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

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)