Volumetric Super-Resolution Forests for MRI Super-Resolution
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README.md

Volumetric Super-Resolution Forests (VSRF)

Volumetric Super-Resolution Forests for MRI Super-Resolution

This is the source code to the conference article accepted at ICIP 2018.

Citation

The source code is only for academic use, no commercial use is allowed. If you use or adapt our code in your research, please cite our ICIP article:

  @INPROCEEDINGS{8451320,
	author={A. Sindel and K. Breininger and J. K\"a{\ss}er and A. Hess and A. Maier and T. K\"ohler},
	booktitle={2018 25th IEEE International Conference on Image Processing (ICIP)},
	title={Learning from a Handful Volumes: MRI Resolution Enhancement with Volumetric Super-Resolution Forests},
	year={2018},
	pages={1453-1457},
	doi={10.1109/ICIP.2018.8451320},
	ISSN={2381-8549},
	month={Oct}
  }

Requirements

  • The code was developed with MATLAB R2017a and tested under Windows 10 (for some functions, e.g. imresize3 MATLAB 2017a is required)
  • Required libraries/toolboxes:
    • libEigen (for the mex/cpp files)
    • SPM12 (to convert .nii to .mat and save the super-resolved images as .nii)
  • Files from MATLAB file exchange:

Usage

Run the example script to get an impression for the usage of VSRF. Some settings have to be specified as described in the code.

Data

To run the example code with the Kirby 21 human brain MRI [1] dataset you can download the MPRAGE files here. A script for preprocessing the data and converting the .nii files to .mat file is provided in \preprocessing.

Building MEX Files

A pre-compiled MEX file is provided for Windows 64 bit, for other operating systems the MEX file can be build with the script method\compile_forestRegrInference.m.

Training

VSRF is fast to train, depending on your hardware you can run the training in parallel. For training either a set of low- and high-resolution MR volumes (mat files) can be used or the high-resolution volumes can be downscaled. These settings have to be defined in the example script run_VSRF.m. The training process stores a .mat file containing the learned tree structure in \method\models for further usage.

Inference

After training the trained forest is applied to the defined test MR volumes (see run_VSRF.m and main_VSRF_MRI.m). Then the super-resolved results are evaluated with the peak signal-to-noise ratio (PSNR) and the structural similarity (SSIM) [2] and the volumes are written to disk.

The code is based on [3], [4] and [5].

@author Aline Sindel

References

[1] B. A. Landman, A. J. Huang, A. Gifford, D. S. Vikram, I. A. L. Lim, J. A. D. Farrell, J. A. Bogovic, J. Hua, M. Chen, S. Jarso, S. A. Smith, S. Joel, S. Mori, J. J. Pekar, P. B. Barker, J. L. Prince, and P. C. M. van Zijl, “Multi-parametric neuroimaging reproducibility: A 3-T resource study,” NeuroImage, vol. 54, no. 4, pp. 2854 – 2866, 2011.

[2] Z. Wang, A. C. Bovik, H. R. Sheikh, and E. P. Simoncelli, “Image quality assessment: from error visibility to structural similarity,” IEEE Trans. Image Process., vol. 13, no. 4, pp. 600–612, 2004.

[3] S. Schulter, C. Leistner, and H. Bischof. Fast and accurate image upscaling with super-resolution forests. CVPR 2015.

[4] R. Timofte, V. De Smet, L. van Gool. Anchored Neighborhood Regression for Fast Example-Based Super- Resolution. ICCV 2013."

[5] P. Dollar. Piotr's Computer Vision Matlab Toolbox (PMT). http://vision.ucsd.edu/~pdollar/toolbox/doc/index.html