The Creation of a Brain Atlas for Image Guided Neurosurgery Using Serial Histological Data. - M. Mallar Chakravarty; Gilles Bertrand 002; Maxime Descoteaux; Abbas F. Sadikot; D. Louis Collins (MICCAI (1), 2003)

Anatomical and Electrophysiological Validation of an Atlas for Neurosurgical Planning. - M. Mallar Chakravarty; Abbas F. Sadikot; Jürgen Germann; Gilles Bertrand 002; D. Louis Collins (MICCAI (2), 2005)

Towards a Multi-modal Atlas for Neurosurgical Planning. - M. Mallar Chakravarty; Abbas F. Sadikot; Sanjay Mongia; Gilles Bertrand 002; D. Louis Collins (MICCAI (2), 2006)

The creation of a brain atlas for image guided neurosurgery using serial histological data. - M. Mallar Chakravarty; Gilles Bertrand 002; Charles P. Hodge; Abbas F. Sadikot; D. Louis Collins (NeuroImage, 2006)

Three-dimensional reconstruction of serial histological mouse brain sections. - M. Mallar Chakravarty; Barry J. Bedell; Simone P. Zehntner; Alan C. Evans; D. Louis Collins (ISBI, 2008)

Development of FMRI techniques for planning in functional neurosurgery for Parkinson's disease. - M. Mallar Chakravarty; Pedro Rosa-Neto; Scott Broadbent; Alan C. Evans; D. Louis Collins (ISBI, 2008)

The Connectivity of the Human Pulvinar: A Diffusion Tensor Imaging Tractography Study. - Sandra E. Leh; M. Mallar Chakravarty; Alain Ptito (Int. J. Biomed. Imaging, 2008)

Towards a validation of atlas warping techniques. - M. Mallar Chakravarty; Abbas F. Sadikot; Jürgen Germann; Gilles Bertrand 002; D. Louis Collins (Medical Image Anal., 2008)

Blindsight Mediated by an S-Cone-independent Collicular Pathway: An fMRI Study in Hemispherectomized Subjects. - Sandra E. Leh; Alain Ptito; Marc Schönwiesner; M. Mallar Chakravarty; Kathy T. Mullen (J. Cogn. Neurosci., 2010)

Neurite density from magnetic resonance diffusion measurements at ultrahigh field: Comparison with light microscopy and electron microscopy. - Sune Nørhøj Jespersen; Carsten Reidies Bjarkam; Jens R. Nyengaard; M. Mallar Chakravarty; Brian Hansen; Thomas Vosegaard; Leif Østergaard; Dmitriy A. Yablonskiy; Niels Chr. Nielsen; Peter Vestergaard-Poulsen (NeuroImage, 2010)

An MRI based average macaque monkey stereotaxic atlas and space (MNI monkey space). - Stephen Frey; Deepak N. Pandya; M. Mallar Chakravarty; Lara Bailey; Michael Petrides; D. Louis Collins (NeuroImage, 2011)

Atlas-Based Segmentation of the Subthalamic Nucleus, Red Nucleus, and Substantia Nigra for Deep Brain Stimulation by Incorporating Multiple MRI Contrasts. - Yiming Xiao; Lara Bailey; M. Mallar Chakravarty; Silvain Bériault; Abbas F. Sadikot; G. Bruce Pike; D. Louis Collins (IPCAI, 2012)

Mapping registration sensitivity in MR mouse brain images. - Matthijs C. van Eede; Jan Scholz; M. Mallar Chakravarty; R. Mark Henkelman; Jason P. Lerch (NeuroImage, 2013)

Does skull shape mediate the relationship between objective features and subjective impressions about the face? - Klára Marecková; M. Mallar Chakravarty; Mei Huang; Claire Lawrence; Gabriel Leonard; Michel Perron; G. Bruce Pike; Louis Richer; Suzanne Veillette; Zdenka Pausova; Tomás Paus (NeuroImage, 2013)

A novel in vivo atlas of human hippocampal subfields using high-resolution 3 T magnetic resonance imaging. - Julie L. Winterburn; Jens C. Pruessner; Sofia Chavez; Mark M. Schira; Nancy J. Lobaugh; Aristotle N. Voineskos; M. Mallar Chakravarty (NeuroImage, 2013)

