ISMRM Raw data format: A proposed standard for MRI raw datasets

Purpose This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format consisting of a flexible header and tagged frames of k‐space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB,...

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Published inMagnetic resonance in medicine Vol. 77; no. 1; pp. 411 - 421
Main Authors Inati, Souheil J., Naegele, Joseph D., Zwart, Nicholas R., Roopchansingh, Vinai, Lizak, Martin J., Hansen, David C., Liu, Chia‐Ying, Atkinson, David, Kellman, Peter, Kozerke, Sebastian, Xue, Hui, Campbell‐Washburn, Adrienne E., Sørensen, Thomas S., Hansen, Michael S.
Format Journal Article
LanguageEnglish
Published United States Wiley Subscription Services, Inc 01.01.2017
Subjects
Algorithms
C (programming language)
C plus plus
Converters
Data retrieval
Databases, Factual
Format
Image processing
Image Processing, Computer-Assisted - methods
Image reconstruction
Interfaces
Magnetic resonance imaging
Magnetic Resonance Imaging - methods
Matlab
NMR
Nuclear magnetic resonance
open source
Phantoms, Imaging
raw data format
Scanners
Signal-To-Noise Ratio
Software
Source code
magnetic resonance imaging
open source
image reconstruction
raw data format
Online AccessGet full text
ISSN0740-3194
1522-2594
1522-2594
DOI10.1002/mrm.26089

