Henning, von Polier, Georg, Shook, Devon, Muetzel, Ryan, Chakravarty, M Mallar, Konrad, Kerstin, Durston, Sarah, White, Tonya, "A multicohort, longitudinal study of cerebellar development in attention deficit hyperactivity disorder." Journal of child psychology and psychiatry, and allied disciplines, 2018. http://dx.doi.org/10.1111/jcpp.12920
A 3D MRI-based atlas of a lizard brain
Published in The Journal of comparative neurology, 2018
Hoops, Daniel, Desfilis, Ester, Ullmann, Jeremy F P, Janke, Andrew L, Stait-Gardner, Timothy, Devenyi, Gabriel A, Price, William S, Medina, Loreta, Whiting, Martin J, Keogh, J Scott, "A 3D MRI-based atlas of a lizard brain." The Journal of comparative neurology, 2018. http://dx.doi.org/10.1002/cne.24480
Dissecting genetic cross-talk between ADHD and other neurodevelopmental disorders: Evidence from behavioural, pharmacological and brain imaging investigations
Published in Psychiatry research, 2018
Sengupta, Sarojini M, Fotopoulos, Nellie, Devenyi, Gabriel A, Fortier, Marie-Ève, Ter-Stepanian, Marina, Sagliker, Saba, Karama, Sherif, Mallar Chakravarty, M, Labbe, Aurelie, Grizenko, Natalie, Joober, Ridha, "Dissecting genetic cross-talk between ADHD and other neurodevelopmental disorders: Evidence from behavioural, pharmacological and brain imaging investigations." Psychiatry research, 2018. http://dx.doi.org/10.1016/j.psychres.2018.08.080
Epitaxial thin film transfer for flexible devices from reusable substrates
Published in Materials Research Express, 2018
Jovanovic, S M, Devenyi, G A, Kuyanov, P, Carvalho, J L, Meinander, K, LaPierre, R R, Preston, J S, "Epitaxial thin film transfer for flexible devices from reusable substrates." Materials Research Express, 2018. https://iopscience.iop.org/article/10.1088/2053-1591/aaf264/meta
Reduced resting-state functional connectivity of the basolateral amygdala to the medial prefrontal cortex in preweaning rats exposed to chronic early-life stress
Published in Brain structure & function, 2018
Guadagno, Angela, Kang, Min Su, Devenyi, Gabriel A, Mathieu, Axel P, Rosa-Neto, Pedro, Chakravarty, Mallar, Walker, Claire-Dominique, "Reduced resting-state functional connectivity of the basolateral amygdala to the medial prefrontal cortex in preweaning rats exposed to chronic early-life stress." Brain structure & function, 2018. http://dx.doi.org/10.1007/s00429-018-1720-3
Focused ultrasound thalamotomy location determines clinical benefits in patients with essential tremor
Published in Brain: a journal of neurology, 2018
Boutet, Alexandre, Ranjan, Manish, Zhong, Jidan, Germann, Jurgen, Xu, David, Schwartz, Michael L, Lipsman, Nir, Hynynen, Kullervo, Devenyi, Gabriel A, Chakravarty, Mallar, Hlasny, Eugen, Llinas, Maheleth, Lozano, Christopher S, Elias, Gavin J B, Chan, Jason, Coblentz, Ailish, Fasano, Alfonso, Kucharczyk, Walter, Hodaie, Mojgan, Lozano, Andres M, "Focused ultrasound thalamotomy location determines clinical benefits in patients with essential tremor." Brain: a journal of neurology, 2018. http://dx.doi.org/10.1093/brain/awy278
Contributions of a high-fat diet to Alzheimer's disease-related decline: A longitudinal behavioural and structural neuroimaging study in mouse models
Published in NeuroImage. Clinical, 2019
Rollins, Colleen P E, Gallino, Daniel, Kong, Vincent, Ayranci, Gülebru, Devenyi, Gabriel A, Germann, Jürgen, Chakravarty, M Mallar, "Contributions of a high-fat diet to Alzheimer's disease-related decline: A longitudinal behavioural and structural neuroimaging study in mouse models." NeuroImage. Clinical, 2019. http://dx.doi.org/10.1016/j.nicl.2018.11.016
Clinical, imaging genetics and deformation based morphometry study of longitudinal changes after surgery for intractable aggressive behaviour
Published in bioRxiv, 2019
