Epiphyseal Cartilage Vascular Architecture at the Distal Humeral Osteochondritis Dissecans Predilection Site in Juvenile Pigs

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

Epiphyseal Cartilage Vascular Architecture at the Distal Humeral Osteochondritis Dissecans Predilection Site in Juvenile Pigs

Journal of Orthopaedic Research | DOI:  https://doi.org/10.1002/jor.25732

Ferenc Tóth, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota
Mikko J. Nissi, Department of Technical Physics, University of Eastern Finland  
Alexandra R. Armstrong, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota
Erick O. Buko, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota; Center for Magnetic Resonance Research, University of Minnesota  
Casey P. Johnson, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota; Center for Magnetic Resonance Research, University of Minnesota

Corresponding author (whole study):
Ferenc Tóth
The University of Minnesota
1365 Gortner Ave., St. Paul, MN 55108
Tel.: [phone]
Fax.: [phone]
email: [e-mail]

Corresponding author (data set):
Mikko J. Nissi
Department of Technical Physics
University of Eastern Finland
POB 1627, FI-70211, Kuopio, Finland
[phone]
[e-mail]

Keywords: OCD, MRI, humerus, vasculature, pathogenesis, quantitative susceptibility mapping

Included folders and files are:
3-D_visualizations
   - 3D_models: 3-D models of the specimens (Rhinoceros .3dm files)
   - Raw_Animation_files: .png format animation image exports
   - Ready_Animation_videos: .mp4 / .mov supplementary animation movie clips and Blender video edition files
   - Visualizations_w_different_lambda: visualizations of the resulting 3-D models with different MEDI L1 lambda values

Figure_parts
   - Sub-parts of various manuscript figures

Histo_images
   - Collections of histological images of the specimens in a powerpoint file

raw_MRI_data
   - RAW Varian/Agilent MRI data for all specimens
   - Pre-processed data for each specimen:
       - Segmentation masks (epiphyseal cartilage, SOC) and ROI files (for Aedes)
       - QSM data processed as described in the manuscript, using the mask provided (VSHARP + MEDI), using MEDI-toolbox
       - Binary image created from the QSM data via highest-correlating binary threshold
       - 3-D .stl files for
           - AECC (articular-epiphyseal cartilage-complex)
           - SOC (secondary ossification center)
           - vasculature (from the binary-threshold-QSM data)

matlab_functions
   - Collection of matlab functions the analysis script requires

data_processing_script.m:  Matlab script for producing data visualizations for most of the manuscript figures  
scan_protocol_by_sample.xls:  Excel file listing the primary scan parameters for each specimen
README.txt:  this file

(Mikko Nissi, Nov 17, 2023)