Literature DB >> 29092948

dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM.

Christian Herz1,2, Jean-Christophe Fillion-Robin3, Michael Onken4, Jörg Riesmeier5, Andras Lasso6, Csaba Pinter6, Gabor Fichtinger6, Steve Pieper7, David Clunie8, Ron Kikinis1,2,9,10, Andriy Fedorov11,2.   

Abstract

Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology. dcmqi (DICOM for Quantitative Imaging) is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation. dcmqi source code is distributed under BSD-style license. It is freely available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. Installation and usage instructions are provided in the GitHub repository at https://github.com/qiicr/dcmqi Cancer Res; 77(21); e87-90. ©2017 AACR. ©2017 American Association for Cancer Research.

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Year:  2017        PMID: 29092948      PMCID: PMC5675033          DOI: 10.1158/0008-5472.CAN-17-0336

Source DB:  PubMed          Journal:  Cancer Res        ISSN: 0008-5472            Impact factor:   12.701


  8 in total

1.  3D Slicer as an image computing platform for the Quantitative Imaging Network.

Authors:  Andriy Fedorov; Reinhard Beichel; Jayashree Kalpathy-Cramer; Julien Finet; Jean-Christophe Fillion-Robin; Sonia Pujol; Christian Bauer; Dominique Jennings; Fiona Fennessy; Milan Sonka; John Buatti; Stephen Aylward; James V Miller; Steve Pieper; Ron Kikinis
Journal:  Magn Reson Imaging       Date:  2012-07-06       Impact factor: 2.546

2.  User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.

Authors:  Paul A Yushkevich; Joseph Piven; Heather Cody Hazlett; Rachel Gimpel Smith; Sean Ho; James C Gee; Guido Gerig
Journal:  Neuroimage       Date:  2006-03-20       Impact factor: 6.556

Review 3.  Understanding and using DICOM, the data interchange standard for biomedical imaging.

Authors:  W D Bidgood; S C Horii; F W Prior; D E Van Syckle
Journal:  J Am Med Inform Assoc       Date:  1997 May-Jun       Impact factor: 4.497

4.  Relationship between apparent diffusion coefficients at 3.0-T MR imaging and Gleason grade in peripheral zone prostate cancer.

Authors:  Thomas Hambrock; Diederik M Somford; Henkjan J Huisman; Inge M van Oort; J Alfred Witjes; Christina A Hulsbergen-van de Kaa; Thomas Scheenen; Jelle O Barentsz
Journal:  Radiology       Date:  2011-05       Impact factor: 11.105

Review 5.  Radiomics: extracting more information from medical images using advanced feature analysis.

Authors:  Philippe Lambin; Emmanuel Rios-Velazquez; Ralph Leijenaar; Sara Carvalho; Ruud G P M van Stiphout; Patrick Granton; Catharina M L Zegers; Robert Gillies; Ronald Boellard; André Dekker; Hugo J W L Aerts
Journal:  Eur J Cancer       Date:  2012-01-16       Impact factor: 9.162

6.  Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach.

Authors:  Hugo J W L Aerts; Emmanuel Rios Velazquez; Ralph T H Leijenaar; Chintan Parmar; Patrick Grossmann; Sara Carvalho; Sara Cavalho; Johan Bussink; René Monshouwer; Benjamin Haibe-Kains; Derek Rietveld; Frank Hoebers; Michelle M Rietbergen; C René Leemans; Andre Dekker; John Quackenbush; Robert J Gillies; Philippe Lambin
Journal:  Nat Commun       Date:  2014-06-03       Impact factor: 14.919

7.  DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research.

Authors:  Andriy Fedorov; David Clunie; Ethan Ulrich; Christian Bauer; Andreas Wahle; Bartley Brown; Michael Onken; Jörg Riesmeier; Steve Pieper; Ron Kikinis; John Buatti; Reinhard R Beichel
Journal:  PeerJ       Date:  2016-05-24       Impact factor: 2.984

8.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

  8 in total
  10 in total

1.  SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality.

Authors:  Csaba Pinter; Andras Lasso; Saleh Choueib; Mark Asselin; Jean-Christophe Fillion-Robin; Jean-Baptiste Vimort; Ken Martin; Matthew A Jolley; Gabor Fichtinger
Journal:  IEEE Trans Med Robot Bionics       Date:  2020-03-26

