Multiclass Spinal Cord Tumor Segmentation on MRI with Deep Learning
Polytechnique Montreal（蒙特利尔理工学院）；Mila, Quebec AI Institute（米拉魁北克人工智能研究所）；Beijing Tiantan Hospital, Capital Medical University（首都医科大学附属北京天坛医院）；Université de Montréal（蒙特利尔大学）
Andreanne Lemay, Charley Gros, Zhizheng Zhuo, Jie Zhang, Yunyun Duan, Julien Cohen-Adad, Yaou Liu
Spinal cord tumors lead to neurological morbidity and mortality. Being able to obtain morphometric quantification (size, location, growth rate) of the tumor, edema, and cavity can result in improved monitoring and treatment planning. Such quantification requires the segmentation of these structures into three separate classes. However, manual segmentation of 3-dimensional structures is time-consuming and tedious, motivating the development of automated methods. Here, we tailor a model adapted to the spinal cord tumor segmentation task. Data were obtained from 343 patients using gadolinium-enhanced T1-weighted and T2-weighted MRI scans with cervical, thoracic, and/or lumbar coverage. The dataset includes the three most common intramedullary spinal cord tumor types: astrocytomas, ependymomas, and hemangioblastomas. The proposed approach is a cascaded architecture with U-Net-based models that segments tumors in a two-stage process: locate and label. The model first finds the spinal cord and generates bounding box coordinates. The images are cropped according to this output, leading to a reduced field of view, which mitigates class imbalance. The tumor is then segmented. The segmentation of the tumor, cavity, and edema (as a single class) reached 76.7 $\pm$ 1.5% of Dice score and the segmentation of tumors alone reached 61.8 $\pm$ 4.0% Dice score. The true positive detection rate was above 87% for tumor, edema, and cavity. To the best of our knowledge, this is the first fully automatic deep learning model for spinal cord tumor segmentation. The multiclass segmentation pipeline is available in the Spinal Cord Toolbox (https://spinalcordtoolbox.com/). It can be run with custom data on a regular computer within seconds.
University College London（伦敦大学学院）；University Hospital Zurich（苏黎世大学医院）；University of Zurich（苏黎世大学）
In this paper we will focus on the potential and on the challenges associated with the development of an integrated brain and spinal cord modelling framework for processing MR neuroimaging data. The aim of the work is to explore how a hierarchical generative model of imaging data, which captures simultaneously the distribution of signal intensities and the variability of anatomical shapes across a large population of subjects, can serve to quantitatively investigate, in vivo, the morphology of the central nervous system (CNS). In fact, the generality of the proposed Bayesian approach, which ex…
Polytechnique Montreal（蒙特利尔高等理工学院）；Duke University Medical Center（杜克大学医学中心）；University of California San Francisco（加州大学旧金山分校）；Université de Montréal（蒙特利尔大学）
Gray matter (GM) tissue changes have been associated with a wide range of neurological disorders and was also recently found relevant as a biomarker for disability in amyotrophic lateral sclerosis. The ability to automatically segment the GM is, therefore, an important task for modern studies of the spinal cord. In this work, we devise a modern, simple and end-to-end fully automated human spinal cord gray matter segmentation method using Deep Learning, that works both on in vivo and ex vivo MRI acquisitions. We evaluate our method against six independently developed methods on a GM segmentatio…
Don Bosco Institute of Technology（唐博斯科理工学院）；R. V College of Engineering（R. V工程学院）；Dayananda Sagar College of Engineering（达亚南达·萨加尔工程学院）
