Orientation anisotropy of quantitative MRI relaxation parameters in ordered tissue

This dataset contains all the raw source data and MATLAB analysis functions that comprise the study:

Orientation anisotropy of quantitative MRI relaxation parameters in ordered tissue

Scientific Reports | DOI:10.1038/s41598-017-10053-2

Hänninen Nina(1,2), Rautiainen Jari(1), Rieppo Lassi(2,3), Saarakkala Simo(2,3,4) 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. Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland

*Corresponding author:
Mikko J. Nissi
Department of Applied Physics,
University of Eastern Finland
POB 1627
FI-70211, Kuopio, Finland
mikko.nissi@uef.fi
+358-50-5955517

Keywords: relaxation anisotropy, orientation, cartilage, MRI, quantitative

Included folders and files are:

• article_figures: all figures published in the manuscript
• data: MRI measurement data and pre-processed PLM measurement data
• matlab_functions: matlab functions used in data analysis with subfolders:
  • aedes_plugins: plugins for aedes (http://aedes.uef.fi) for calculation of relaxation time maps
  • fitting_functions: miscellaneous functions for fitting relaxation times etc, 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
• plm_new_data: histological data measured by quantitative polarized light microscopy.
• sample_holder_3D_model: .stl files for the 3-D printable sample-holder which allows rotation of the specimen
• carbon_data_collector_ROT_for_publication.m: master data collection and analysis script that reads in all the data and performs all the calculations to produce the images of the study. This function relies on all the matlab-functions in the subfolder (i.e. the subfolders need to be indexable by matlab) and Aedes analysis software (http://aedes.uef.fi) and matlab R2013b or later.
• 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: readfid (old)
• Orient: no

See more info in separate readme files included in each folder.

(Mikko Nissi, Aug 15, 2017)