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Jan Valosek

Postdoctorat - Polytechnique
Superviseur⋅e principal⋅e
Sujets de recherche
Apprentissage automatique médical
Apprentissage profond

Publications

Monitoring morphometric drift in lifelong learning segmentation of the spinal cord
Enamundram Naga Karthik
Sandrine Bédard
Christoph S. Aigner
Elise Bannier
Josef Bednařík
Virginie Callot
Anna Combes
Armin Curt
Gergely David
Falk Eippert
Lynn Farner
Michael G Fehlings
Patrick Freund
Tobias Granberg
Cristina Granziera
Rhscir Network Imaging Group
Ulrike Horn
Tomáš Horák … (voir 36 de plus)
Suzanne Humphreys
Markus Hupp
Anne Kerbrat
Nawal Kinany
Shannon Kolind
Anna Lebret
Petr Kudlička
Lisa Eunyoung Lee
Caterina Mainero
Allan R. Martin
Megan McGrath
Govind Nair
Kristin P. O’Grady
Jiwon Oh
Russell Ouellette
Nikolai Pfender
Dario Pfyffer
P. Pradat
Alexandre Prat
Emanuele Pravatà
Daniel S. Reich
Ilaria Ricchi
Naama Rotem-Kohavi
Simon Schading-Sassenhausen
Maryam Seif
Andrew C. Smith
Seth Aaron Smith
Grace Sweeney
Roger Tam
Anthony Traboulsee
Constantina A. Treaba
Charidimos Tsagkas
Zachary Vavasour
Dimitri Van De Ville
Kenneth A. Weber
Rootlets-based registration to the spinal cord PAM50 template
Sandrine Bédard
Valeria Oliva
Kenneth A. Weber
Normalizing Spinal Cord Compression Measures in Degenerative Cervical Myelopathy.
Sandrine Bédard
Maryam Seif
Armin Curt
Simon Schading-Sassenhausen
Nikolai Pfender
P. Freund
Markus Hupp
Automatic segmentation of spinal cord lesions in MS: A robust tool for axial T2-weighted MRI scans
Enamundram Naga Karthik
Julian McGinnis
Ricarda Wurm
Sebastian Ruehling
Robert Graf
Pierre-Louis Benveniste
Markus Lauerer
Jason Talbott
Rohit Bakshi
Shahamat Tauhid
Timothy Shepherd
Achim Berthele
Claus Zimmer
Bernhard Hemmer
Daniel Rueckert
Benedikt Wiestler
Jan S. Kirschke
Mark Mühlau
Deep learning models have achieved remarkable success in segmenting brain white matter lesions in multiple sclerosis (MS), becoming integral… (voir plus) to both research and clinical workflows. While brain lesions have gained significant attention in MS research, the involvement of spinal cord lesions in MS is relatively understudied. This is largely owed to the variability in spinal cord magnetic resonance imaging (MRI) acquisition protocols, high individual anatomical differences, the complex morphology and size of spinal cord lesions - and lastly, the scarcity of labeled datasets required to develop robust segmentation tools. As a result, automatic segmentation of spinal cord MS lesions remains a significant challenge. Although some segmentation tools exist for spinal cord lesions, most have been developed using sagittal T2-weighted (T2w) sequences primarily focusing on cervical spines. With the growing importance of spinal cord imaging in MS, axial T2w scans are becoming increasingly relevant due to their superior sensitivity in detecting lesions compared to sagittal acquisition protocols. However, most existing segmentation methods struggle to effectively generalize to axial sequences due to differences in image characteristics caused by the highly anisotropic spinal cord scans. To address these challenges, we developed a robust, open-source lesion segmentation tool tailored specifically for axial T2w scans covering the whole spinal cord. We investigated key factors influencing lesion segmentation, including the impact of stitching together individually acquired spinal regions, straightening the spinal cord, and comparing the effectiveness of 2D and 3D convolutional neural networks (CNNs). Drawing on these insights, we trained a multi-center model using an extensive dataset of 582 MS patients, resulting in a dataset comprising an entirety of 2,167 scans. We empirically evaluated the model's segmentation performance across various spinal segments for lesions with varying sizes. Our model significantly outperforms the current state-of-the-art methods, providing consistent segmentation across cervical, thoracic and lumbar regions. To support the broader research community, we integrate our model into the widely-used Spinal Cord Toolbox (v7.0 and above), making it accessible via the command sct_deepseg -task seg_sc_ms_lesion_axial_t2w -i .