This paper presents a new approach for contrast enhancement of spinal cord medical images based on multirate scheme incorporated into multiscale retinex algorithm. The proposed work here uses HSV color space, since HSV color space separates color details from intensity. The enhancement of medical image is achieved by down sampling the original image into five versions, namely, tiny, small, medium, fine, and normal scale. This is due to the fact that the each versions of the image when independently enhanced and reconstructed results in enormous improvement in the visual quality. Further, the c…
University of Oxford（牛津大学）；Plexalis Ltd（Plexalis有限公司）
This paper proposes a novel transformer-based model architecture for medical imaging problems involving analysis of vertebrae. It considers two applications of such models in MR images: (a) detection of spinal metastases and the related conditions of vertebral fractures and metastatic cord compression, (b) radiological grading of common degenerative changes in intervertebral discs. Our contributions are as follows: (i) We propose a Spinal Context Transformer (SCT), a deep-learning architecture suited for the analysis of repeated anatomical structures in medical imaging such as vertebral bodies…
U2AD: Uncertainty-based Unsupervised Anomaly Detection Framework for Detecting T2 Hyperintensity in MRI Spinal Cord
School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）；Renji Hospital, School of Medicine, Shanghai Jiao Tong University（上海交通大学医学院附属仁济医院）；Ruijin Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属瑞金医院）；National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT)（先进磁共振诊疗技术国家工程研究中心）；Med-X Research Institute, Shanghai Jiao Tong University（上海交通大学Med-X研究院）
Rootlets-based registration to the spinal cord PAM50 template
Polytechnique Montreal（蒙特利尔理工学院）；Mila - Quebec AI Institute（米拉-魁北克人工智能研究所）；Palacký University Olomouc（帕拉茨基大学奥洛穆茨分校）；Stanford School of Medicine（斯坦福医学院）；Italian National Institute of Health（意大利国家卫生研究院）；Université de Montréal（蒙特利尔大学）；Centre de Recherche du CHU Sainte-Justine（圣贾斯汀大学医学中心研究中心）
Towards contrast-agnostic soft segmentation of the spinal cord
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montréal（神经Poly实验室，生物医学工程学院，蒙特利尔理工学院）；Mila - Québec Artificial Intelligence Institute（魁北克人工智能研究所）；Translational Imaging in Neurology (ThINK) Basel（神经学转化成像（ThINK）巴塞尔）；Department of Biomedical Engineering, Faculty of Medicine, University Hospital Basel and University of Basel（生物医学工程系，医学学院，巴塞尔大学医院和巴塞尔大学）；Department of Neurology, University Hospital Basel（神经病学系，巴塞尔大学医院）；Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel and University of Basel（临床神经免疫学和神经科学巴塞尔研究中心（RC2NB），巴塞尔大学医院和巴塞尔大学）；Neuroradiology Department, Neurocenter of Southern Switzerland, Ospedale Regionale di Lugano（神经放射科，瑞士南部神经中心，卢加诺地区医院）；Department of Physical Medicine and Rehabilitation Physical Therapy Program, University of Colorado School of Medicine（康复医学系，科罗拉多大学医学院物理治疗项目）；Division of Pain Medicine, Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine（疼痛医学科，麻醉学、围手术期和疼痛医学部，斯坦福大学医学院）；Functional Neuroimaging Unit, CRIUGM, University of Montreal（功能神经影像单元，CRIUGM，蒙特利尔大学）
Aix Marseille Univ（艾克斯-马赛大学）；CNRS（法国国家科学研究中心）；CRMBM（生物医学与医学影像学研究中心）；APHM（Assistance Publique - Hôpitaux de Marseille（马赛公立医院系统））；CHU Timone（蒂莫讷大学医院）；CEMEREM（马赛医学研究中心）；NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montréal（蒙特利尔理工大学生物医学工程系NeuroPoly实验室）；MILA - Québec AI Institute（魁北克人工智能研究所（MILA））
