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An End-to-End Geometry-Based Pipeline for Automatic Preoperative Surgical Planning of Pelvic Fracture Reduction and Fixation
Jiaxuan Liu;Haitao Li;Bolun Zeng;Huixiang Wang;Ron Kikinis;Leo Joskowicz;Xiaojun Chen
Computer-assisted preoperative planning of pelvic fracture reduction surgery has the potential to increase the accuracy of the surgery and to reduce complications. However, the diversity of the pelvic fractures and the disturbance of small fracture fragments present a great challenge to perform reliable automatic preoperative planning. In this paper, we present a comprehensive and automatic preope...Show More
A Registration- and Uncertainty-Based Framework for White Matter Tract Segmentation with Only One Annotated Subject
Hao Xu;Tengfei Xue;Dongnan Liu;Fan Zhang;Carl-Fredrik Westin;Ron Kikinis;Lauren J. O’Donnell;Weidong Cai
2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)
Year: 2023 | Conference Paper |
Cited by: Papers (3)
White matter (WM) tract segmentation based on diffusion magnetic resonance imaging (dMRI) plays an important role in the analysis of human health and brain diseases. However, the annotation of WM tracts is time-consuming and needs experienced neuroanatomists. In this study, to explore tract segmentation in the challenging setting of minimal annotations, we propose a novel framework utilizing only ...Show More
DEEPRGVP: A novel microstructure-informed supervised contrastive learning framework for automated identification of the retinogeniculate pathway using dMRI tractography
Sipei Li;Jianzhong He;Tengfei Xue;Guoqiang Xie;Shun Yao;Yuqian Chen;Erickson F. Torio;Yuanjing Feng;Dhiego CA Bastos;Yogesh Rathi;Nikos Makris;Ron Kikinis;Wenya Linda Bi;Alexandra J Golby;Lauren J O’Donnell;Fan Zhang
2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI)
Year: 2023 | Conference Paper |
Cited by: Papers (2)
The retinogeniculate pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3...Show More
DEEPRGVP: A novel microstructure-informed supervised contrastive learning framework for automated identification of the retinogeniculate pathway using dMRI tractography
Sipei Li;Jianzhong He;Tengfei Xue;Guoqiang Xie;Shun Yao;Yuqian Chen;Erickson F. Torio;Yuanjing Feng;Dhiego CA Bastos;Yogesh Rathi;Nikos Makris;Ron Kikinis;Wenya Linda Bi;Alexandra J Golby;Lauren J O’Donnell;Fan Zhang
Year: 2023 | Conference Paper |
A Review of Low-Cost Ultrasound Compatible Phantoms
Leah A. Groves;Mohamed Keita;Saidou Talla;Ron Kikinis;Gabor Fichtinger;Parvin Mousavi;Mamadou Camara
Ultrasound-compatible phantoms are used to develop novel US-based systems and train simulated medical interventions. The price difference between lab-made and commercially available ultrasound-compatible phantoms lead to the publication of many papers categorized as low-cost in the literature. The aim of this review was to improve the phantom selection process by summarizing the pertinent literatu...Show More
Open Source Platform for Transperineal In-Bore MRI-Guided Targeted Prostate Biopsy
Christian Herz;Kyle MacNeil;Peter A. Behringer;Junichi Tokuda;Alireza Mehrtash;Parvin Mousavi;Ron Kikinis;Fiona M. Fennessy;Clare M. Tempany;Kemal Tuncali;Andriy Fedorov
Objective: Accurate biopsy sampling of the suspected lesions is critical for the diagnosis and clinical management of prostate cancer. Transperineal in-bore MRI-guided prostate biopsy (tpMRgBx) is a targeted biopsy technique that was shown to be safe, efficient, and accurate. Our goal was to develop an open source software platform to support evaluation, refinement, and translation of this biopsy ...Show More
Automatic Needle Segmentation and Localization in MRI With 3-D Convolutional Neural Networks: Application to MRI-Targeted Prostate Biopsy
