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Early steps of an Ontology for Magnetic Resonance Imaging: MRIO

Lucas M. Serra, Michael G. Dwyer, William D. Duncan, Alexander D. Diehl
2019 International Conference on Biomedical Ontology  
The Magnetic Resonance Imaging Ontology (MRIO) is an application ontology that represents numerous entities in the domain of magnetic resonance imaging (MRI) including MRI analysis and MRI sequences.  ...  The current work represents the beginnings of a full-fledged imaging ontology and automated analysis pipeline, which we plan to further develop.  ...  Introduction The Fundamentals of Magnetic Resonance Imaging Magnetic resonance imaging (MRI) is a mainstay of modern medicine that has rapidly integrated itself into a myriad of diagnostic algorithms and  ... 
dblp:conf/icbo/SerraDDD19 fatcat:ur6scesbvrhk7pqqmxwy4l7eca

Ontology for fMRI as a Biomedical Informatics Method

Toshiharu NAKAI, Epifanio BAGARINAO, Yoshio TANAKA, Kayako MATSUO, Daniel RACOCEANU
2008 Magnetic Resonance in Medical Sciences  
Neuroimaging modalities, such as functional magnetic resonance imaging (fMRI), magnetoencephalography (MEG), electroencephalography (EEG), and near infrared spectroscopy (NIRS), share similar application  ...  purposes, imaging protocol, analyzing methods, and data structure; semantic gaps that remain among the modalities will be bridged as ontology develops.  ...  This should be represented in the ontology of each type of functional magnetic resonance imaging (fMRI) usage.  ... 
doi:10.2463/mrms.7.141 pmid:18827457 fatcat:z4qijfvlqzfojllunm47furzkq

Towards the Creation of the Cardiovascular Magnetic Resonance Quality Assessment Ontology (CMR-QA)

Ernesto Jiménez-Ruiz, Valentina Carapella, Elena Lukaschuk, Nay Aung, Kenneth Fung, José Miguel Paiva, Mihir Sanghvi, Stefan Neubauer, Steffen E. Petersen, Ian Horrocks, Stefan K. Piechnik
2016 Workshop on Semantic Web Applications and Tools for Life Sciences  
SEP, SN and SP acknowledge the British Heart Foundation (BHF) for funding the manual analysis to create a cardiovascular magnetic resonance imaging reference standard for the UK Biobank imaging resource  ...  Magnetic Resonance Quality Assessment).  ...  In particular, a number of Cardiac Magnetic Resonance Imaging (CMR) sequences are employed to evaluate cardiac function: cine-MRI, tag-MRI, T1-mapping and blood flow imaging [3].  ... 
dblp:conf/swat4ls/Jimenez-RuizCLA16 fatcat:6chysyaqfbdetkbutbmhthgqee

BCIO: Brain Computer Interface Ontology

Muhammad Siddiq, Sheikh Kashif Raffat, Farhan Shafiq
2012 International Journal of Computer Applications  
Nowadays ontology for representing knowledge is becoming more popular in researchers to describe, share and integrate their scientific data.  ...  If the information, algorithms and results are stored in the form of ontological content, it will provide the efficient way to use and reuse the data related to BCI and will help to BCI researchers for  ...  RELATED WORK Magnetic Resonance Images (MRI) is using in neuro-surgery but the functional Magnetic Resonance Images (fMRI) have been used to control the robot in real time trough the brain signals [4]  ... 
doi:10.5120/5511-7502 fatcat:ipn2xuoz2vcnbowqklh4h2muhi

Some critical remarks on the epistemology of functional magnetic resonance imaging (fMRI)

Alexandre Métraux
2020 Science & Philosophy  
The article examines epistemological and ontological underpinnings of reasearch performed by means of magnetic resonance imaging (MRI) and functional magnetic resonance imaging (fMRI).  ...  Thus, when the objects of examination (human and animal brains, e.g.) are subjected to 2 or more Tesla in fMRI, a strength of magnetic field never occuring in earthly nature, technical means literally  ...  Therefore, he is often seen as a father of functional magnetic resonance imaging (Sandone et al., 2014) .  ... 
doi:10.23756/sp.v8i1.493 doaj:8bdd683b18244b539a05c5ab23caef8e fatcat:7ea6lf24o5gevd35zx7klggyza