Automatic segmentation of spinal cord lesions in MS: A robust tool for axial T2-weighted MRI scans
Enamundram Naga Karthik
J. McGinnis
R. Wurm
S. Ruehling
R. Graf
Pierre-Louis Benveniste
M. Lauerer
J. Talbott
R. Bakshi
S. Tauhid
T. Shepherd
A. Berthele
C. Zimmer
B. Hemmer
D. Rueckert
B. Wiestler
J. Kirschke
M. Muehlau
Deep learning models have achieved remarkable success in segmenting brain white matter lesions in multiple sclerosis (MS), becoming integral… (voir plus) to both research and clinical workflows. While brain lesions have gained significant attention in MS research, the involvement of spinal cord lesions in MS is relatively understudied. This is largely owed to the variability in spinal cord magnetic resonance imaging (MRI) acquisition protocols, high individual anatomical differences, the complex morphology and size of spinal cord lesions - and lastly, the scarcity of labeled datasets required to develop robust segmentation tools. As a result, automatic segmentation of spinal cord MS lesions remains a significant challenge. Although some segmentation tools exist for spinal cord lesions, most have been developed using sagittal T2-weighted (T2w) sequences primarily focusing on cervical spines. With the growing importance of spinal cord imaging in MS, axial T2w scans are becoming increasingly relevant due to their superior sensitivity in detecting lesions compared to sagittal acquisition protocols. However, most existing segmentation methods struggle to effectively generalize to axial sequences due to differences in image characteristics caused by the highly anisotropic spinal cord scans. To address these challenges, we developed a robust, open-source lesion segmentation tool tailored specifically for axial T2w scans covering the whole spinal cord. We investigated key factors influencing lesion segmentation, including the impact of stitching together individually acquired spinal regions, straightening the spinal cord, and comparing the effectiveness of 2D and 3D convolutional neural networks (CNNs). Drawing on these insights, we trained a multi-center model using an extensive dataset of 582 MS patients, resulting in a dataset comprising an entirety of 2,167 scans. We empirically evaluated the model's segmentation performance across various spinal segments for lesions with varying sizes. Our model significantly outperforms the current state-of-the-art methods, providing consistent segmentation across cervical, thoracic and lumbar regions. To support the broader research community, we integrate our model into the widely-used Spinal Cord Toolbox (v7.0 and above), making it accessible via the command sct_deepseg -task seg_sc_ms_lesion_axial_t2w -i .
Body size and intracranial volume interact with the structure of the central nervous system: A multi-center in vivo neuroimaging study
René Labounek
Monica T. Bondy
Amy L. Paulson
Sandrine Bédard
Mihael Abramovic
Eva Alonso‐Ortiz
Nicole Atcheson
Laura R. Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew D. Budde
Virginie Callot
Anna Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Doyon … (voir 74 de plus)
Adam Dvorak
Falk Eippert
Karla R. Epperson
Kevin S. Epperson
Patrick Freund
Jürgen Finsterbusch
Alexandru Foias
Michela Fratini
Issei Fukunaga
Claudia A. M. Gandini Wheeler-Kingshott
Giancarlo Germani
Guillaume Gilbert
Federico Giove
Francesco Grussu
Akifumi Hagiwara
Pierre-Gilles Henry
Tomáš Horák
Masaaki Hori
James Joers
Kouhei Kamiya
Haleh Karbasforoushan
Miloš Keřkovský
Ali Khatibi
Joo-won Kim
Nawal Kinany
Hagen H. Kitzler
Shannon Kolind
Yazhuo Kong
Petr Kudlička
Paul Kuntke
Nyoman D. Kurniawan
Slawomir Kusmia
Maria Marcella Lagana
Cornelia Laule
Christine S. W. Law
Csw Law
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Allan R. Martin
Eloy Martinez-Heras
Loan Mattera
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran Prados
Àlex Rovira
Marc J. Ruitenberg
Rebecca S. Samson
Giovanni Savini
Maryam Seif
Alan C. Seifert
Alex K. Smith
Seth Aaron Smith
Zachary A. Smith
Elisabeth Solana
Yuichi Suzuki
George Tackley
Alexandra Tinnermann
Dimitri Van De Ville
Marios C. Yiannakas
Kenneth A. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
Christophe Lenglet
Igor Nestrašil
SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-weighted MRI Scans.
