Many of the publications from my group build upon the Michigan Image Reconstruction Toolbox (MIRT) and, in the spirit of reproducible research, many of the algorithms in those papers are included as examples in MIRT.

This directory contains the data and code for reproducing the results in some of the group's publications. These are distributed here, rather than within MIRT, because the data sizes involved would make MIRT undesirably large. However, a version of MIRT is needed to use the code in many cases.

More recent papers tend to have github repos cited in the paper itself, so may not be listed here. Check the paper first, then here, and then email the first author and Prof. Fessler if you still cannot find it.

Todo: make DOIs for citeable code

2023

• Il Yong Chun, Zhengyu Huang, Hongki Lim, J A Fessler.
  Momentum-Net: Fast and convergent iterative neural network for inverse problems.
  IEEE Trans. Patt. Anal. Mach. Int., 45(4):4915-31, Apr., 2023.
  github code repository (matlab/python)

  2022

  2021

• David Hong, Kyle Gilman, Laura Balzano, J A Fessler.
  HePPCAT: probabilistic PCA for data with heteroscedastic noise.
  IEEE Trans. Sig. Proc., 69:4819-34, Aug. 2021.
  http://arxiv.org/abs/2101.03468
  gitlab code repository (julia)
• Mingjie Gao, J A Fessler, Heang-Ping Chan.
  Deep convolutional neural network with adversarial training for denoising for digital breast tomosynthesis images
  IEEE Trans. Med. Im., 40(7)1805-16, July, 2021.
  github code repository (python)

  2020

• Il Yong Chun, J A Fessler.
  Convolutional analysis operator learning: acceleration and convergence.
  IEEE Trans. Im. Proc., 29(1):2108-22, Jan. 2020.
  github code repository (matlab)
  Julia package ConvolutionalOperatorLearning.jl
• Hongki Lim, Il Yong Chun, Yuni K Dewaraja, J A Fessler.
  Improved low-count quantitative PET reconstruction with a variational neural network.
  IEEE Trans. Med. Imag., 39(11):3512-22, Nov. 2020.
  github code (matlab/python)
• Claire Yilin Lin, J A Fessler.
  Efficient regularized field map estimation in 3D MRI.
  IEEE Trans. Computational Imaging, 6:1451-8, 2020.
  github code (matlab) and data
• Brian E Moore, Saiprasad Ravishankar, Raj Rao Nadakuditi, J A Fessler.
  Online adaptive image reconstruction using (OnAIR) using dictionary models.
  IEEE Trans. on Computational Imaging, 6:153-66, 2020.
  github code (matlab), data
• Steven T Whitaker, Jon-Fredrik Nielsen, J A Fessler.
  Myelin water fraction estimation using small-tip fast recovery MRI.
  Mag. Res. Med., 84(4):1977-90, Oct. 2020.
  github code repo (Julia)
  raw data on deep blue
• Haowei Xiang, Hongki Lim, J A Fessler, Yuni Dewaraja.
  A deep neural network for fast and accurate scatter estimation in quantitative SPECT/CT under challenging scatter conditions.
  Eur. J. Nuc. Med. Mol. Im., ?. 2020.
  github code (python/jupyter notebook), github phantom data, deep blue spect patient data
• Siqi Ye, Saiprasad Ravishankar, Yong Long, J A Fessler.
  SPULTRA: low-dose CT image reconstruction with joint statistical and learned image models.
  IEEE Trans. Med. Imag., 39(3):729-41, Mar. 2020.
  github code repository (matlab)
• Mónica Abella, Cristobal Martinez, Manuel Desco, Juan José Vaquero, J A Fessler
  Simplified statistical image reconstruction for X-ray CT with beam-hardening artifact compensation
  IEEE Trans. Medical Imaging, 39(1):111-18 Jan., 2019.
  code
• Zhengyu Huang, J A Fessler, Theodore B Norris, Il Yong Chun.
  Light-field reconstruction and depth estimation from focal stack images using convolutional neural networks.
  Proc. IEEE Conf. Acoust. Speech Sig. Proc., pp. 8648-52, 2020.
  github code repository

  2019

• Claire Yilin Lin, J A Fessler
  Efficient dynamic parallel MRI reconstruction for the low-rank plus sparse model.
  IEEE Trans. Computational Imaging, 5(1):17-26, Mar. 2019.
  github code repository data directory

  2018

• Il Yong Chun, J A Fessler.
  Convolutional dictionary learning: acceleration and convergence.
  IEEE Trans. Im. Proc., 27(4):1697-712, Apr. 2018.
  arXiv version github code repository
• Donghwan Kim, J A Fessler.
  Adaptive restart of the optimized gradient method for convex optimization.
  J. Optim. Theory Appl., 178(1):240-63, Jul. 2018.
  gitlab code repository
• Hongki Lim, Yuni K Dewaraja, J A Fessler.
  A PET reconstruction formulation that enforces non-negativity in projection space for bias reduction in Y-90 imaging.
  Phys. Med. Biol., 63(3):035042, Feb. 2018.
  github code repository
• Gopal Nataraj, Jon-Fredrik Nielsen, Clayton D Scott, J A Fessler.
  Dictionary-free MRI PERK: Parameter estimation via regression with kernels.
  IEEE Trans. Med. Imag., 37(9):2103-14, Sep. 2018.
  github code repository
• Valur T Olafsson, Douglas C Noll, J A Fessler.
  Fast spatial resolution analysis of quadratic penalized least-squares image reconstruction with separate real and imaginary roughness penalty: application to MRI.
  IEEE Trans. Med. Imag., 37(2):604-14, Feb. 2018.
  code/data
• Sydney N Williams, Jon-Fredrik Nielsen, J A Fessler, Douglas C Noll.
  Design of spectral-spatial phase prewinding pulses and their use in small-tip fast recovery steady-state imaging.
  Mag. Res. Med., 79(3):1377-86, Mar. 2018.
  github code repository
• Xuehang Zheng, Saiprasad Ravishankar, Yong Long, J A Fessler.
  PWLS-ULTRA: An efficient clustering and learning-based approach for low-dose 3D CT image reconstruction.
  IEEE Trans. Med. Imag., 37(6):1498-510, Jun. 2018.
  github code repository