Towards the Semantic Enrichment of Free-Text Annotation of Image Quality Assessment for UK Biobank Cardiac Cine MRI Scans [chapter]

Valentina Carapella, Ernesto Jiménez-Ruiz, Elena Lukaschuk, Nay Aung, Kenneth Fung, Jose Paiva, Mihir Sanghvi, Stefan Neubauer, Steffen Petersen, Ian Horrocks, Stefan Piechnik
2016 Lecture Notes in Computer Science  
This semantic layer will be a powerful tool to automatically infer or validate quality scores for clinical images and efficiently query image databases based on quality information extracted from the annotations  ...  In this paper we motivate the need for this semantic layer, present an initial version of our ontology as well as preliminary results.  ...  Acknowledgements SEP, SN and SP acknowledge the British Heart Foundation (BHF) for funding the manual analysis to create a cardiovascular magnetic resonance imaging reference standard for the UK Biobank  ... 
doi:10.1007/978-3-319-46976-8_25 fatcat:cyecs7wdp5bk3natqqk344p4tu

HealthAgents: distributed multi-agent brain tumor diagnosis and prognosis

Horacio González-Vélez, Mariola Mier, Margarida Julià-Sapé, Theodoros N. Arvanitis, Juan M. García-Gómez, Montserrat Robles, Paul H. Lewis, Srinandan Dasmahapatra, David Dupplaw, Andrew Peet, Carles Arús, Bernardo Celda (+2 others)
2007 Applied intelligence (Boston)  
Spinning Nuclear Magnetic Resonance (HR-MAS) and DNA micro-array data.  ...  The HealthAgents system is implementing novel pattern recognition discrimination methods, in order to analyse in vivo Magnetic Resonance Spectroscopy (MRS) and ex vivo/in vitro High Resolution Magic Angle  ...  produced Magnetic Resonance Spectroscopic Imaging (MRSI) [26, 45] . 2.  ... 
doi:10.1007/s10489-007-0085-8 fatcat:kefcix5l7zcy7kahfujyjxeq4m

Sharing object models for multi-modality medical image simulation: A semantic approach

Germain Forestier, Adrien Marion, Hugues Benoit-Cattin, Patrick Clarysse, Denis Friboulet, Tristan Glatard, Patrick Hugonnard, Carole Lartizien, Herve Liebgott, Joachim Tabary, Bernard Gibaud
2011 2011 24th International Symposium on Computer-Based Medical Systems (CBMS)  
In particular, we developed an ontology that contains the relevant concepts and relations of the domain of object models for image simulation.  ...  We address this issue by explicitly describing object models using a semantic approach.  ...  Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET) and Ultrasound imaging (US).  ... 
doi:10.1109/cbms.2011.5999167 dblp:conf/cbms/ForestierMBCFGHLLTG11 fatcat:gdpcnfg3djbfzfasbqsw3ywf64

OntoVIP: An ontology for the annotation of object models used for medical image simulation

Bernard Gibaud, Germain Forestier, Hugues Benoit-Cattin, Frédéric Cervenansky, Patrick Clarysse, Denis Friboulet, Alban Gaignard, Patrick Hugonnard, Carole Lartizien, Hervé Liebgott, Johan Montagnat, Joachim Tabary (+1 others)
2014 Journal of Biomedical Informatics  
The goal is to create an application ontology that can be used to annotate the models in a repository integrated in the Virtual Imaging Platform (VIP), to facilitate their sharing and reuse.  ...  This paper describes the creation of a comprehensive conceptualization of object models used in medical image simulation, suitable for major imaging modalities and simulators.  ...  Appendix A This Appendix contains an example of vSPARQL [16] query designed to create a module in OntoVIP. We use as illustration the anatomical objects extracted from the FMA.  ... 
doi:10.1016/j.jbi.2014.07.008 pmid:25038553 pmcid:PMC5943577 fatcat:33kxzx22ozgw5airtyltyfmlyi

The clinical perspective of large scale projects: A case study of multiparametric MR imaging of pediatric brain tumors

