MatMRI
Toolbox for MRI image reconstruction using only core or toolbox Matlab functions (i.e., no mex files or pre-compiled binaries). This philosophy is used to enable easy integration with built-in Matlab GPU functionality, and to minimize dependencies.
Summary
| Latest Version | Unknown |
|---|---|
| License | Unknown |
| CI Status | Failing |
| Stars | 4 |
| Forks | 4 |
| Open Issues | 0 |
| Last Commit | 2026-02-25 |
| Downloads | 0 |
| Last Indexed | 2026-07-31 04:41 |
Installation
nimble install MatMRI
choosenim install MatMRI
git clone https://gitlab.com/cfmm/matlab/matmri
OS Compatibility
| Platform | Linux | macOS | Windows | FreeBSD | OpenBSD | NetBSD | Android | iOS | WASM | Embedded |
|---|---|---|---|---|---|---|---|---|---|---|
| MatMRI | ✓ | ✓ | ✓ | - | - | - | - | - | - | - |
Source
| Repository | https://gitlab.com/cfmm/matlab/matmri |
|---|---|
| Homepage | https://gitlab.com/cfmm/matlab/matmri |
| Registry Source | gitlab |
README
Package for MRI. Supports: - Reconstruction - non-Cartesian regridding - iterative SENSE (Cartesian or non-Cartesian) - iterative SENSE for higher order models that may include: - a B0 map - time varying spherical harmonics of phase accrual - diffusion MRI fitting - spatially regularized diffusion kurtosis fitting with an axially symmetric model (nii2kurt.m) - free water corrected kurtosis and micro-FA (nii2uFA_fwe.m). Cite with doi: 10.3389/fnins.2023.1074730
Before Usage - run setPath.m to add all the directories to the Matlab path
Includes a basic image viewer and ROI drawing tool called "bview" - enter "bview" in the Matlab command prompt to use
Tips - step through the demos in the demos folder - recommended order is demo_regridding, demo_regSENSE, demo_highOrder - open files to read usage info
Notes - Matlab gpuArray functionality is used whenever possible, so a compatible GPU is strongly recommended
Acknowledgement
- Cite as:
1. Varela-Mattatall G, Dubovan PI, Santini T, Gilbert KM, Menon RS, Baron CA. Single-shot spiral diffusion-weighted imaging at 7T using expanded encoding with compressed sensing. Magn Reson Med. 2023 Apr 10. doi: 10.1002/mrm.29666
2. Baron CA (2021, February 2). MatMRI: A GPU enabled package for model based MRI image reconstruction. Zenodo. http://doi.org/10.5281/zenodo.4495476
- Additionally, please reference the following works for usage of the below functions:
- nii2kurt: Hamilton, J., Xu, K., Geremia, N., Prado, V. F., Prado, M. A. M., Brown, A., & Baron, C. A. (2024). Robust frequency-dependent diffusional kurtosis computation using an efficient direction scheme, axisymmetric modelling, and spatial regularization. Imaging Neuroscience, 2, 1–22.
- nii2uFA_fwe: Arezza NJJ, Santini T, Omer M, Baron CA. Estimation of free water-corrected microscopic fractional anisotropy. Front Neurosci. 2023 Mar 7;17:1074730. doi: 10.3389/fnins.2023.1074730.
- harmonicsFromRaw: Dubovan PI, Gilbert KM, Baron CA. A correction algorithm for improved magnetic field monitoring with distal field probes. Magn Reson Med. 2023 Dec;90(6):2242-2260. doi: 10.1002/mrm.29781
- findDelAuto: Dubovan PI, Baron CA. Model-based determination of the synchronization delay between MRI and trajectory data. Magn Reson Med. 2022 Sep 26. doi:10.1002/mrm.29460.
- nufftOp: Baron CA, Dwork N, Pauly JM, Nishimura DG. Rapid compressed sensing reconstruction of 3D non-Cartesian MRI. Magn. Reson. Med. 2018;79:2685–2692.
- sampHighOrder:
- Wilm BJ, Barmet C, Pruessmann KP. Fast higher-order MR image reconstruction using singular-vector separation. IEEE Trans Med Imaging. 2012 Jul;31(7):1396-403. doi: 10.1109/TMI.2012.2190991. Epub 2012 Mar 14. Erratum in: IEEE Trans Med Imaging. 2012 Sep;31(9):1833.
- Baron CA, Dwork N, Pauly JM, Nishimura DG. Rapid compressed sensing reconstruction of 3D non-Cartesian MRI. Magn. Reson. Med. 2018;79:2685–2692.
(c) 2020, Corey Baron