Alireza Mehrtash;Mohsen Ghafoorian;Guillaume Pernelle;Alireza Ziaei;Friso G. Heslinga;Kemal Tuncali;Andriy Fedorov;Ron Kikinis;Clare M. Tempany;William M. Wells;Purang Abolmaesumi;Tina Kapur
Image guidance improves tissue sampling during biopsy by allowing the physician to visualize the tip and trajectory of the biopsy needle relative to the target in MRI, CT, ultrasound, or other relevant imagery. This paper reports a system for fast automatic needle tip and trajectory localization and visualization in MRI that has been developed and tested in the context of an active clinical resear...Show More
Automatic Needle Segmentation and Localization in MRI With 3-D Convolutional Neural Networks: Application to MRI-Targeted Prostate Biopsy
Alireza Mehrtash;Mohsen Ghafoorian;Guillaume Pernelle;Alireza Ziaei;Friso G. Heslinga;Kemal Tuncali;Andriy Fedorov;Ron Kikinis;Clare M. Tempany;William M. Wells;Purang Abolmaesumi;Tina Kapur
Train the Trainers: Medical Technology for the Sustainable Development of Africa
Juan Ruiz-Alzola;Asmaa Skareb;Ahmedou Moulaye Idriss;Babacar Diao;Joseane Da Rosa De Pina Ferreira;María Alexandra Fernandes Rodrigues;Luis López Rivero;Ron Kikinis
2018 IEEE Global Humanitarian Technology Conference (GHTC)
Year: 2018 | Conference Paper |
Cited by: Papers (3)
The role of technology as a key driver of sustainable development has long been recognized. Technology leverages total-factor productivity and contributes to the growth of welfare. The lack of adequate financial and human capital hampers the adoption of technology in many parts of Africa. On September 2015, the General Assembly of United Nations adopted as a consensus resolution the 2030 Developme...Show More
Large Scale Cloud-Based Deformable Registration for Image Guided Therapy
Shahram Mohrehkesh;Andriy Fedorov;Arun Brahmavar Vishwanatha;Fotis Drakopoulos;Ron Kikinis;Nikos Chrisochoides
2016 IEEE First International Conference on Connected Health: Applications, Systems and Engineering Technologies (CHASE)
Year: 2016 | Conference Paper |
We present a feasibility study using cloud resources for computing the deformable registration or non-rigid registration (NRR) of brain MR images for Image Guided Neurosurgery (IGNS). We consider the use of cloud resources in two scenarios. First, we describe a workflow implementation to enable speculative computation of registration to improve confidence in the result and assist in retrospective ...Show More
Pairwise Latent Semantic Association for Similarity Computation in Medical Imaging
Fan Zhang;Yang Song;Weidong Cai;Sidong Liu;Siqi Liu;Sonia Pujol;Ron Kikinis;Yong Xia;Michael J. Fulham;David Dagan Feng;Alzheimer's Disease Neuroimaging Initiative
Retrieving medical images that present similar diseases is an active research area for diagnostics and therapy. However, it can be problematic given the visual variations between anatomical structures. In this paper, we propose a new feature extraction method for similarity computation in medical imaging. Instead of the low-level visual appearance, we design a CCA-PairLDA feature representation me...Show More
Subject-centered multi-view feature fusion for neuroimaging retrieval and classification
Sidong Liu;Weidong Cai;Siqi Liu;Sonia Pujol;Ron Kikinis;Dagan Feng
2015 IEEE International Conference on Image Processing (ICIP)
Year: 2015 | Conference Paper |
Cited by: Papers (2)
Multi-View neuroimaging retrieval and classification play an important role in computer-aided-diagnosis of brain disorders, as multi-view features could provide more insights of the disease pathology and potentially lead to more accurate diagnosis than single-view features. The large inter-feature and inter-subject variations make the multi-view neuroimaging analysis a challenging task. Many multi...Show More
Longitudinal brain MR retrieval with diffeomorphic demons registration: What happened to those patients with similar changes?
Siqi Liu;Sidong Liu;Fan Zhang;Weidong Cai;Sonia Pujol;Ron Kikinis;Dagan Feng
2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)
Year: 2015 | Conference Paper |
Cited by: Papers (10)
Current medical content-based retrieval (MCBR) systems for neuroimaging data mainly focus on retrieving the cross-sectional neuroimaging data with similar regional or global measurements. The longitudinal pathological changes along different time-points are usually neglected in such MCBR systems. We propose the cross-registration based retrieval for longitudinal MR data to retrieve patients with s...Show More
Multimodal Neuroimaging Feature Learning for Multiclass Diagnosis of Alzheimer's Disease
Siqi Liu;Sidong Liu;Weidong Cai;Hangyu Che;Sonia Pujol;Ron Kikinis;Dagan Feng;Michael J. Fulham;ADNI
The accurate diagnosis of Alzheimer's disease (AD) is essential for patient care and will be increasingly important as disease modifying agents become available, early in the course of the disease. Although studies have applied machine learning methods for the computer-aided diagnosis of AD, a bottleneck in the diagnostic performance was shown in previous methods, due to the lacking of efficient s...Show More
A 3D difference-of-Gaussian-based lesion detector for brain PET
Weidong Cai;Sidong Liu;Yang Song;Sonia Pujol;Ron Kikinis;Dagan Feng
2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI)
Year: 2014 | Conference Paper |
Cited by: Papers (12)
Positron emission tomography (PET) plays an important role in neurodegenerative disorder diagnosis and neurooncology applications, especially detecting the early metabolism anomalies in human brains. Current lesion detection algorithms can be roughly classified into voxel-based, region of interest (ROI)-based, and global algorithms. These methods may capture the scale and/or location of the lesion...Show More
Propagation graph fusion for multi-modal medical content-based retrieval
Sidong Liu;Siqi Liu;Sonia Pujol;Ron Kikinis;Dagan Feng;Weidong Cai
2014 13th International Conference on Control Automation Robotics & Vision (ICARCV)
Year: 2014 | Conference Paper |
Cited by: Papers (10)
Medical content-based retrieval (MCBR) plays an important role in computer aided diagnosis and clinical decision support. Multi-modal imaging data have been increasingly used in MCBR, as they could provide more insights of the diseases and complement the deficiencies of single-modal data. However, it is very challenging to fuse data in different modalities since they have different physical fundam...Show More
Latent Semantic Association for Medical Image Retrieval
Fan Zhang;Yang Song;Sidong Liu;Sonia Pujol;Ron Kikinis;Dagan Feng;Weidong Cai
2014 International Conference on Digital Image Computing: Techniques and Applications (DICTA)
Year: 2014 | Conference Paper |
Cited by: Papers (2)
In this work, we propose a Latent Semantic Association Retrieval(LSAR) method to break the bottleneck of the low-level feature based medical image retrieval. The method constructs the high-level semantic correlations among patients based on the low-level feature set extracted from the images. Specifically, a Pair-LDA model is firstly designed to refine the topic generation process of traditional L...Show More
Early diagnosis of Alzheimer's disease with deep learning
Siqi Liu;Sidong Liu;Weidong Cai;Sonia Pujol;Ron Kikinis;Dagan Feng
2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI)
Year: 2014 | Conference Paper |
Cited by: Papers (319)
The accurate diagnosis of Alzheimer's disease (AD) plays a significant role in patient care, especially at the early stage, because the consciousness of the severity and the progression risks allows the patients to take prevention measures before irreversible brain damages are shaped. Although many studies have applied machine learning methods for computer-aided-diagnosis (CAD) of AD recently, a b...Show More
Co-neighbor multi-view spectral embedding for medical content-based retrieval
Hangyu Che;Sidong Liu;Weidong Cai;Sonia Pujol;Ron Kikinis;Dagan Feng
2014 IEEE 11th International Symposium on Biomedical Imaging (ISBI)
Year: 2014 | Conference Paper |
Cited by: Papers (9)
Multimodal medical data from various information sources are often used to depict patients. We refer to each source as a `view'. Multi-view features could provide complementary information to each other; thus by fusing the multi-view features, we could greatly enhance the current medical content-based retrieval framework. In this paper, we propose a Co-neighbor Multi-view Spectral Embedding (CMSE)...Show More
Application of Tolerance Limits to the Characterization of Image Registration Performance
Andriy Fedorov;William M. Wells;Ron Kikinis;Clare M. Tempany;Mark G. Vangel
Deformable image registration is used increasingly in image-guided interventions and other applications. However, validation and characterization of registration performance remain areas that require further study. We propose an analysis methodology for deriving tolerance limits on the initial conditions for deformable registration that reliably lead to a successful registration. This approach res...Show More