Gouveia, Flavia Venetucci, Germann, Jurgen, de Morais, Rosa Magaly Campelo Borba, Fonoff, Erich Talamoni, Hamani, Clement, Alho, Eduardo Joaquim, Brentani, Helena, Martins, Ana Paula, Devenyi, Gabriel A, Patel, Raihaan, Steele, Christopher J, Gramer, Robert, Mallar Chakravarty, M, Martinez, Raquel Chacon Ruiz, "Clinical, imaging genetics and deformation based morphometry study of longitudinal changes after surgery for intractable aggressive behaviour." bioRxiv, 2019. https://www.biorxiv.org/content/10.1101/548826v1.abstract
Polygenic Risk and Neural Substrates of Attention-Deficit/Hyperactivity Disorder Symptoms in Youths With a History of Mild Traumatic Brain Injury
Published in Biological psychiatry, 2019
Stojanovski, Sonja, Felsky, Daniel, Viviano, Joseph D, Shahab, Saba, Bangali, Rutwik, Burton, Christie L, Devenyi, Gabriel A, O'Donnell, Lauren J, Szatmari, Peter, Chakravarty, M Mallar, Ameis, Stephanie, Schachar, Russell, Voineskos, Aristotle N, Wheeler, Anne L, "Polygenic Risk and Neural Substrates of Attention-Deficit/Hyperactivity Disorder Symptoms in Youths With a History of Mild Traumatic Brain Injury." Biological psychiatry, 2019. http://dx.doi.org/10.1016/j.biopsych.2018.06.024
Role of D3 dopamine receptors in modulating neuroanatomical changes in response to antipsychotic administration
Published in Scientific reports, 2019
Guma, Elisa, Rocchetti, Jill, Devenyi, Gabriel A, Tanti, Arnaud, Mathieu, Axel P, Lerch, Jason P, Elgbeili, Guillaume, Courcot, Blandine, Mechawar, Naguib, Chakravarty, M Mallar, Giros, Bruno, "Role of D3 dopamine receptors in modulating neuroanatomical changes in response to antipsychotic administration." Scientific reports, 2019. http://dx.doi.org/10.1038/s41598-019-43955-4
Spatial patterning of tissue volume deformation in schizophrenia reflects brain network architecture
Published in bioRxiv, 2019
Shafiei, Golia, Markello, Ross D, Talpalaru, Alexandra, Makowski, Carolina, Kirschner, Matthias, Devenyi, Gabriel A, Hagmann, Patric, Cashman, Neil R, Lepage, Martin, Mallar Chakravarty, M, Dagher, Alain, Mišić, Bratislav, "Spatial patterning of tissue volume deformation in schizophrenia reflects brain network architecture." bioRxiv, 2019. https://www.biorxiv.org/content/10.1101/626168v1.abstract
Longitudinal assessment of the neuroanatomical consequences of deep brain stimulation: Application of fornical DBS in an Alzheimer's mouse model
Published in Brain research, 2019
Gallino, Daniel, Devenyi, Gabriel A, Germann, Jürgen, Guma, Elisa, Anastassiadis, Chloe, Chakravarty, M Mallar, "Longitudinal assessment of the neuroanatomical consequences of deep brain stimulation: Application of fornical DBS in an Alzheimer's mouse model." Brain research, 2019. http://dx.doi.org/10.1016/j.brainres.2019.03.030
Tractography-based targeting of the ventral intermediate nucleus: accuracy and clinical utility in MRgFUS thalamotomy
Published in Journal of neurosurgery, 2019
Ranjan, Manish, Elias, Gavin J B, Boutet, Alexandre, Zhong, Jidan, Chu, Powell, Germann, Jurgen, Devenyi, Gabriel A, Chakravarty, M Mallar, Fasano, Alfonso, Hynynen, Kullervo, Lipsman, Nir, Hamani, Clement, Kucharczyk, Walter, Schwartz, Michael L, Lozano, Andres M, Hodaie, Mojgan, "Tractography-based targeting of the ventral intermediate nucleus: accuracy and clinical utility in MRgFUS thalamotomy." Journal of neurosurgery, 2019. http://dx.doi.org/10.3171/2019.6.JNS19612
Can we accurately classify schizophrenia patients from healthy controls using magnetic resonance imaging and machine learning? A multi-method and multi-dataset study
Published in Schizophrenia research, 2019