Enamundram Naga Karthik
Andrew C. Smith
Dario Pfyffer
Simon Schading-Sassenhausen
Lynn Farner
KA Weber
Patrick Freund
"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This ar… (voir plus)ticle will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To develop a deep learning tool for the automatic segmentation of the spinal cord and intramedullary lesions in spinal cord injury (SCI) on T2-weighted MRI scans. Materials and Methods This retrospective study included MRI data acquired between July 2002 and February 2023 from 191 patients with SCI (mean age, 48.1 years ± 17.9 [SD]; 142 males). The data consisted of T2-weighted MRI acquired using different scanner manufacturers with various image resolutions (isotropic and anisotropic) and orientations (axial and sagittal). Patients had different lesion etiologies (traumatic, ischemic, and hemorrhagic) and lesion locations across the cervical, thoracic and lumbar spine. A deep learning model, SCIseg, was trained in a three-phase process involving active learning for the automatic segmentation of intramedullary SCI lesions and the spinal cord. The segmentations from the proposed model were visually and quantitatively compared with those from three other open-source methods (PropSeg, DeepSeg and contrast-agnostic, all part of the Spinal Cord Toolbox). Wilcoxon signed-rank test was used to compare quantitative MRI biomarkers of SCI (lesion volume, lesion length, and maximal axial damage ratio) derived from the manual reference standard lesion masks and biomarkers obtained automatically with SCIseg segmentations. Results SCIseg achieved a Dice score of 0.92 ± 0.07 (mean ± SD) and 0.61 ± 0.27 for spinal cord and SCI lesion segmentation, respectively. There was no evidence of a difference between lesion length (P = .42) and maximal axial damage ratio (P = .16) computed from manually annotated lesions and the lesion segmentations obtained using SCIseg. Conclusion SCIseg accurately segmented intramedullary lesions on a diverse dataset of T2-weighted MRI scans and extracted relevant lesion biomarkers (namely, lesion volume, lesion length, and maximal axial damage ratio). SCIseg is open-source and accessible through the Spinal Cord Toolbox (v6.2 and above). Published under a CC BY 4.0 license.
SCIseg: Automatic Segmentation of Intramedullary Lesions in Spinal Cord Injury on T2-weighted MRI Scans.
Enamundram Naga Karthik
Andrew C. Smith
Dario Pfyffer
Simon Schading-Sassenhausen
Lynn Farner
KA Weber
Kenneth A. Weber
Patrick Freund
"Just Accepted" papers have undergone full peer review and have been accepted for publication in Radiology: Artificial Intelligence. This ar… (voir plus)ticle will undergo copyediting, layout, and proof review before it is published in its final version. Please note that during production of the final copyedited article, errors may be discovered which could affect the content. Purpose To develop a deep learning tool for the automatic segmentation of the spinal cord and intramedullary lesions in spinal cord injury (SCI) on T2-weighted MRI scans. Materials and Methods This retrospective study included MRI data acquired between July 2002 and February 2023 from 191 patients with SCI (mean age, 48.1 years ± 17.9 [SD]; 142 males). The data consisted of T2-weighted MRI acquired using different scanner manufacturers with various image resolutions (isotropic and anisotropic) and orientations (axial and sagittal). Patients had different lesion etiologies (traumatic, ischemic, and hemorrhagic) and lesion locations across the cervical, thoracic and lumbar spine. A deep learning model, SCIseg, was trained in a three-phase process involving active learning for the automatic segmentation of intramedullary SCI lesions and the spinal cord. The segmentations from the proposed model were visually and quantitatively compared with those from three other open-source methods (PropSeg, DeepSeg and contrast-agnostic, all part of the Spinal Cord Toolbox). Wilcoxon signed-rank test was used to compare quantitative MRI biomarkers of SCI (lesion volume, lesion length, and maximal axial damage ratio) derived from the manual reference standard lesion masks and biomarkers obtained automatically with SCIseg segmentations. Results SCIseg achieved a Dice score of 0.92 ± 0.07 (mean ± SD) and 0.61 ± 0.27 for spinal cord and SCI lesion segmentation, respectively. There was no evidence of a difference between lesion length (P = .42) and maximal axial damage ratio (P = .16) computed from manually annotated lesions and the lesion segmentations obtained using SCIseg. Conclusion SCIseg accurately segmented intramedullary lesions on a diverse dataset of T2-weighted MRI scans and extracted relevant lesion biomarkers (namely, lesion volume, lesion length, and maximal axial damage ratio). SCIseg is open-source and accessible through the Spinal Cord Toolbox (v6.2 and above). Published under a CC BY 4.0 license.
SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spinal Cord Injury
Enamundram Naga Karthik
Lynn Farner
Dario Pfyffer
Simon Schading-Sassenhausen
A. Lebret
Gergely David
Andrew Smith
Kenneth A. Weber
Maryam Seif
Rhscir Network Imaging Group
Patrick Freund
Spinal cord injury (SCI) is a devastating incidence leading to permanent paralysis and loss of sensory-motor functions potentially resulting… (voir plus) in the formation of lesions within the spinal cord. Imaging biomarkers obtained from magnetic resonance imaging (MRI) scans can predict the functional recovery of individuals with SCI and help choose the optimal treatment strategy. Currently, most studies employ manual quantification of these MRI-derived biomarkers, which is a subjective and tedious task. In this work, we propose (i) a universal tool for the automatic segmentation of intramedullary SCI lesions, dubbed \texttt{SCIsegV2}, and (ii) a method to automatically compute the width of the tissue bridges from the segmented lesion. Tissue bridges represent the spared spinal tissue adjacent to the lesion, which is associated with functional recovery in SCI patients. The tool was trained and validated on a heterogeneous dataset from 7 sites comprising patients from different SCI phases (acute, sub-acute, and chronic) and etiologies (traumatic SCI, ischemic SCI, and degenerative cervical myelopathy). Tissue bridges quantified automatically did not significantly differ from those computed manually, suggesting that the proposed automatic tool can be used to derive relevant MRI biomarkers. \texttt{SCIsegV2} and the automatic tissue bridges computation are open-source and available in Spinal Cord Toolbox (v6.4 and above) via the \texttt{sct\_deepseg -task seg\_sc\_lesion\_t2w\_sci} and \texttt{sct\_analyze\_lesion} functions, respectively.
Automatic Segmentation of the Spinal Cord Nerve Rootlets
Theo Mathieu
Raphaëlle Schlienger
Olivia S. Kowalczyk
Precise identification of spinal nerve rootlets is relevant to delineate spinal levels for the study of functional activity in the spinal co… (voir plus)rd. The goal of this study was to develop an automatic method for the semantic segmentation of spinal nerve rootlets from T2-weighted magnetic resonance imaging (MRI) scans. Images from two open-access MRI datasets were used to train a 3D multi-class convolutional neural network using an active learning approach to segment C2-C8 dorsal nerve rootlets. Each output class corresponds to a spinal level. The method was tested on 3T T2-weighted images from datasets unseen during training to assess inter-site, inter-session, and inter-resolution variability. The test Dice score was 0.67 +- 0.16 (mean +- standard deviation across rootlets levels), suggesting a good performance. The method also demonstrated low inter-vendor and inter-site variability (coefficient of variation= 1.41 %), as well as low inter-session variability (coefficient of variation= 1.30 %) indicating stable predictions across different MRI
Body size interacts with the structure of the central nervous system: A multi-center in vivo neuroimaging study
René Labounek
Monica T. Bondy
Amy L. Paulson
Sandrine Bédard
Mihael Abramovic
Eva Alonso‐Ortiz
Nicole Atcheson
Laura R. Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew D. Budde
Virginie Callot
Anna Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Doyon … (voir 74 de plus)
Adam Dvorak
Falk Eippert
Karla R. Epperson
Kevin S. Epperson
Patrick Freund
Jürgen Finsterbusch
Alexandru Foias
Michela Fratini
Issei Fukunaga
Claudia A. M. Gandini Wheeler-Kingshott
Giancarlo Germani
Guillaume Gilbert
Federico Giove
Francesco Grussu
Akifumi Hagiwara
Pierre-Gilles Henry
Tomáš Horák
Masaaki Hori
James M. Joers
Kouhei Kamiya
Haleh Karbasforoushan
Miloš Keřkovský
Ali Khatibi
Joo‐Won Kim
Nawal Kinany
Hagen H. Kitzler
Shannon Kolind
Yazhuo Kong
Petr Kudlička
Paul Kuntke
Nyoman D. Kurniawan
Slawomir Kusmia
Maria Marcella Lagana
Cornelia Laule
Christine S. W. Law
Csw Law
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Allan R. Martin
Eloy Martinez-Heras
Loan Mattera
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran Prados
Àlex Rovira
Marc J. Ruitenberg
Rebecca S. Samson
Giovanni Savini
Maryam Seif
Alan C. Seifert
Alex K. Smith
Seth A. Smith
Zachary A. Smith
Elisabeth Solana
Yuichi Suzuki
George Tackley
Alexandra Tinnermann
Dimitri Van De Ville
Marios C. Yiannakas
Kenneth A. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
Christophe Lenglet
Igor Nestrašil
Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controllin… (voir plus)g for sources of biological variation such as subject’s sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1±6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44≤r≤0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (-0.21≥r≥-0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (-0.20≥r≥-0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=-0.20) and dorsal columns (-0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39≤r≤0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (-0.22≥r≥-0.25). Linear mixture of sex and age explained 26±10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33±11% when body height was added into the mixture model. Age itself explained only 2±2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.