Pydpiper: a flexible toolkit for constructing novel registration pipelines. - Miriam Friedel; Matthijs C. van Eede; Jon Pipitone; M. Mallar Chakravarty; Jason P. Lerch (Frontiers Neuroinformatics, 2014)

Derivation of high-resolution MRI atlases of the human cerebellum at 3 T and segmentation using multiple automatically generated templates. - Min Tae M. Park; Jon Pipitone; Lawrence H. Baer; Julie L. Winterburn; Yashvi Shah; Sofia Chavez; Mark M. Schira; Nancy J. Lobaugh; Jason P. Lerch; Aristotle N. Voineskos; M. Mallar Chakravarty (NeuroImage, 2014)

Multi-atlas segmentation of the whole hippocampus and subfields using multiple automatically generated templates. - Jon Pipitone; Min Tae M. Park; Julie L. Winterburn; Tristram A. Lett; Jason P. Lerch; Jens C. Pruessner; Martin D. Lepage; Aristotle N. Voineskos; M. Mallar Chakravarty (NeuroImage, 2014)

Estimating volumes of the pituitary gland from T1-weighted magnetic-resonance images: Effects of age, puberty, testosterone, and estradiol. - Angelita Pui-Yee Wong; Jon Pipitone; Min Tae M. Park; Erin W. Dickie; Gabriel Leonard; Michel Perron; G. Bruce Pike; Louis Richer; Suzanne Veillette; M. Mallar Chakravarty; Zdenka Pausova; Tomás Paus (NeuroImage, 2014)

Improving multi-atlas segmentation accuracy by leveraging local neighborhood information during label-fusion. - Nikhil Bhagwat; Jon Pipitone; Aristotle N. Voineskos; Jens C. Pruessner; M. Mallar Chakravarty (ISBI, 2015)

Multi-contrast unbiased MRI atlas of a Parkinson's disease population. - Yiming Xiao; Vladimir S. Fonov; Silvain Bériault; Fahd Al Subaie; M. Mallar Chakravarty; Abbas F. Sadikot; G. Bruce Pike; D. Louis Collins (Int. J. Comput. Assist. Radiol. Surg., 2015)

Regional cerebellar volumes are related to early musical training and finger tapping performance. - Lawrence H. Baer; Min Tae M. Park; Jennifer Anne Bailey; M. Mallar Chakravarty; K. Z. H. Li; Virginia B. Penhune (NeuroImage, 2015)

Quantitative comparison of 21 protocols for labeling hippocampal subfields and parahippocampal subregions in in vivo MRI: Towards a harmonized segmentation protocol. - Paul A. Yushkevich; Robert S. C. Amaral; Jean C. Augustinack; Andrew R. Bender; Jeffrey D. Bernstein; Marina Boccardi; Martina Bocchetta; Alison C. Burggren; Valerie A. Carr; M. Mallar Chakravarty; Gaël Chételat; Ana M. Daugherty; et al. (NeuroImage, 2015)

Gene Prioritization for Imaging Genetics Studies Using Gene Ontology and a Stratified False Discovery Rate Approach. - Sejal Patel; Min Tae M. Park; M. Mallar Chakravarty; Jo Knight (Frontiers Neuroinformatics, 2016)

Deep brain stimulation of the ventromedial prefrontal cortex causes reorganization of neuronal processes and vasculature. - M. Mallar Chakravarty; Clement Hamani; Alonso Martinez-Canabal; Jacob Ellegood; Christine L. Laliberté; José N. Nobrega; Tejas Sankar; Andres M. Lozano; Paul W. Frankland; Jason P. Lerch (NeuroImage, 2016)

Hippocampus and amygdala volumes from magnetic resonance images in children: Assessing accuracy of FreeSurfer and FSL against manual segmentation. - Dorothee Schoemaker; Claudia Buss; Kevin Head; Curt A. Sandman; Elysia Poggi Davis; M. Mallar Chakravarty; Serge Gauthier; Jens C. Pruessner (NeuroImage, 2016)

CERES: A new cerebellum lobule segmentation method. - José E. Romero; Pierrick Coupé; Rémi Giraud; Vinh-Thong Ta 002; Vladimir S. Fonov; Min Tae M. Park; M. Mallar Chakravarty; Aristotle N. Voineskos; José V. Manjón (NeuroImage, 2017)

BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods. - Krzysztof J. Gorgolewski; Fidel Alfaro-Almagro; Tibor Auer; Pierre Bellec; Mihai Capota; M. Mallar Chakravarty; Nathan William Churchill; Alexander Li Cohen; R. Cameron Craddock; Gabriel A. Devenyi; Anders Eklund 002; Oscar Esteban; et al. (PLoS Comput. Biol., 2017)

Learning to Unlearn: Building Immunity to Dataset Bias in Medical Imaging Studies. - Ahmed Ashraf 001; Shehroz S. Khan; Nikhil Bhagwat; M. Mallar Chakravarty; Babak Taati (CoRR, 2018)

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. - Robert S. C. Amaral; Min Tae M. Park; Gabriel A. Devenyi; Vivian Lynn; Jon Pipitone; Julie L. Winterburn; Sofia Chavez; Mark M. Schira; Nancy J. Lobaugh; Aristotle N. Voineskos; Jens C. Pruessner; M. Mallar Chakravarty (NeuroImage, 2018)

Toward defining deep brain stimulation targets in MNI space: A subcortical atlas based on multimodal MRI, histology and structural connectivity. - Siobhan Ewert; Philip Plettig; Ningfei Li; M. Mallar Chakravarty; D. Louis Collins; Todd M. Herrington; Andrea A. Kühn; Andreas Horn (NeuroImage, 2018)

Regional brain volume changes following chronic antipsychotic administration are mediated by the dopamine D2 receptor. - Elisa Guma; Jill Rocchetti; Gabriel A. Devenyi; Arnaud Tanti; Axel Mathieu; Jason P. Lerch; Guillaume Elgbeili; Blandine Courcot; Naguib Mechawar; M. Mallar Chakravarty; Bruno Giros (NeuroImage, 2018)

Evaluating accuracy of striatal, pallidal, and thalamic segmentation methods: Comparing automated approaches to manual delineation. - Carolina Makowski; Sophie Béland; Penelope Kostopoulos; Nikhil Bhagwat; Gabriel A. Devenyi; Ashok K. Malla; Ridha Joober; Martin D. Lepage; M. Mallar Chakravarty (NeuroImage, 2018)

Heritability estimates of cortical anatomy: The influence and reliability of different estimation strategies. - Sejal Patel; Raihaan Patel; Min Tae M. Park; Mario Masellis; Jo Knight; M. Mallar Chakravarty (NeuroImage, 2018)

Corrigendum to "Hippocampus and amygdala volumes from magnetic resonance images in children: Assessing accuracy of FreeSurfer and FSL against manual segmentation"[NeuroImage 129 (2016) 1-14]. - Dorothee Schoemaker; Claudia Buss; Kevin Head; Curt A. Sandman; Elysia Poggi Davis; M. Mallar Chakravarty; Serge Gauthier; Jens C. Pruessner (NeuroImage, 2018)

Gray-matter structural variability in the human cerebellum: Lobule-specific differences across sex and hemisphere. - Christopher John Steele; M. Mallar Chakravarty (NeuroImage, 2018)

Modeling and prediction of clinical symptom trajectories in Alzheimer's disease using longitudinal data. - Nikhil Bhagwat; Joseph D. Viviano; Aristotle N. Voineskos; M. Mallar Chakravarty; Alzheimer's Disease Neuroimaging Initiative (PLoS Comput. Biol., 2018)

Animal Functional Magnetic Resonance Imaging: Trends and Path Toward Standardization. - Francesca Mandino; Domenic H. Cerri; Clément M. Garin; Milou Straathof; Geralda A. F. van Tilborg; M. Mallar Chakravarty; Marc Dhenain; Rick M. Dijkhuizen; Alessandro Gozzi; Andreas Hess 001; Shella D. Keilholz; Jason P. Lerch; et al. (Frontiers Neuroinformatics, 2019)

White matter injury in term neonates with congenital heart diseases: Topology & comparison with preterm newborns. - Ting Guo; Vann Chau; Shabnam Peyvandi; Beatrice Latal; Patrick S. McQuillen; Walter Knirsch; Anne Synnes; Maria Feldmann; Nadja Naef; M. Mallar Chakravarty; Alessandra De Petrillo; Emma G. Duerden; et al. (NeuroImage, 2019)