Winterburn, Julie L, Voineskos, Aristotle N, Devenyi, Gabriel A, Plitman, Eric, de la Fuente-Sandoval, Camilo, Bhagwat, Nikhil, Graff-Guerrero, Ariel, Knight, Jo, Chakravarty, M Mallar, "Can we accurately classify schizophrenia patients from healthy controls using magnetic resonance imaging and machine learning? A multi-method and multi-dataset study." Schizophrenia research, 2019. http://dx.doi.org/10.1016/j.schres.2017.11.038
Identifying schizophrenia subgroups using clustering and supervised learning
Published in Schizophrenia research, 2019
Talpalaru, Alexandra, Bhagwat, Nikhil, Devenyi, Gabriel A, Lepage, Martin, Chakravarty, M Mallar, "Identifying schizophrenia subgroups using clustering and supervised learning." Schizophrenia research, 2019. http://dx.doi.org/10.1016/j.schres.2019.05.044
MR-based age-related effects on the striatum, globus pallidus, and thalamus in healthy individuals across the adult lifespan
Published in Human brain mapping, 2019
Tullo, Stephanie, Patel, Raihaan, Devenyi, Gabriel A, Salaciak, Alyssa, Bedford, Saashi A, Farzin, Sarah, Wlodarski, Nancy, Tardif, Christine L, {PREVENT-AD Research Group}, Breitner, John C S, Chakravarty, M Mallar, "MR-based age-related effects on the striatum, globus pallidus, and thalamus in healthy individuals across the adult lifespan." Human brain mapping, 2019. http://dx.doi.org/10.1002/hbm.24771
Investigating microstructural variation in the human hippocampus using non-negative matrix factorization
Published in NeuroImage, 2020
Patel, Raihaan, Steele, Christopher J, Chen, Anthony G X, Patel, Sejal, Devenyi, Gabriel A, Germann, Jürgen, Tardif, Christine L, Chakravarty, M Mallar, "Investigating microstructural variation in the human hippocampus using non-negative matrix factorization." NeuroImage, 2020. http://dx.doi.org/10.1016/j.neuroimage.2019.116348
Altered neurotransmission and neuroimaging biomarkers of chronic arsenic poisoning in wild muskrats (Ondatra zibethicus) and red squirrels (Tamiasciurus hudsonicus) breeding near the City of Yellowknife, Northwest Territories (Canada)
Published in The Science of the total environment, 2020
Amuno, S, Rudko, D A, Gallino, D, Tuznik, M, Shekh, K, Kodzhahinchev, V, Niyogi, S, Chakravarty, M M, Devenyi, G A, "Altered neurotransmission and neuroimaging biomarkers of chronic arsenic poisoning in wild muskrats (Ondatra zibethicus) and red squirrels (Tamiasciurus hudsonicus) breeding near the City of Yellowknife, Northwest Territories (Canada)." The Science of the total environment, 2020. http://dx.doi.org/10.1016/j.scitotenv.2019.135556
Large-scale analyses of the relationship between sex, age and intelligence quotient heterogeneity and cortical morphometry in autism spectrum disorder
Published in Molecular psychiatry, 2020
Bedford, Saashi A, Park, Min Tae M, Devenyi, Gabriel A, Tullo, Stephanie, Germann, Jurgen, Patel, Raihaan, Anagnostou, Evdokia, Baron-Cohen, Simon, Bullmore, Edward T, Chura, Lindsay R, Craig, Michael C, Ecker, Christine, Floris, Dorothea L, Holt, Rosemary J, Lenroot, Rhoshel, Lerch, Jason P, Lombardo, Michael V, Murphy, Declan G M, Raznahan, Armin, Ruigrok, Amber N V, Smith, Elizabeth, Spencer, Michael D, Suckling, John, Taylor, Margot J, Thurm, Audrey, {MRC AIMS Consortium}, Lai, Meng-Chuan, Chakravarty, M Mallar, "Large-scale analyses of the relationship between sex, age and intelligence quotient heterogeneity and cortical morphometry in autism spectrum disorder." Molecular psychiatry, 2020. http://dx.doi.org/10.1038/s41380-019-0420-6
An MRI-Derived Neuroanatomical Atlas of the Fischer 344 Rat Brain
Published in Scientific reports, 2020
Goerzen, Dana, Fowler, Caitlin, Devenyi, Gabriel A, Germann, Jurgen, Madularu, Dan, Chakravarty, M Mallar, Near, Jamie, "An MRI-Derived Neuroanatomical Atlas of the Fischer 344 Rat Brain." Scientific reports, 2020. http://dx.doi.org/10.1038/s41598-020-63965-x
Spatial Patterning of Tissue Volume Loss in Schizophrenia Reflects Brain Network Architecture