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Abstract Purpose This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format consisting of a flexible header and tagged frames of k‐space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python). Results Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research. Conclusion The proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community‐driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411–421, 2017. © 2016 Wiley Periodicals, Inc.
AbstractList Purpose This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format consisting of a flexible header and tagged frames of k‐space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python). Results Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research. Conclusion The proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community‐driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411–421, 2017. © 2016 Wiley Periodicals, Inc.
PurposeThis work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing.MethodsA file format consisting of a flexible header and tagged frames of k‐space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python).ResultsImages were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research.ConclusionThe proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community‐driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411–421, 2017. © 2016 Wiley Periodicals, Inc.
Purpose This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format consisting of a flexible header and tagged frames of k-space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python). Results Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research. Conclusion The proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community-driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411-421, 2017. © 2016 Wiley Periodicals, Inc.
This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. A file format consisting of a flexible header and tagged frames of k-space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python). Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research. The proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community-driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411-421, 2017. © 2016 Wiley Periodicals, Inc.
This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing.PURPOSEThis work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing.A file format consisting of a flexible header and tagged frames of k-space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python).METHODSA file format consisting of a flexible header and tagged frames of k-space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python).Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research.RESULTSImages were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research.The proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community-driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411-421, 2017. © 2016 Wiley Periodicals, Inc.CONCLUSIONThe proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community-driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411-421, 2017. © 2016 Wiley Periodicals, Inc.
Purpose This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format consisting of a flexible header and tagged frames of k-space data was designed. Application Programming Interfaces were implemented in C/C++, MATLAB, and Python. Converters for Bruker, General Electric, Philips, and Siemens proprietary file formats were implemented in C++. Raw data were collected using magnetic resonance imaging scanners from four vendors, converted to ISMRM Raw Data format, and reconstructed using software implemented in three programming languages (C++, MATLAB, Python). Results Images were obtained by reconstructing the raw data from all vendors. The source code, raw data, and images comprising this work are shared online, serving as an example of an image reconstruction project following a paradigm of reproducible research. Conclusion The proposed raw data format solves a practical problem for the magnetic resonance imaging community. It may serve as a foundation for reproducible research and collaborations. The ISMRM Raw Data format is a completely open and community-driven format, and the scientific community is invited (including commercial vendors) to participate either as users or developers. Magn Reson Med 77:411-421, 2017.
Author Sørensen, Thomas S.
Liu, Chia‐Ying
Kellman, Peter
Hansen, David C.
Inati, Souheil J.
Zwart, Nicholas R.
Roopchansingh, Vinai
Atkinson, David
Lizak, Martin J.
Xue, Hui
Hansen, Michael S.
Naegele, Joseph D.
Campbell‐Washburn, Adrienne E.
Kozerke, Sebastian
AuthorAffiliation 7 National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
8 Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
6 Centre for Medical Image Computing, University College London, United Kingdom
1 National Institute of Mental Health, National Institutes of Health, Bethesda, MD
5 Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD
9 Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
4 Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
2 Keller Center for Imaging Innovation, Barrow Neurological Institute, Phoenix, AZ
3 National Institute of Neurologic Disease and Stroke, National Institutes of Health, Bethesda, MD
AuthorAffiliation_xml – name: 2 Keller Center for Imaging Innovation, Barrow Neurological Institute, Phoenix, AZ
– name: 5 Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD
– name: 8 Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
– name: 7 National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
– name: 4 Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
– name: 9 Institute for Biomedical Engineering, University and ETH Zurich, Zurich, Switzerland
– name: 1 National Institute of Mental Health, National Institutes of Health, Bethesda, MD
– name: 3 National Institute of Neurologic Disease and Stroke, National Institutes of Health, Bethesda, MD
– name: 6 Centre for Medical Image Computing, University College London, United Kingdom
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  organization: National Institute of Mental Health, National Institutes of Health
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  surname: Naegele
  fullname: Naegele, Joseph D.
  organization: National Institute of Mental Health, National Institutes of Health
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  surname: Zwart
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  surname: Roopchansingh
  fullname: Roopchansingh, Vinai
  organization: National Institute of Mental Health, National Institutes of Health
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  givenname: Martin J.
  surname: Lizak
  fullname: Lizak, Martin J.
  organization: National Institute of Neurologic Disease and Stroke, National Institutes of Health
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  surname: Hansen
  fullname: Hansen, David C.
  organization: Aarhus University Hospital
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  givenname: Chia‐Ying
  surname: Liu
  fullname: Liu, Chia‐Ying
  organization: Clinical Center, National Institutes of Health
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  givenname: David
  surname: Atkinson
  fullname: Atkinson, David
  organization: Centre for Medical Image Computing, University College
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  fullname: Kellman, Peter
  organization: National Heart, Lung, and Blood Institute, National Institutes of Health
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  givenname: Sebastian
  surname: Kozerke
  fullname: Kozerke, Sebastian
  organization: University and ETH Zurich
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  givenname: Hui
  surname: Xue
  fullname: Xue, Hui
  organization: National Heart, Lung, and Blood Institute, National Institutes of Health
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  surname: Campbell‐Washburn
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  givenname: Michael S.
  surname: Hansen
  fullname: Hansen, Michael S.
  email: michael.hansen@nih.gov
  organization: National Heart, Lung, and Blood Institute, National Institutes of Health
BackLink https://www.ncbi.nlm.nih.gov/pubmed/26822475$$D View this record in MEDLINE/PubMed
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Copyright 2016 Wiley Periodicals, Inc.
2017 International Society for Magnetic Resonance in Medicine
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Keywords magnetic resonance imaging
open source
image reconstruction
raw data format
Language English
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Snippet Purpose This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format...
This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. A file format consisting of a flexible...
Purpose This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing. Methods A file format...
PurposeThis work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing.MethodsA file format consisting...
This work proposes the ISMRM Raw Data format as a common MR raw data format, which promotes algorithm and data sharing.PURPOSEThis work proposes the ISMRM Raw...
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StartPage 411
SubjectTerms Algorithms
C (programming language)
C plus plus
Converters
Data retrieval
Databases, Factual
Format
Image processing
Image Processing, Computer-Assisted - methods
Image reconstruction
Interfaces
Magnetic resonance imaging
Magnetic Resonance Imaging - methods
Matlab
NMR
Nuclear magnetic resonance
open source
Phantoms, Imaging
raw data format
Scanners
Signal-To-Noise Ratio
Software
Source code
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Title ISMRM Raw data format: A proposed standard for MRI raw datasets
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