L. Astrakas, Song Ye, M. Zarifi, F. Makedon, A. Tzika
2006 Oncology Reports  
For example, a pediatric brain tumor database of magnetic resonance imaging data, including conventional MRI imaging, hemodynamic MRI, diffusion weighted MRI and MR spectroscopic imaging, combined with  ...  Such a system will greatly enhance the utility of different data sets to a wide array of scientists.  ...  DAML+OIL (16, 17) , a language with which to create ontologies and mark up information, is used in layer 3 to define a negotiation ontology.  ... 
doi:10.3892/or.15.4.1065 fatcat:3qsmzyt4nnbhzi3jl6nlopt44q

Ontology-Based Classification of Radiological Procedures for Consistent Sharing in Clinical Data Warehouses

Pierre Lemordant, Bernard Gibaud, Cyril Garde, Sébastien Delarche, Didier Goudet, Marc Cuggia
2020 International Conference on Biomedical Ontology  
Then, we developed a proof of concept of a radiological procedures data classifier that exploits the richness of RadLex ontology and the ontological reasoning and we assessed it using medical imaging data  ...  This work concerns the management of medical imaging data in CDWs. It proposes a data-driven approach for classifying radiological procedures using an ontology-based approach.  ...  Figure 1 shows a few columns of the Playbook, in this example the value "RID13060" in the set of values of column RIDS refers to the MODALITY column and represents the "magnetic resonance imaging" class  ... 
dblp:conf/icbo/LemordantGGDGC20 fatcat:lg53sjzkqrffjofijw7kadghxu

Extending the Foundational Model of Anatomy with Automatically Acquired Spatial Relations

Manuel Möller, Christian Folz, Michael Sintek, Sascha Seifert, Pinar Wennerberg
2009 Nature Precedings  
Our ultimate goals are to use spatial knowledge from the FMA (1) to improve automatic parsing algorithms for 3D volume data sets generated by Computed Tomography and Magnetic Resonance Imaging and (2)  ...  Formal ontologies have made significant impact in bioscience over the last ten years.  ...  (CT) or Magnetic Resonance Imaging (MRI).  ... 
doi:10.1038/npre.2009.3471.1 fatcat:zu23w3lbtrgg3h34z2z5xiz4nq

Non-manifold Mesh Extraction from Time-varying Segmented Volumes used for Modeling a Human Heart [article]

Martin Bertram, Gerd Reis, Rolf H. Van Lengen, Sascha Köhn, Hans Hagen
2005 EUROVIS 2005: Eurographics / IEEE VGTC Symposium on Visualization  
Finally, the mesh geometry is relaxed in a constrained fairing process. We use our algorithm to construct a heart model from segmented time-varying magnetic resonance images.  ...  Information concerning the heart ontology is used to merge certain structures to functional units.  ...  Figure 1 : 1 Figure 1: Magnetic resonance image (left) and segmented image (right).  ... 
doi:10.2312/vissym/eurovis05/199-206 fatcat:iznnl3rq55g4fofx5qvsstrgmq

Open Biomedical Ontologies Applied to Prostate Cancer

James Overton, James Overton, Cesare Romagnoli, Rethy Chhem
2009 Nature Precedings  
We then briefly describe the database-backed website we have created around the relevant OBO ontologies, and provide excerpts of reports from radiology, surgery, and pathology which we have hyperlinked  ...  to the ontology terms.  ...  annotations for medical images. • Medical Image Magnetic Resonance Imaging (MRI) Image • T1 Weighted MRI Image MRI Image without Contrast MRI Image with Contrast • Static Contrast MRI Image • Dynamic  ... 
doi:10.1038/npre.2009.3589 fatcat:mqgpyjlctjagzfdmj4jdcfmfpu

Open Biomedical Ontologies Applied to Prostate Cancer

James Overton, James Overton, Cesare Romagnoli, Rethy Chhem
2009 Nature Precedings  
We then briefly describe the database-backed website we have created around the relevant OBO ontologies, and provide excerpts of reports from radiology, surgery, and pathology which we have hyperlinked  ...  to the ontology terms.  ...  annotations for medical images. • Medical Image Magnetic Resonance Imaging (MRI) Image • T1 Weighted MRI Image MRI Image without Contrast MRI Image with Contrast • Static Contrast MRI Image • Dynamic  ... 
doi:10.1038/npre.2009.3570 fatcat:db4i6hi2orfw3cnznvbwvq2m7y
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