The spinal cord (SC), which conveys information between the brain and the peripheral nervous system, plays a key role in various neurological disorders such as multiple sclerosis (MS) and amyotrophic lateral sclerosis (ALS), in which both gray matter (GM) and white matter (WM) may be impaired. While automated methods for WM/GM segmentation are now largely available, these techniques, developed for conventional systems (3T or lower) do not necessarily perform well on 7T MRI data, which feature finer details, contrasts, but also different artifacts or signal dropout. The primary goal of this stu…
Background: Magnetic field inhomogeneities generate important geometric distortions in reconstructed echo-planar images. Various procedures were proposed for correcting these distortions on brain images; yet, few neuroimaging studies tailored and incorporated the use of these techniques in spinal cord diffusion MRI. Purpose: We present a comparative evaluation of distortion correction methods that use the reversed gradient polarity technique on spinal cord. We propose novel geometric metrics to measure the alignment of the reconstructed diffusion model with the apparent centerline of the spina…
Obtaining high quality images of the spinal cord with MRI is difficult, partly due to the fact that the spinal cord is surrounded by a number of structures that have differing magnetic susceptibility. This causes inhomogeneities in the magnetic field, which in turn lead to image artifacts. In order to address this issue, linear compensation gradients can be employed. The latter can be generated using an MRI scanner's first order gradient coils and adjusted on a per-slice basis, in order to correct for through-plane ("z") magnetic field gradients. This approach is referred to as z-shimming. The…
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal（蒙特利尔理工学院生物医学工程研究所NeuroPoly实验室）；Mila - Quebec AI Institute（Mila-魁北克人工智能研究所）；Functional Neuroimaging Unit, CRIUGM, Université de Montréal（蒙特利尔大学CRIUGM功能神经影像单元）
While multiple studies have explored the relation between inter-rater variability and deep learning model uncertainty in medical segmentation tasks, little is known about the impact of individual rater style. This study quantifies rater style in the form of bias and consistency and explores their impacts when used to train deep learning models. Two multi-rater public datasets were used, consisting of brain multiple sclerosis lesion and spinal cord grey matter segmentation. On both datasets, results show a correlation ($R^2 = 0.60$ and $0.93$) between rater bias and deep learning uncertainty. T…
Optimization in Sparse 2D to Dense 3D Weakly Supervised Learning: Application to Multi-Label Segmentation of Large ex vivo MRI Data
NeuroPoly Lab, Institute of Biomedical Engineering, Polytechnique Montreal（神经多极实验室，生物医学工程学院，蒙特利尔理工学院）；École Centrale de Lyon（里昂中央理工学院）；Mila - Quebec AI Institute（魁北克人工智能研究所）；Functional Neuroimaging Unit, CRIUGM, University of Montreal（功能神经影像单元，CRIUGM，蒙特利尔大学）；Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health（转化神经放射学部门，国家神经疾病与中风研究所，国家卫生研究院）；Translational Imaging in Neurology (ThINk) Basel, Department of Biomedical Engineering, Faculty of Medicine, University Hospital Basel and University of Basel（神经学转化成像（ThINk）巴塞尔，生物医学工程系，医学院，巴塞尔大学医院和巴塞尔大学）；Neurologic Clinic and Policlinic, Departments of Medicine, University Hospital Basel, Switzerland（神经科诊所和多科诊所，医学院，巴塞尔大学医院，瑞士）；Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel and University of Basel, Switzerland（临床神经免疫学和神经科学巴塞尔研究中心（RC2NB），巴塞尔大学医院和巴塞尔大学，瑞士）；National Institute of Neurological Disorders and Stroke, National Institutes of Health（国家神经疾病与中风研究所，国家卫生研究院）；Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montreal, QC, Canada（圣朱斯特医院研究中心，蒙特利尔大学，蒙特利尔，魁北克，加拿大）；Quantitative MRI core facility, NINDS, NIH（定量MRI核心设施，NINDS，NIH）；Experimental Immunotherapeutics Unit, Division of Neuroimmunology and Neurovirology, NINDS, NIH（实验免疫治疗单元，神经免疫学和神经病毒学部门，NINDS，NIH）