Published in Biological psychiatry, 2020
Shafiei, Golia, Markello, Ross D, Makowski, Carolina, Talpalaru, Alexandra, Kirschner, Matthias, Devenyi, Gabriel A, Guma, Elisa, Hagmann, Patric, Cashman, Neil R, Lepage, Martin, Chakravarty, M Mallar, Dagher, Alain, Mišić, Bratislav, "Spatial Patterning of Tissue Volume Loss in Schizophrenia Reflects Brain Network Architecture." Biological psychiatry, 2020. http://dx.doi.org/10.1016/j.biopsych.2019.09.031
Using Non-Negative Matrix Factorization to Examine Treatment Resistance and Response in Patients With Schizophrenia: A Multimodal Imaging Study
Published in Biological psychiatry, 2020
Plitman, Eric, Ochi, Ryo, Patel, Raihaan, Tsugawa, Sakiko, Tarumi, Ryosuke, Honda, Shiori, Matsushita, Karin, Fujii, Shinya, Uchida, Hiroyuki, Mimura, Masaru, Noda, Yoshihiro, Devenyi, Gabriel A, Nakajima, Shinichiro, Chakravarty, Mallar, "Using Non-Negative Matrix Factorization to Examine Treatment Resistance and Response in Patients With Schizophrenia: A Multimodal Imaging Study." Biological psychiatry, 2020. https://linkinghub.elsevier.com/retrieve/pii/S0006322320310118
Amyloid-beta modulates the association between neurofilament light chain and brain atrophy in Alzheimer's disease
Published in Molecular psychiatry, 2020
Kang, Min Su, Aliaga, Arturo Aliaga, Shin, Monica, Mathotaarachchi, Sulantha, Benedet, Andrea L, Pascoal, Tharick A, Therriault, Joseph, Chamoun, Mira, Savard, Melissa, Devenyi, Gabriel A, Mathieu, Axel, Chakravarty, M Mallar, Sandelius, Åsa, Blennow, Kaj, Zetterberg, Henrik, Soucy, Jean-Paul, Cuello, A Claudio, Massarweh, Gassan, Gauthier, Serge, Rosa-Neto, Pedro, {Alzheimer's Disease Neuroimaging Initiative}, "Amyloid-beta modulates the association between neurofilament light chain and brain atrophy in Alzheimer's disease." Molecular psychiatry, 2020. http://dx.doi.org/10.1038/s41380-020-0818-1
Refractoriness of aggressive behaviour to pharmacological treatment: cortical thickness analysis in autism spectrum disorder
Published in BJPsych open, 2020
Gouveia, Flavia Venetucci, Germann, Jürgen, Devenyi, Gabriel A, Morais, Rosa M C B, Santos, Ana Paula M, Fonoff, Erich T, Hamani, Clement, Brentani, Helena, Chakravarty, M Mallar, Martinez, Raquel C R, "Refractoriness of aggressive behaviour to pharmacological treatment: cortical thickness analysis in autism spectrum disorder." BJPsych open, 2020. http://dx.doi.org/10.1192/bjo.2020.71
Fully Automated Habenula Segmentation Provides Robust and Reliable Volume Estimation Across Large Magnetic Resonance Imaging Datasets, Suggesting Intriguing Developmental Trajectories in Psychiatric Disease
Published in Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 2020
Germann, Jürgen, Gouveia, Flavia Venetucci, Martinez, Raquel C R, Zanetti, Marcus Vinicius, de Souza Duran, Fábio Luís, Chaim-Avancini, Tiffany M, Serpa, Mauricio H, Chakravarty, M Mallar, Devenyi, Gabriel A, "Fully Automated Habenula Segmentation Provides Robust and Reliable Volume Estimation Across Large Magnetic Resonance Imaging Datasets, Suggesting Intriguing Developmental Trajectories in Psychiatric Disease." Biological Psychiatry: Cognitive Neuroscience and Neuroimaging, 2020. http://www.sciencedirect.com/science/article/pii/S2451902220300227
The ratio of posterior-anterior medial temporal lobe volumes predicts source memory performance in healthy young adults
Published in Hippocampus, 2020
Snytte, Jamie, Elshiekh, Abdelhalim, Subramaniapillai, Sivaniya, Manning, Lyssa, Pasvanis, Stamatoula, Devenyi, Gabriel A, Olsen, Rosanna K, Rajah, Maria Natasha, "The ratio of posterior-anterior medial temporal lobe volumes predicts source memory performance in healthy young adults." Hippocampus, 2020. http://dx.doi.org/10.1002/hipo.23251
