Matthias J. Ehrhardt

About me CV Research Teaching Software

Software

Reproducible Research
This page is intended to give access to the software of my published articles. Please feel free to download and make use of it. If you find bugs in our code please let me know: m.ehrhardt@bath.ac.uk.

I not only hope that this page can be useful to you but it also may encourage you to make your research accessible and reproducible. I followed the guideline to reproducible research by Patrick Vandewalle.

Quick links to all software
For more software see my github page.
Multi-Contrast MRI Reconstruction with Structure-Guided Total Variation
M. J. Ehrhardt, M. M. Betcke

Paper: [SIAM.org] [arxiv]

Download software: [7 MB]

Tested Configurations: The software was tested on Ubuntu 12.04 LTS with Matlab 2015a and Mac OS X with Matlab 2015a.


Motivation: Different scan parameters lead to different contrasts in MRI.

Idea: Structure can be either based on the location or direction of edges.
Reference: M. J. Ehrhardt and M. M. Betcke, Multi-Contrast MRI Reconstruction with Structure-Guided Total Variation, SIAM Journal on Imaging Sciences 9(3), pp. 1084–1106, 2016

Acknowledgements: The simulation results are based on BrainWeb data and patient data kindly provided by Ninon Burgos and Jonathan Schott from the University College London, UK.


Example Result: Reconstructions with different a priori knowledge. The reconstruction quality improves visually significantly from left to right.
Joint Reconstruction of PET-MRI by Exploiting Structural Similarity
M. J. Ehrhardt, K. Thielemans, L. Pizarro, D. Atkinson, S. Ourselin, B. F. Hutton, S. R. Arridge

Paper: [IOP science]

Download software: [59 MB]

Tested Configurations: The software was tested on Ubuntu 12.04 LTS with Matlab 2013a.

Reference: M. J. Ehrhardt, K. Thielemans, L. Pizarro, D. Atkinson, S. Ourselin, B. F. Hutton and S. R. Arridge, Joint reconstruction of PET-MRI by exploiting structural similarity, Inverse Problems 31(1), 015001, 2015


Motivation: PET and MRI images show structural similarity due to the same anatomy.

Acknowledgements: The software uses L-BFGS-B to solve the constrained minimization problem which needs to be downloaded separately. The Fortan code can be obtained from [link, accessed September 2014] and the Matlab interface from [link, accessed September 2014].

Example Result: Reconstructions of simulated PET and undersampled MRI are shown. Separate reconstructions (left) show low resolution in PET and ghosting in MRI. Joint reconstruction (right) results in better defined PET images and removes ghosting artefacts in MRI.
Vector-Valued Image Processing by Parallel Level Sets
M. J. Ehrhardt, S. R. Arridge

Paper: [IEEE Xplore] [preprint (11 MB)]

Download software: [14 MB]

Tested Configurations: The software was tested on Ubuntu 12.04 LTS with Matlab 2013a.

Reference: M. J. Ehrhardt and S. R. Arridge, Vector-Valued Image Processing by Parallel Level Sets , IEEE Transactions on Image Processing, Volume 23, Number 1, Pages 9-18, 2014


Idea: By penalizing parallel level sets two images evolve to a common shape.
Example Result: Demosaicking of the image "leopard" (left) with the noisy data zero filled at missing values (middle). Using parallel level sets one recovers the image visually perfect (right).

Acknowledgements: The original images are part of the training data set of the Berkeley Segmentation Dataset, [download (21 MB), accessed March 2013]. The images have different names in the data base: leopard = 159029, lake = 176035, pyramid = 299091, bugs = 35008, wolf = 42078. The noisy images can be found on Francisco J. Estrada's web page, [download (1 GB), accessed March 2013]. The images have different names on this page: leopard = 0072, lake = 0094, pyramid = 0194, bugs = 0213, wolf = 0246.
We used the Structural Similarity as a figure of merit. To make use of it in the software please download the file ssim_index.m [download (6 KB), accessed March 2013] available from the author's web page.

© 2014-2018 Matthias J. Ehrhardt - m.ehrhardt@bath.ac.uk - last updated: Sep 2018