  2017

• Mai Le, J A Fessler.
  Efficient, convergent SENSE MRI reconstruction for non-periodic boundary conditions via tridiagonal solvers.
  IEEE Trans. Computational Imaging, 3(1):11-21, Mar. 2017.
  github code repository
• Saiprasad Ravishankar, Brian E Moore, Raj Rao Nadakuditi, J A Fessler.
  Low-rank and adaptive sparse signal (LASSI) models for highly accelerated dynamic imaging.
  IEEE Trans. Med. Imag., 36(5):1116-28, May 2017.
  code/data gitlab.com code repository
• Saiprasad Ravishankar, Raj Rao Nadakuditi, J A Fessler.
  Efficient sum of outer products dictionary learning (SOUP-DIL) and its application to inverse problems.
  IEEE Trans. Computational Imaging, 3(4):694-709, Dec. 2017.
  gitlab code repository
  python version of SOUP-DIL
  python notebook example

  2016

• Hung Nien, J A Fessler.
  Relaxed linearized algorithms for faster X-ray CT image reconstruction.
  IEEE Trans. Med. Imag., 35(4):1090-8, Apr. 2016.
  code/data

  2015

• Matthew J Muckley, Douglas C Noll, J A Fessler.
  Fast parallel MR image reconstruction via B1-based, adaptive restart, iterative soft thresholding algorithms (BARISTA).
  IEEE Trans. Med. Imag., 34(2):578-88, Feb. 2015.
  code/data
• Daniel S Weller, Ayelet Pnueli, Gilad Divon, Ori Radzyner, Yonina C Eldar, J A Fessler.
  Undersampled phase retrieval with outliers.
  IEEE Trans. Computational Imaging, 1(4):247-58, Dec. 2015.
  gitlab code repository (matlab)

  2014

• Yong Long, J A Fessler.
  Multi-material decomposition using statistical image reconstruction for spectral CT.
  IEEE Trans. Med. Imag., 33(8):1614-26, Aug. 2014.
  code
• Daniel Weller, Sathish Ramani, J A Fessler.
  Augmented Lagrangian with variable splitting for faster non-Cartesian L1-SPIRiT MR image reconstruction.
  IEEE Trans. Med. Imag., 33(2):351-61, Feb. 2014.
  code/data
• Daniel S Weller, Sathish Ramani, Jon-Fredrik Nielsen, J A Fessler.
  Monte Carlo SURE-based parameter selection for parallel magnetic resonance imaging reconstruction.
  Mag. Res. Med., 71(5):1760-70, May 2014.
  code/data

  2013

• Antonios Matakos, Sathish Ramani, J A Fessler.
  Accelerated edge-preserving image restoration without boundary artifacts.
  IEEE Trans. Im. Proc., 22(5):2019-29, May 2013.
  code/data

  2012

• Sathish Ramani, J A Fessler.
  A splitting-based iterative algorithm for accelerated statistical X-ray CT reconstruction.
  IEEE Trans. Med. Imag., 31(3):677-88, Mar. 2012.
  code
• Sathish Ramani, Zhihao Liu, Jeffrey Rosen, Jon-Fredrik Nielsen, J A Fessler.
  Regularization parameter selection for nonlinear iterative image restoration and MRI reconstruction using GCV and SURE-based methods.
  IEEE Trans. Im. Proc., 21(8):3659-72, Aug. 2012.
  code/data
• Feng Zhao, Douglas Noll, Jon-Frederick Nielsen, J A Fessler.
  Separate magnitude and phase regularization via compressed sensing.
  IEEE Trans. Med. Imag., 31(9):1713-23, Sep. 2012.
  code/data

  2011

• Sathish Ramani, J A Fessler.
  Parallel MR image reconstruction using augmented Lagrangian methods.
  IEEE Trans. Med. Imag., 30(3):694-706, Mar. 2011.
  code/data

  2009

• Joonki Noh, J A Fessler, Paul E Kinahan.
  Statistical sinogram restoration in dual-energy CT for PET attenuation correction.
  IEEE Trans. Med. Imag., 28(11):1688-702, Nov. 2009.
  code

  2004

• Bradley P Sutton, Douglas C Noll, J A Fessler.
  Dynamic field map estimation using a spiral-in / spiral-out acquisition.
  Mag. Res. Med., 51(6):1194-204, Jun. 2004.
  code

  2002

• Daniel F Yu, J A Fessler.
  Edge-preserving tomographic reconstruction with nonlocal regularization.
  IEEE Trans. Med. Imag., 21(2):159-73, Feb. 2002.
  code/data