Body size interacts with the structure of the central nervous system: A multi-center in vivo neuroimaging study
René Labounek
Monica T. Bondy
Amy L. Paulson
Sandrine Bédard
Mihael Abramovic
Eva Alonso‐Ortiz
Nicole Atcheson
Laura R. Barlow
Robert L. Barry
Markus Barth
Marco Battiston
Christian Büchel
Matthew D. Budde
Virginie Callot
Anna Combes
Benjamin De Leener
Maxime Descoteaux
Paulo Loureiro de Sousa
Marek Dostál
Julien Doyon … (voir 73 de plus)
Adam Dvorak
Falk Eippert
Karla R. Epperson
Kevin S. Epperson
Patrick Freund
Jürgen Finsterbusch
Alexandru Foias
Michela Fratini
Issei Fukunaga
Claudia A. M. Gandini Wheeler-Kingshott
Giancarlo Germani
Guillaume Gilbert
Federico Giove
Francesco Grussu
Akifumi Hagiwara
Pierre-Gilles Henry
Tomáš Horák
Masaaki Hori
James M. Joers
Kouhei Kamiya
Haleh Karbasforoushan
Miloš Keřkovský
Ali Khatibi
Joo‐Won Kim
Nawal Kinany
Hagen H. Kitzler
Shannon Kolind
Yazhuo Kong
Petr Kudlička
Paul Kuntke
Nyoman D. Kurniawan
Slawomir Kusmia
Maria Marcella Lagana
Cornelia Laule
Csw Law
Tobias Leutritz
Yaou Liu
Sara Llufriu
Sean Mackey
Allan R. Martin
Eloy Martinez-Heras
Loan Mattera
Kristin P. O’Grady
Nico Papinutto
Daniel Papp
Deborah Pareto
Todd B. Parrish
Anna Pichiecchio
Ferran Prados
Àlex Rovira
Marc J. Ruitenberg
Rebecca S. Samson
Giovanni Savini
Maryam Seif
Alan C. Seifert
Alex K. Smith
Seth A. Smith
Zachary A. Smith
Elisabeth Solana
Yuichi Suzuki
George Tackley
Alexandra Tinnermann
Dimitri Van De Ville
Marios C. Yiannakas
Kenneth A. Weber
Nikolaus Weiskopf
Richard G. Wise
Patrik O. Wyss
Junqian Xu
Christophe Lenglet
Igor Nestrašil
Clinical research emphasizes the implementation of rigorous and reproducible study designs that rely on between-group matching or controllin… (voir plus)g for sources of biological variation such as subject’s sex and age. However, corrections for body size (i.e. height and weight) are mostly lacking in clinical neuroimaging designs. This study investigates the importance of body size parameters in their relationship with spinal cord (SC) and brain magnetic resonance imaging (MRI) metrics. Data were derived from a cosmopolitan population of 267 healthy human adults (age 30.1±6.6 years old, 125 females). We show that body height correlated strongly or moderately with brain gray matter (GM) volume, cortical GM volume, total cerebellar volume, brainstem volume, and cross-sectional area (CSA) of cervical SC white matter (CSA-WM; 0.44≤r≤0.62). In comparison, age correlated weakly with cortical GM volume, precentral GM volume, and cortical thickness (-0.21≥r≥-0.27). Body weight correlated weakly with magnetization transfer ratio in the SC WM, dorsal columns, and lateral corticospinal tracts (-0.20≥r≥-0.23). Body weight further correlated weakly with the mean diffusivity derived from diffusion tensor imaging (DTI) in SC WM (r=-0.20) and dorsal columns (-0.21), but only in males. CSA-WM correlated strongly or moderately with brain volumes (0.39≤r≤0.64), and weakly with precentral gyrus thickness and DTI-based fractional anisotropy in SC dorsal columns and SC lateral corticospinal tracts (-0.22≥r≥-0.25). Linear mixture of sex and age explained 26±10% of data variance in brain volumetry and SC CSA. The amount of explained variance increased at 33±11% when body height was added into the mixture model. Age itself explained only 2±2% of such variance. In conclusion, body size is a significant biological variable. Along with sex and age, body size should therefore be included as a mandatory variable in the design of clinical neuroimaging studies examining SC and brain structure.