Quantitative susceptibility mapping of articular cartilage: ex vivo findings at multiple orientations and following different degradation treatments

Nykänen, Olli,Department of Applied Physics, University of Eastern Finland; Rieppo, Lassi,Research Unit of Medical Imaging, Physics and Technology, University of Oulu; Medical Research Center Oulu, University of Oulu and Oulu University Hospital; Töyräs, Juha,Department of Applied Physics, University of Eastern Finland; Diagnostic Imaging Center, Kuopio University Hospital; Kolehmainen, Ville,Department of Applied Physics, University of Eastern Finland; Saarakkala, Simo,Research Unit of Medical Imaging, Physics and Technology, University of Oulu; Medical Research Center Oulu, University of Oulu and Oulu University Hospital;Department of Diagnostic Radiology, Oulu University Hospital; Shmueli, Karin,Department of Medical Physics and Biomedical Engineering, University College London (UCL); Nissi, Mikko Johannes,Department of Applied Physics, University of Eastern Finland

Date

2018-04-19

Author(s)

Nykänen, Olli,Department of Applied Physics, University of Eastern Finland

Rieppo, Lassi,Research Unit of Medical Imaging, Physics and Technology, University of Oulu; Medical Research Center Oulu, University of Oulu and Oulu University Hospital

Töyräs, Juha,Department of Applied Physics, University of Eastern Finland; Diagnostic Imaging Center, Kuopio University Hospital

Kolehmainen, Ville,Department of Applied Physics, University of Eastern Finland

Saarakkala, Simo,Research Unit of Medical Imaging, Physics and Technology, University of Oulu; Medical Research Center Oulu, University of Oulu and Oulu University Hospital;Department of Diagnostic Radiology, Oulu University Hospital

Shmueli, Karin,Department of Medical Physics and Biomedical Engineering, University College London (UCL)

Nissi, Mikko Johannes,Department of Applied Physics, University of Eastern Finland

Unique identifier

10.5281/zenodo.823917

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Citation

Nykänen, Olli,Department of Applied Physics, University of Eastern Finland. Rieppo, Lassi,Research Unit of Medical Imaging, Physics and Technology, University of Oulu; Medical Research Center Oulu, University of Oulu and Oulu University Hospital. Töyräs, Juha,Department of Applied Physics, University of Eastern Finland; Diagnostic Imaging Center, Kuopio University Hospital. Kolehmainen, Ville,Department of Applied Physics, University of Eastern Finland. Saarakkala, Simo,Research Unit of Medical Imaging, Physics and Technology, University of Oulu; Medical Research Center Oulu, University of Oulu and Oulu University Hospital;Department of Diagnostic Radiology, Oulu University Hospital. Shmueli, Karin,Department of Medical Physics and Biomedical Engineering, University College London (UCL). Nissi, Mikko Johannes,Department of Applied Physics, University of Eastern Finland. , Quantitative susceptibility mapping of articular cartilage: ex vivo findings at multiple orientations and following different degradation treatments, 2018, 10.5281/zenodo.823917.

Abstract

This dataset contains all the raw source data and MATLAB analysis functions that comprise the study: Quantitative susceptibility mapping of articular cartilage: Ex vivo findings at multiple orientations and following different degradation treatments Magnetic Resonance in Medicine | DOI: 10.1002/mrm.27216 Nykänen Olli(1*), Rieppo Lassi(2,3), Töyräs Juha(1,4), Kolehmainen Ville(1), Saarakkala Simo(2,3,5), Shmueli Karin(6) and Nissi Mikko Johannes(1) (1) Department of Applied Physics, University of Eastern Finland, POB 1627, FI-70211 Kuopio, Finland (2) Research Unit of Medical Imaging, Physics and Technology, University of Oulu, POB 5000, FI-90014 Oulu, Finland (3) Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland (4) Diagnostic Imaging Center, Kuopio University Hospital, Kuopio, Finland (5) Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland (6) Department of Medical Physics & Biomedical Engineering, University College London(UCL), London, United Kingdom *Corresponding author: Olli Nykänen Department of Applied Physics, University of Eastern Finland POB 1627 FI-70211, Kuopio, Finland olli.nykanen@uef.fi +358-50-5556357 Keywords: cartilage, collagen matrix, quantitative susceptibility mapping, MRI, osteoarthritis Included folders and files are: - article_figures: all figures published in the manuscript - data: all MRI, histological, and PLM data used in this article - matlab_functions: matlab functions used in data analysis with subfolders: - aedes_plugins: plugins for aedes (http://aedes.uef.fi) for calculation of QS- and T2* maps - fitting_functions: functions for fitting relaxation times or TKD-method for QSM, used by the functions in above folder - miscellaneous_functions: small helper functions for a number of small tasks utilized by the other scripts and functions - ReadMe.txt: this file Notes for setting up Aedes correctly for this dataset: Run Aedes -> Tools -> Edit VNMR Defaults: - Return: FT + K-space - DC: off - Zeropadding: off - Sorting & fastread: on - Precision: single - Read_fcn: readvnmr - Orient: no See more info in separate readme files included in each folder. (Olli Nykänen, Apr 17, 2018)