├── 01-gridding-reconstruction.ipynb ├── 02-parallel-imaging-compressed-sensing-reconstruction.ipynb ├── 03-building-an-l1-wavelet-recon-app.ipynb ├── LICENSE ├── README.md ├── data ├── cartesian_ksp.npy ├── projection_coord.npy └── projection_ksp.npy └── requirements.txt /LICENSE: -------------------------------------------------------------------------------- 1 | BSD 3-Clause License 2 | 3 | Copyright (c) 2019, mikgroup 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions are met: 8 | 9 | 1. Redistributions of source code must retain the above copyright notice, this 10 | list of conditions and the following disclaimer. 11 | 12 | 2. Redistributions in binary form must reproduce the above copyright notice, 13 | this list of conditions and the following disclaimer in the documentation 14 | and/or other materials provided with the distribution. 15 | 16 | 3. Neither the name of the copyright holder nor the names of its 17 | contributors may be used to endorse or promote products derived from 18 | this software without specific prior written permission. 19 | 20 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 21 | AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 22 | IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 23 | DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 24 | FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 25 | DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 26 | SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 27 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 28 | OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 29 | OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 30 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # SigPy for MRI Tutorial 2 | 3 | [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/mikgroup/sigpy-mri-tutorial/master) 4 | 5 | In this tutorial, you will learn how to use [SigPy](https://github.com/mikgroup/sigpy) for MRI reconstruction. 6 | 7 | There are three parts of the tutorial: 8 | 9 | 1. [Gridding Reconstruction](01-gridding-reconstruction.ipynb): This notebook goes through basic features of SigPy using the gridding reconstruction as an example usage. 10 | 2. [Parallel Imaging Compressed Sensing Reconstruction](02-parallel-imaging-compressed-sensing-reconstruction.ipynb): This notebook shows how to run Apps in SigPy to perform parallel imaging compressed sensing reconstructions. 11 | 3. [Buiding a Parallel Imaging Compressed Sensing App](03-building-an-l1-wavelet-recon-app.ipynb): This notebook shows how to create an L1 wavelet regularized reconstruction App from scratch. 12 | 13 | 14 | Some topics that are not covered in this tutorial: 15 | 16 | - Non-Cartesian support in MRI Apps. 17 | - MRI simulation functions, such as generating Poisson disk sampling using `poisson`. 18 | - Plotting functions. 19 | - Multi-CPU and GPUs using MPI. 20 | - PyTorch interopability. 21 | -------------------------------------------------------------------------------- /data/cartesian_ksp.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikgroup/sigpy-mri-tutorial/b21dcdcfac8557ebb4c2bda1e9faf2cb1e1b6a33/data/cartesian_ksp.npy -------------------------------------------------------------------------------- /data/projection_coord.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikgroup/sigpy-mri-tutorial/b21dcdcfac8557ebb4c2bda1e9faf2cb1e1b6a33/data/projection_coord.npy -------------------------------------------------------------------------------- /data/projection_ksp.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mikgroup/sigpy-mri-tutorial/b21dcdcfac8557ebb4c2bda1e9faf2cb1e1b6a33/data/projection_ksp.npy -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | numpy 2 | scipy 3 | PyWavelets 4 | matplotlib 5 | numba 6 | tqdm 7 | sigpy 8 | --------------------------------------------------------------------------------