Measuring hand use in the home after cervical spinal cord injury using egocentric video
KITE Research Institute, University Health Network（KITE研究所（大学健康网络））；The BioRobotics Institute, Scuola Superiore Sant’Anna（圣安娜高等学校生物机器人研究所）；Institute of Biomedical Engineering, University of Toronto（多伦多大学生物医学工程研究所）；Sunnybrook Research Institute, Sunnybrook Health Sciences Centre（桑尼布鲁克健康科学中心桑尼布鲁克研究所）；Temerty Faculty of Medicine, University of Toronto（多伦多大学特默蒂医学院）；Brain and Spinal Cord Rehabilitation Program, Toronto Rehabilitation Institute – University Health Network（大学健康网络多伦多康复研究所脑与脊髓康复项目）；Department of Physical Therapy, University of Toronto（多伦多大学物理治疗系）；Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto（多伦多大学爱德华·S·罗杰斯 Sr. 电气与计算机工程系）
SpineReport: Automated 3D Quantification and Reporting of Lumbar Spine Degeneration on MRI
NeuroPoly, Institute of Biomedical Engineering, Polytechnique Montreal（NeuroPoly，生物医学工程研究所，蒙特利尔大学）；Mila, Quebec AI Institute, Montreal（Mila，魁北克人工智能研究所，蒙特利尔）；Department of Radiology, Balgrist University Hospital, Zurich（放射科，巴尔格里斯大学医院，苏黎世）；Faculty of Medicine, University of Zurich（医学学院，苏黎世大学）；Department of Neurosurgery, Brain & Spine, University of South Florida（神经外科，脑与脊柱，佛罗里达大学）；Center for Neuromusculoskeletal Research, University of South Florida（神经肌肉研究中心，佛罗里达大学）；Department of Medical Engineering, University of South Florida（医学工程系，佛罗里达大学）；Stanford School of Medicine, Stanford（斯坦福医学院，斯坦福）；Functional Neuroimaging Unit, CRIUGM, Université de Montréal（功能神经影像单元，CRIUGM，蒙特利尔大学）；Centre de recherche du CHU Sainte-Justine, Université de Montréal（圣若泽中心研究，蒙特利尔大学）
University of Oulu（奥卢大学）；KFUPM（法赫德国王石油与矿业大学）；King Fahd Specialist Hospital Dammam（达曼法赫德国王专科医院）
Introduction: Multiple Sclerosis (MS) is a chronic disease that affects millions of people across the globe. MS can critically affect different organs of the central nervous system such as the eyes, the spinal cord, and the brain. Background: To help physicians in diagnosing MS lesions, computer-aided methods are widely used. In this regard, a considerable research has been carried out in the area of automatic detection and segmentation of MS lesions in magnetic resonance images (MRIs). Methodology: In this study, we review the different approaches that have been used in computer-aided detecti…
SPINEPS -- Automatic Whole Spine Segmentation of T2-weighted MR images using a Two-Phase Approach to Multi-class Semantic and Instance Segmentation
Technical University of Munich（慕尼黑工业大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；University of Zurich（苏黎世大学）；Imperial College London（帝国理工学院）；Helmholtz Munich（亥姆霍兹慕尼黑中心）；University Medical Center Rostock（罗斯托克大学医学中心）；University of Freiburg（弗赖堡大学）；University Hospital Augsburg（奥格斯堡大学医院）；Augsburg University（奥格斯堡大学）
Robust High-Resolution Multi-Organ Diffusion MRI Using Synthetic-Data-Tuned Prompt Learning
Xiamen University（厦门大学）；Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University（厦门大学萨本栋微纳米科学技术研究院）；The Second Hospital of Shandong University（山东大学第二医院）；Zhongshan Hospital, Fudan University (Xiamen Branch)（复旦大学附属中山医院厦门医院）；Neusoft Medical Systems（东软医疗系统股份有限公司）；United Imaging Healthcare（上海联影医疗科技股份有限公司）；Lishui Central Hospital（丽水市中心医院）；Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University（厦门大学附属翔安医院）；Zhongshan Hospital Affiliated to Xiamen University（厦门大学附属中山医院）；Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology（湖北科技学院附属第一医院（咸宁市中心医院））；th Hospital of PLA Joint Logistic Support Force, Dongfang Hospital of Xiamen University, School of Medicine, Xiamen University（厦门大学附属东方医院（解放军联勤保障部队第九〇〇医院））；The First Affiliated Hospital of the Medical College of Shantou University（汕头大学医学院第一附属医院）；The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University（厦门大学附属第一医院）；Xiamen University of Technology（厦门理工学院）
