Advanced toolbox for design and analysis of radiofrequency (RF) pulses, and processing of magnetic resonance spectroscopy data.
Jamie Near1,2,3, Robin Simpson4, Peter Jezzard5, Philip Cowen6, Gabriel Devenyi1, Philip Ehses7,8,9, Martyn Klassen10,11, Richard Edden12,13, Ashley Harris14,15,16,17, Kimberly Chan12,13,18, Mark Mikkelsen12, Chathura Kumaragamage1,2, Jay Hennessy1,2, Elvisha Dhamala19, Franck Lamberton20, and Esin Ozturk21.
The FID Appliance (FID-A) is an open-source software package for simulation of MRS experiments, design and analysis of radiofrequency (RF) pulses, and processing of MRS data. The FID-A software package consists of four separate toolboxes:
- the Simulation Toolbox for simulation of in vivo MRS experiments;
- the RF-pulse Toolbox, for designing and simulating radiofrequency pulse waveforms;
- the Input-output Toolbox, for reading and writing data between MATLAB and other useful data formats;
- the Processing toolbox, for processing of in vivo MRS data.
In addition to the toolboxes listed above, FID-A also comes with a library of Example Run Scripts, which provide examples of useful “pipelines” for NMR simulation and data processing. The example run scripts each make use of combinations of the various functions within the FID-A toolboxes. A library of Example Data, consisting of actual in vivo and in vitro MRS data in a few different vendor formats, is also provided with the FID-A toolkit, and can be used to test the functionality of some of the Example Run Scripts. Finally, although the FID-A toolbox is primarily MATLAB command-line based, a few graphical user interfaces are also provided to assist with processing tasks in which visual feedback is required, such as manual phasing of spectra, and visual alignment of spectra or sub-spectra prior to subtraction.
1Brain Imaging Centre, Douglas Mental Health University Institute, Montreal, Canada.
2Department of Biomedical Engineering, McGill University, Montreal, Canada.
3Department of Psychiatry, McGill University, Montreal, Canada.
4Department of Radiology, Medical Physics, Freiburg University, Freiburg, Germany.
5FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
6 Department of Psychiatry, Oxford University, Oxford OX3 7JX, United Kingdom.
7Department for Biomedical Magnetic Resonance, University of Tübingen, Tübingen, Germany.
8High‐Field MR Center, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
9German Center for Neurodegenerative Diseases (DZNE)Bonn, Germany.
10Centre for Functional and Metabolic Mapping, Robarts Research Institute, London, Ontario, Canada.
11Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada.
12Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
13F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, Maryland, USA.
14Department of Radiology, University of Calgary, Calgary, AB, Canada.
15Child and Adolescent Imaging Research (CAIR) Program, Alberta.
16Children’s Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
17Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
18Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
19School of Physical and Occupational Therapy, McGill University, Montreal, Canada.
20CERMEP, Imagerie du vivant, Bron 69677, France.
21Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey.