APILab

Codes Available

This package provides the main components of the pulmonary MRI and CT biomarker framework, including:

The software GUI (need Visual C++ Redistributable Packages for Visual Studio 2013 to run). The source code and the .exe GUI-based 3D visualizer are not provided because of copyright issues. However, readers who are interested in the visuaizer can contact Dr. Aaron Fenster at: afenster@robarts.ca

Three representative biomarker modules (the remainder will be added soon):
1. Whole lung and lobar noble gas MRI ventillation measurements
  
  Guo, Fumin, et al. "Globally optimal co-segmentation of three-dimensional pulmonary ¹H and hyperpolarized ³He MRI with spatial consistence prior." Medical image analysis 23.1 (2015): 43-55.
  
  Guo, Fumin, et al. "Thoracic CT-MRI coregistration for regional pulmonary structure-function measurements of obstructive lung disease." Medical physics 44.5 (2017): 1718-1733.
2. Multi-volume UTE MRI dynamic proton density maps
  
  Sheikh, Khadija, et al. "Ultrashort echo time MRI biomarkers of asthma." Journal of Magnetic Resonance Imaging 45.4 (2017): 1204-1215.
3. Inspiration and expiration CT (MRI) parametric response maps
  
  Capaldi, Dante PI, et al. "Pulmonary imaging biomarkers of gas trapping and emphysema in COPD: ³He MR imaging and CT parametric response maps." Radiology 279.2 (2016): 597-608.
4. Fourier decomposition of free breathing ¹H MRI ventilation measurements
5. ¹H MRI specific ventilation measurements (not provided as this work is protected)
  
  Capaldi, Dante PI, et al. "Free-Breathing Pulmonary MR Imaging to Quantify Regional Ventilation." Radiology 287.2 (2018): 693-704.
Commonly used Matlab functionalities (these .m files need to be added to Matlab path) - Please refer to the "RunMe.txt" in each folder for specific components