Polytechnique Montreal（蒙特利尔综合理工学院）；Ecole Centrale de Lille（里尔中央理工学院）；Ecole Centrale de Nantes（南特中央理工学院）；Université de Montréal（蒙特利尔大学）
Segmentation of axon and myelin from microscopy images of the nervous system provides useful quantitative information about the tissue microstructure, such as axon density and myelin thickness. This could be used for instance to document cell morphometry across species, or to validate novel non-invasive quantitative magnetic resonance imaging techniques. Most currently-available segmentation algorithms are based on standard image processing and usually require multiple processing steps and/or parameter tuning by the user to adapt to different modalities. Moreover, only few methods are publicly…
Georgia Institute of Technology（佐治亚理工学院）；Emory University（埃默里大学）；Georgia Tech Research Institute（佐治亚理工研究院）
This paper presents a method of navigating a surgical robot beyond the resolution of magnetic resonance imaging (MRI) by using a resolution enhancement technique enabled by high-precision piezoelectric actuation. The surgical robot was specifically designed for injecting stem cells into the spinal cord. This particular therapy can be performed in a shorter time by using a MRI-compatible robotic platform than by using a manual needle positioning platform. Imaging resolution of fiducial markers attached to the needle guide tubing was enhanced by reconstructing a high-resolution image from multip…
Glioma is one of the most common types of brain tumors; it arises in the glial cells in the human brain and in the spinal cord. In addition to having a high mortality rate, glioma treatment is also very expensive. Hence, automatic and accurate segmentation and measurement from the early stages are critical in order to prolong the survival rates of the patients and to reduce the costs of the treatment. In the present work, we propose a novel end-to-end cascaded network for semantic segmentation that utilizes the hierarchical structure of the tumor sub-regions with ResNet-like blocks and Squeeze…
VIBESegmentator: Full Body MRI Segmentation for the NAKO and UK Biobank
TUM University Hospital（慕尼黑工业大学附属医院）；Technical University of Munich（慕尼黑工业大学）；University Medicine Greifswald（格赖夫斯瓦尔德大学医学中心）；University Medical Center Freiburg（弗赖堡大学医学中心）；University of Freiburg（弗赖堡大学）；Weill Cornell Medicine（威尔康奈尔医学院）；Imperial College London（伦敦帝国理工学院）
Pathology-Guided AI System for Accurate Segmentation and Diagnosis of Cervical Spondylosis
School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）；National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT)（先进磁共振诊断与治疗技术国家工程研究中心）；Med-X Research Institute, Shanghai Jiao Tong University（Med-X研究院，上海交通大学）；Department of Spine Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University（上海交通大学医学院附属仁济医院脊柱外科部）；Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属瑞金医院放射科）；Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University（上海交通大学医学院附属仁济医院放射科）
Today, over 700,000 people are living with brain tumors in the United States. Brain tumors can spread very quickly to other parts of the brain and the spinal cord unless necessary preventive action is taken. Thus, the survival rate for this disease is less than 40% for both men and women. A conclusive and early diagnosis of a brain tumor could be the difference between life and death for some. However, brain tumor detection and segmentation are tedious and time-consuming processes as it can only be done by radiologists and clinical experts. The use of computer vision techniques, such as Mask R…