Maternal cafeteria diet exposure primes depression-like behavior in the offspring evoking lower brain volume related to changes in synaptic terminals and gliosis
Published in Translational psychiatry, 2021
Trujillo-Villarreal, Luis A, Romero-Díaz, Viktor J, Marino-Martínez, Iván Alberto, Fuentes-Mera, Lizeth, Ponce-Camacho, Marco Antonio, Devenyi, Gabriel A, Mallar Chakravarty, M, Camacho-Morales, Alberto, Garza-Villarreal, Eduardo E, "Maternal cafeteria diet exposure primes depression-like behavior in the offspring evoking lower brain volume related to changes in synaptic terminals and gliosis." Translational psychiatry, 2021. https://www.nature.com/articles/s41398-020-01157-x
The ANTsX ecosystem for quantitative biological and medical imaging
Published in Scientific reports, 2021
Tustison, Nicholas J, Cook, Philip A, Holbrook, Andrew J, Johnson, Hans J, Muschelli, John, Devenyi, Gabriel A, Duda, Jeffrey T, Das, Sandhitsu R, Cullen, Nicholas C, Gillen, Daniel L, Yassa, Michael A, Stone, James R, Gee, James C, Avants, Brian B, "The ANTsX ecosystem for quantitative biological and medical imaging." Scientific reports, 2021. http://dx.doi.org/10.1038/s41598-021-87564-6
Cumulative exposure to ADHD medication is inversely related to hippocampus subregional volume in children
Published in NeuroImage: Clinical, 2021
Fotopoulos, Nellie H, Devenyi, Gabriel A, Guay, Stephanie, Sengupta, Sarojini M, Mallar Chakravarty, M, Grizenko, Natalie, Karama, Sherif, Joober, Ridha, "Cumulative exposure to ADHD medication is inversely related to hippocampus subregional volume in children." NeuroImage: Clinical, 2021. https://www.sciencedirect.com/science/article/pii/S221315822100139X
Longitudinal quantification of metabolites and macromolecules reveals age- and sex-related changes in the healthy Fischer 344 rat brain
Published in Neurobiology of aging, 2021
Fowler, Caitlin F, Madularu, Dan, Dehghani, Masoumeh, Devenyi, Gabriel A, Near, Jamie, "Longitudinal quantification of metabolites and macromolecules reveals age- and sex-related changes in the healthy Fischer 344 rat brain." Neurobiology of aging, 2021. http://dx.doi.org/10.1016/j.neurobiolaging.2020.12.012
Bilateral Amygdala Radio-Frequency Ablation for Refractory Aggressive Behavior Alters Local Cortical Thickness to a Pattern Found in Non-refractory Patients
Published in Frontiers in human neuroscience, 2021
Gouveia, Flavia Venetucci, Germann, Jürgen, Devenyi, Gabriel A, Fonoff, Erich T, Morais, Rosa M C B, Brentani, Helena, Chakravarty, M Mallar, Martinez, Raquel C R, "Bilateral Amygdala Radio-Frequency Ablation for Refractory Aggressive Behavior Alters Local Cortical Thickness to a Pattern Found in Non-refractory Patients." Frontiers in human neuroscience, 2021. http://dx.doi.org/10.3389/fnhum.2021.653631
Examining the Boundary Sharpness Coefficient as an Index of Cortical Microstructure in Autism Spectrum Disorder
Published in Cerebral cortex, 2021
Olafson, Emily, Bedford, Saashi A, Devenyi, Gabriel A, Patel, Raihaan, Tullo, Stephanie, Park, Min Tae M, Parent, Olivier, Anagnostou, Evdokia, Baron-Cohen, Simon, Bullmore, Edward T, Chura, Lindsay R, Craig, Michael C, Ecker, Christine, Floris, Dorothea L, Holt, Rosemary J, Lenroot, Rhoshel, Lerch, Jason P, Lombardo, Michael V, Murphy, Declan G M, Raznahan, Armin, Ruigrok, Amber N V, Spencer, Michael D, Suckling, John, Taylor, Margot J, {MRC AIMS Consortium}, Lai, Meng-Chuan, Chakravarty, M Mallar, "Examining the Boundary Sharpness Coefficient as an Index of Cortical Microstructure in Autism Spectrum Disorder." Cerebral cortex, 2021. http://dx.doi.org/10.1093/cercor/bhab015
Hippocampal subfield volumes across the healthy lifespan and the effects of MR sequence on estimates
Published in NeuroImage, 2021