2.  The Cancer Imaging Phenomics Toolkit (CaPTk): Technical Overview.

Authors:  Sarthak Pati; Ashish Singh; Saima Rathore; Aimilia Gastounioti; Mark Bergman; Phuc Ngo; Sung Min Ha; Dimitrios Bounias; James Minock; Grayson Murphy; Hongming Li; Amit Bhattarai; Adam Wolf; Patmaa Sridaran; Ratheesh Kalarot; Hamed Akbari; Aristeidis Sotiras; Siddhesh P Thakur; Ragini Verma; Russell T Shinohara; Paul Yushkevich; Yong Fan; Despina Kontos; Christos Davatzikos; Spyridon Bakas
Journal:  Brainlesion       Date:  2020-05-19

3.  DeepNeuro: an open-source deep learning toolbox for neuroimaging.

Authors:  Andrew Beers; James Brown; Ken Chang; Katharina Hoebel; Jay Patel; K Ina Ly; Sara M Tolaney; Priscilla Brastianos; Bruce Rosen; Elizabeth R Gerstner; Jayashree Kalpathy-Cramer
Journal:  Neuroinformatics       Date:  2021-01

4.  Toward uniform implementation of parametric map Digital Imaging and Communication in Medicine standard in multisite quantitative diffusion imaging studies.

Authors:  Dariya Malyarenko; Andriy Fedorov; Laura Bell; Melissa Prah; Stefanie Hectors; Lori Arlinghaus; Mark Muzi; Meiyappan Solaiyappan; Michael Jacobs; Maggie Fung; Amita Shukla-Dave; Kevin McManus; Michael Boss; Bachir Taouli; Thomas E Yankeelov; Christopher Chad Quarles; Kathleen Schmainda; Thomas L Chenevert; David C Newitt
Journal:  J Med Imaging (Bellingham)       Date:  2017-10-30

5.  An annotated test-retest collection of prostate multiparametric MRI.

Authors:  Andriy Fedorov; Michael Schwier; David Clunie; Christian Herz; Steve Pieper; Ron Kikinis; Clare Tempany; Fiona Fennessy
Journal:  Sci Data       Date:  2018-12-04       Impact factor: 6.444

6.  ePAD: An Image Annotation and Analysis Platform for Quantitative Imaging.

Authors:  Daniel L Rubin; Mete Ugur Akdogan; Cavit Altindag; Emel Alkim
Journal:  Tomography       Date:  2019-03

7.  Radiomics Diagnostic Tool Based on Deep Learning for Colposcopy Image Classification.

Authors:  Yuliana Jiménez Gaona; Darwin Castillo Malla; Bernardo Vega Crespo; María José Vicuña; Vivian Alejandra Neira; Santiago Dávila; Veronique Verhoeven
Journal:  Diagnostics (Basel)       Date:  2022-07-12

8.  Integrating Biological and Radiological Data in a Structured Repository: a Data Model Applied to the COSMOS Case Study.

Authors:  Noemi Garau; Alessandro Orro; Paul Summers; Lorenza De Maria; Raffaella Bertolotti; Danny Bassis; Marta Minotti; Elvio De Fiori; Guido Baroni; Chiara Paganelli; Cristiano Rampinelli
Journal:  J Digit Imaging       Date:  2022-03-16       Impact factor: 4.903

9.  Quantitative Imaging Informatics for Cancer Research.

Authors:  Andrey Fedorov; Reinhard Beichel; Jayashree Kalpathy-Cramer; David Clunie; Michael Onken; Jörg Riesmeier; Christian Herz; Christian Bauer; Andrew Beers; Jean-Christophe Fillion-Robin; Andras Lasso; Csaba Pinter; Steve Pieper; Marco Nolden; Klaus Maier-Hein; Markus D Herrmann; Joel Saltz; Fred Prior; Fiona Fennessy; John Buatti; Ron Kikinis
Journal:  JCO Clin Cancer Inform       Date:  2020-05

10.  DICOM re-encoding of volumetrically annotated Lung Imaging Database Consortium (LIDC) nodules.

Authors:  Andrey Fedorov; Matthew Hancock; David Clunie; Mathias Brochhausen; Jonathan Bona; Justin Kirby; John Freymann; Steve Pieper; Hugo J W L Aerts; Ron Kikinis; Fred Prior
Journal:  Med Phys       Date:  2020-09-06       Impact factor: 4.071

  10 in total

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