Localized Sparse Code Gradient in Alzheimer's disease staging
Sidong Liu;Weidong Cai;Yang Song;Sonia Pujol;Ron Kikinis;Lingfeng Wen;David Dagan Feng
2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
Year: 2013 | Conference Paper |
Cited by: Papers (6)
The accurate diagnosis of Alzheimer's disease (AD) at different stages is essential to identify patients at high risk of dementia and plan prevention or treatment measures accordingly. In this study, we proposed a new AD staging method for the entire spectrum of AD including the AD, Mild Cognitive Impairment with and without AD conversions, and Cognitive Normal groups. Our method embedded the high...Show More
High-resolution electroencephalographic forward modeling in traumatic brain injury using the finite element method
S.Y. Matthew Goh;Andrei Irimia;Carinna M. Torgerson;Ron Kikinis;Paul M. Vespa;John D. Van Horn
2013 IEEE 10th International Symposium on Biomedical Imaging
Year: 2013 | Conference Paper |
Localization of electrical brain activity via electroencephalography (EEG) remains a challenging task in traumatic brain injury (TBI) patients, partly due to the complexity of structural brain changes resulting from neurological insult. When localizing EEG-recorded brain activity, the failure to account for pathology-related changes in tissue conductivities may cause forward model inaccuracies whi...Show More
Automatic airway analysis for genome-wide association studies in COPD
Raul San José Estépar;James C. Ross;Gordon L. Kindlmann;Alejandro Diaz;Yuka Okajima;Ron Kikinis;Carl-Fredrik Westin;Edwin K. Silverman;George G. Washko
2012 9th IEEE International Symposium on Biomedical Imaging (ISBI)
Year: 2012 | Conference Paper |
Cited by: Papers (4)
We present an image pipeline for airway phenotype extraction suitable for large-scale genetic and epidemiological studies including genome-wide association studies (GWAS) in Chronic Obstructive Pulmonary Disease (COPD). We use scale-space particles to densely sample intraparenchymal airway locations in a large cohort of high-resolution CT scans. The particle methodology is based on a constrained e...Show More
3D Slicer as a tool for interactive brain tumor segmentation
2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Year: 2011 | Conference Paper |
Cited by: Papers (41)
User interaction is required for reliable segmentation of brain tumors in clinical practice and in clinical research. By incorporating current research tools, 3D Slicer provides a set of interactive, easy to use tools that can be efficiently used for this purpose. One of the modules of 3D Slicer is an interactive editor tool, which contains a variety of interactive segmentation effects. Use of the...Show More
Ontological Labels for Automated Location of Left Ventricular Remodeling
Shane Steinert-Threlkeld;Siamak Ardekani;Jose L.V. Mejino;Landon T. Detwiler;James F. Brinkley;Michael Halle;Ron Kikinis;Raimond L. Winslow;Michael I. Miller;J. Tilak Ratnanather
2011 IEEE Fifth International Conference on Semantic Computing
Year: 2011 | Conference Paper |
In a previous study, Ardekani et. al. used the Large Deformation Diffeomorphic Metric Mapping (LDDMM) image registration algorithm to analyze the left ventricle of 25 human subjects at both end systole (ES) and end diastole (ED) phases of the cardiac cycle. Of these 25 subjects, 12 had nonischemic cardiomyopathy (NICM) and 13 had ischemic cardiomyopathy (ICM). An average template image at each of ...Show More
Real-Time Non-rigid Registration of Medical Images on a Cooperative Parallel Architecture
2009 IEEE International Conference on Bioinformatics and Biomedicine
Year: 2009 | Conference Paper |
Cited by: Papers (8)
Unacceptable execution time of Non-rigid registration (NRR) often presents a major obstacle to its routine clinical use. Parallel computing is an effective way to accelerate NRR. However, development of efficient parallel NRR codes is a very challenging task. One desirable approach is to map the existing sequential algorithm to the parallel architecture to gain speedup instead of designing a new p...Show More
Monitoring slowly evolving tumors
E. Konukoglu;W. M. Wells;S. Novellas;N. Ayache;R. Kikinis;P. M. Black;K. M. Pohl
2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro
Year: 2008 | Conference Paper |
Change detection is a critical task in the diagnosis of many slowly evolving pathologies. This paper describes an approach that semi-automatically performs this task using longitudinal medical images. We are specifically interested in meningiomas, which experts often find difficult to monitor as the tumor evolution can be obscured by image artifacts. We test the method on synthetic data with known...Show More
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