Bussy, Aurélie, Plitman, Eric, Patel, Raihaan, Tullo, Stephanie, Salaciak, Alyssa, Bedford, Saashi A, Farzin, Sarah, Béland, Marie-Lise, Valiquette, Vanessa, Kazazian, Christina, Tardif, Christine Lucas, Devenyi, Gabriel A, Chakravarty, M Mallar, {Alzheimer's Disease Neuroimaging Initiative}, "Hippocampal subfield volumes across the healthy lifespan and the effects of MR sequence on estimates." NeuroImage, 2021. http://dx.doi.org/10.1016/j.neuroimage.2021.117931
A Diagnosis and Biotype Comparison Across the Psychosis Spectrum: Investigating Volume and Shape Amygdala-Hippocampal Differences from the B-SNIP Study
Published in Schizophrenia bulletin, 2021
Guimond, Synthia, Gu, Feng, Shannon, Holly, Kelly, Sinead, Mike, Luke, Devenyi, Gabriel A, Chakravarty, M Mallar, Sweeney, John A, Pearlson, Godfrey, Clementz, Brett A, Tamminga, Carol, Keshavan, Matcheri, "A Diagnosis and Biotype Comparison Across the Psychosis Spectrum: Investigating Volume and Shape Amygdala-Hippocampal Differences from the B-SNIP Study." Schizophrenia bulletin, 2021. http://dx.doi.org/10.1093/schbul/sbab071
talks
The Future of Photovoltaics: Next Generation Materials and Devices at McMaster University Engineering Physics
Published:
Devenyi, Gabriel A, "The Future of Photovoltaics: Next Generation Materials and Devices at McMaster University Engineering Physics." IEEE Hamilton Chapter Monthly Meeting, 2012.
LaTeX for Preparation of Scientific Documents and Theses
Published:
Devenyi, Gabriel A, "LaTeX for Preparation of Scientific Documents and Theses." School of Graduate Studies, McMaster University, 2012.
LaTeX for Preparation of Scientific Documents and Theses
Published:
Devenyi, Gabriel A, "LaTeX for Preparation of Scientific Documents and Theses." School of Graduate Studies, McMaster University, 2013.
LaTeX for Preparation of Scientific Documents and Theses
Published:
Devenyi, Gabriel A, "LaTeX for Preparation of Scientific Documents and Theses." Department of Medical Physics, McMaster University, 2014.
Skills for Scientific Computing
Published:
Wilson, G W, Devenyi, Gabriel A, "Skills for Scientific Computing." Software Carpentry Workshop, Department of Physics & Astronomy, McMaster University, 2014. https://gdevenyi.github.io/2014-05-05-mcmaster/
LaTeX for Preparation of Scientific Documents and Theses
Published:
Devenyi, Gabriel A, "LaTeX for Preparation of Scientific Documents and Theses." Department of Electrical and Computer Engineering, McMaster University, 2014.
Skills for Scientific Computing
Published:
Devenyi, Gabriel A, Ory, Jeremey, "Skills for Scientific Computing." Software Carpentry Workshop, Statistical Computing Unit, Cornell University, 2014. https://gdevenyi.github.io/2014-06-04-cornell/
Skills for Scientific Computing
Published:
Blischak, J D, Haine, D, Corvellec, M, Devenyi, G A, "Skills for Scientific Computing." Software Carpentry Workshop, Faculty of Medicine, University de Montreal, 2014. https://dhaine.github.io/2014-11-06-fmv/
Skills for Scientific Computing
Published:
Devenyi, Gabriel A, Haine, Denis, Corvellec, Marianne, Santos, João F, Kozlov, Igor, "Skills for Scientific Computing." Software Carpentry Workshop, Department of Physics, McGill University, 2015. https://igor-kozlov.github.io/2015-01-10-mcgill/
Skills for Scientific Computing
Published:
Devenyi, Gabriel A, Schwartz, Rachael, "Skills for Scientific Computing." Software Carpentry Workshop, BIO5 Institute & iPlant Collaborative, Arizona State University, 2015. https://rachelss.github.io/2015-04-18-ASU/
MRS Simulation & Preprocessing Using the FID-A Toolkit
Published:
Near, Jamie, Devenyi, Gabriel A, "MRS Simulation & Preprocessing Using the FID-A Toolkit." MR Spectroscopy Study Group, ISMRM Virtual Meetings, 2017. https://www.ismrm.org/virtual-meetings/virtual-meetings-archive/