Sex-biased trajectories of amygdalo-hippocampal morphology change over human development. - Ari M. Fish; Ajay Nadig; Jakob Seidlitz; Paul K. Reardon; Catherine Mankiw; Cassidy L. McDermott; Jonathan D. Blumenthal; Liv S. Clasen; François Lalonde; Jason P. Lerch; M. Mallar Chakravarty; Russell T. Shinohara; et al. (NeuroImage, 2020)

Investigating microstructural variation in the human hippocampus using non-negative matrix factorization. - Raihaan Patel; Christopher John Steele; Anthony G. X. Chen; Sejal Patel; Gabriel A. Devenyi; Jürgen Germann; Christine L. Tardif; M. Mallar Chakravarty (NeuroImage, 2020)

Hippocampal subfield volumes across the healthy lifespan and the effects of MR sequence on estimates. - Aurélie Bussy; Eric Plitman; Raihaan Patel; Stephanie Tullo; Alyssa Salaciak; Saashi A. Bedford; Sarah Farzin; Marie-Lise Béland; Vanessa Valiquette; Christina Kazazian; Christine Lucas Tardif; Gabriel A. Devenyi; et al. (NeuroImage, 2021)

Maturational trajectories of pericortical contrast in typical brain development. - Stefan Drakulich; Anne-Charlotte Thiffault; Emily R. Olafson; Olivier Parent; Aurélie Labbe; Matthew D. Albaugh; Budhachandra S. Khundrakpam; Simon Ducharme; Alan C. Evans; M. Mallar Chakravarty; Sherif Karama (NeuroImage, 2021)

The impact of the Siemens Tim Trio to Prisma upgrade and the addition of volumetric navigators on cortical thickness, structure volume, and 1H-MRS indices: An MRI reliability study with implications for longitudinal study designs. - Eric Plitman; Aurélie Bussy; Vanessa Valiquette; Alyssa Salaciak; Raihaan Patel; Lani Cupo; Marie-Lise Béland; Stephanie Tullo; Christine Lucas Tardif; M. Natasha Rajah; Jamie Near; Gabriel A. Devenyi; et al. (NeuroImage, 2021)

Embracing diversity and inclusivity in an academic setting: Insights from the Organization for Human Brain Mapping. - Athina Tzovara; Ishmael Amarreh; Valentina Borghesani; M. Mallar Chakravarty; Elizabeth Dupre; Christian Grefkes; Amelie Haugg; Lee Jollans; Hyang Woon Lee; Sharlene D. Newman; Rosanna K. Olsen; J. Tilak Ratnanather; et al. (NeuroImage, 2021)

Inter- and intra-individual variation in brain structural-cognition relationships in aging. - Raihaan Patel; Clare E. Mackay; Michelle G. Jansen; Gabriel A. Devenyi; M. Clare O'Donoghue; Mika Kivimäki; Archana Singh-Manoux; Eniko Zsoldos; Klaus P. Ebmeier; M. Mallar Chakravarty; Sana Suri (NeuroImage, 2022)

Analyses of microstructural variation in the human striatum using non-negative matrix factorization. - Corinne Robert; Raihaan Patel; Nadia Blostein; Chrisopher J. Steele; M. Mallar Chakravarty (NeuroImage, 2022)

Mapping pontocerebellar connectivity with diffusion MRI. - Paul-Noel Rousseau; M. Mallar Chakravarty; Christopher John Steele (NeuroImage, 2022)

A cross-sectional and longitudinal study of human brain development: The integration of cortical thickness, surface area, gyrification index, and cortical curvature into a unified analytical framework. - Hadis Kalantar Hormozi; Raihaan Patel; Alyssa Dai; Justine Ziolkowski; Hao-Ming Dong; Avram J. Holmes; Armin Raznahan; Gabriel A. Devenyi; M. Mallar Chakravarty (NeuroImage, 2023)

Examining litter specific variability in mice and its impact on neurodevelopmental studies. - Vanessa Valiquette; Elisa Guma; Lani Cupo; Daniel Gallino; Chloe Anastassiadis; Emily Snook; Gabriel A. Devenyi; M. Mallar Chakravarty (NeuroImage, 2023)

WarpDrive: Improving spatial normalization using manual refinements. - Simon Oxenford; Ana Sofía Ríos; Barbara Hollunder; Clemens Neudorfer; Alexandre Boutet; Gavin J. B. Elias; Jürgen Germann; Aaron Loh; Wissam Deeb; Bryan Salvato; Leonardo Almeida; Kelly D. Foote; et al. (Medical Image Anal., 2024)