cgsense2023 1.0.2
Conjugate Gradient SENSE (CG-SENSE) MRI Reconstruction
License: MIT License
Requires Python: >=3.7
Keywords: mri, reconstruction, cg-sense, conjugate gradient, python

# CG-SENSE HOME


<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->

> Step-by-step tutorial of Conjugate Gradient SENSE (CG-SENSE)
> reconstruction by Hung P. Do.

# Citing this work

## DOI

[![](https://zenodo.org/badge/DOI/10.5281/zenodo.18526383.svg)](https://doi.org/10.5281/zenodo.18526383)

> Do, H. P. (2026). CG-SENSE Tutorial version 1.0.0 (1.0.0). Zenodo.
> https://doi.org/10.5281/zenodo.18526383

# Organization of the tutorial

[This tutorial](https://hdocmsu.github.io/cgsense2023/) was written by
[Hung Do](https://hdocmsu.github.io/) based on the
[RRSG_Challenge_01](https://github.com/ISMRM/rrsg_challenge_01) github
repository.

- [**Original tutorial
  notebook**](https://hdocmsu.github.io/cgsense2023/01_ORIGINAL_tutorial/orig_tuts.html)

- **Original python code:**

  - [helper_fun.py](https://hdocmsu.github.io/cgsense2023/02_ORIGINAL_cgsense/helper_funcs.html)
  - [linop.py](https://hdocmsu.github.io/cgsense2023/02_ORIGINAL_cgsense/linop.html)
  - [solver.py](https://hdocmsu.github.io/cgsense2023/02_ORIGINAL_cgsense/solver.html)
  - [recon.py](https://hdocmsu.github.io/cgsense2023/02_ORIGINAL_cgsense/recon.html)

- **Hung Do’s modifications:**

  - [Modified tutorial
    notebook](https://hdocmsu.github.io/cgsense2023/01_ORIGINAL_tutorial/hpd_tuts.html)
  - [Development notebook for the cgsense2023 PyPI
    package](https://hdocmsu.github.io/cgsense2023/03_HPD_devs/hpd_devs.html)

- [**cgsense2023 PyPI Package
  re-written:**](https://hdocmsu.github.io/cgsense2023/04_HPD_cgsense/plot.html)
  Details can be seen in the P4_HPD_cgsense section.

# My modifications are:

1.  Most importantly, I organized the code into coherent modules and
    repackaged the code into a Python package named
    <a href="https://pypi.org/project/cgsense2023/"
    target="_blank">cgsense2023</a> for easy installation and use. You
    can install the package by running `pip install cgsense2023` in your
    terminal.

2.  For teaching purposes, I created this tutorial for anyone who is
    interested in learning about CG-SENSE and the artifacts that can
    arise from it.

3.  The gridding part was untouched, but I retouched the I/O interface
    such that parameters are consolidated and grouped in one and only
    one central location.

4.  For my own learning purposes, I re-implemented the CG-SENSE
    algorithm from scratch without referring to the original code. There
    are several variations of the CG-SENSE algorithm, but the results
    are generally similar.

5.  Implemented gradient descent (GD) and steepest descent (SD)
    algorithms for comparison with CG-SENSE.

6.  Added code to create k-space trajectories and visualize them.

7.  Added quantitative metrics for evaluating the reconstructed images,
    such as RMSE and SSIM, etc.

8.  Added code to visualize the artifacts in the reconstructed images
    and assess convergence of the CG-SENSE algorithm.

# W.I.P Tasks

Contributions to the below tasks are welcome!

- [ ] Document the standardization of the raw h5-file, otherwise
  [`read_data()`](https://hdocmsu.github.io/cgsense2023/P4_HPD_cgsense/io.html#read_data)
  has to be modified every time a deviation in h5-file is encountered.

- [ ] Refactor, simplify, modularize the gridding reconstructions.
  Currently, it is difficult to understand, especially for new learner.

- [x] Add `dstore` flag in gradient descent or conjugate gradient
  optimization functions to store intermediate reconstruction in each
  iteration.

- [ ] Add theoretical descriptions on MRI, MRI recons, and gradient
  Descent, and gonjugate gradient algorithms.

- [ ] etc.

## How it works

## pip install

The [cgsense2023](https://pypi.org/project/cgsense2023/) package was
uploaded to [PyPI](https://pypi.org/) and can be easily installed using
the below command.

`pip install cgsense2023`

## Plot Module

``` python
from cgsense2023.plot import *
import numpy as np
```

``` python
# Sequential - full - spoke radial trajectory
traj_full = gen_radial_traj(golden=False, full_spoke=True)
show_trajectory(traj_full, golden=True, figsize=(10,8))
```

![](index_files/figure-commonmark/cell-3-output-1.png)

``` python
# golden - full - spoke radial trajectory
traj_full_golden = gen_radial_traj(golden=True, full_spoke=True)
show_trajectory(traj_full_golden, golden=True, figsize=(10,8))
```

![](index_files/figure-commonmark/cell-4-output-1.png)

``` python
Nim, Nx, Ny = 12, 128, 256
x1 = np.random.randn(Nim, Nx, Ny)
x2 = np.random.randn(1, Nx, Ny)
```

``` python
show_image_grid(x1)
```

    Warning: number of images (12) is larger than number of panels (2x5)!

![](index_files/figure-commonmark/cell-6-output-2.png)

``` python
show_image_grid(x2)
```

![](index_files/figure-commonmark/cell-7-output-1.png)

## Metrics Module

``` python
from cgsense2023.metrics import *
import numpy as np
```

``` python
# same dimensions
Nim, Nx, Ny = 11, 128, 256
x1 = np.random.randn(1, Nx, Ny)
x2 = np.random.randn(1, Nx, Ny)
print_metrics(x1, x2)
```

    +---------+-----------+
    | Metrics |   Values  |
    +---------+-----------+
    |   MSE   | 1.999e+00 |
    |   NMSE  | 2.000e+00 |
    |   RMSE  | 1.414e+00 |
    |  NRMSE  | 1.414e+00 |
    |   PSNR  |   14.981  |
    |   SSIM  | 0.0092604 |
    +---------+-----------+

## Gridding Reconstruction

``` python
from cgsense2023.math import *
from cgsense2023.io import *
import cgsense2023 as cgs2003
from cgsense2023.mri import *
from cgsense2023.optimizer import *
import h5py
import numpy as np
import matplotlib.pyplot as plt
```

### Data Paths

``` python
# path to the data file
fpath = '../testdata/rawdata_brain.h5'
# path to the reference results
rpath = '../testdata/CG_reco_inscale_True_denscor_True_reduction_1.h5'
```

``` python
with h5py.File(rpath, 'r') as rf:
    print(list(rf.keys()))
    ref_cg = np.squeeze(rf['CG_reco'][()][-1])
    ref_grid = np.squeeze(rf['Coil_images'][()])
```

    ['CG_reco', 'Coil_images']

``` python
ref_cg.shape, ref_grid.shape
```

    ((300, 300), (12, 300, 300))

### Setup Parameters

``` python
# one stop shop for all Parameters and Data
params = setup_params(fpath, R=1)
```

    ['Coils', 'InScale', 'rawdata', 'trajectory']

### Setup MRI Operator

``` python
# Set up MRI operator
mrimodel = MriImagingModel(params)
mriop = MriOperator(data_par=params["Data"],optimizer_par=params["Optimizer"])
mriop.set_operator(mrimodel)
# Single Coil images after FFT
my_grid = mriop.operator.NuFFT.adjoint(params['Data']['rawdata_density_cor'])
```

``` python
my_grid.shape, ref_grid.shape
```

    ((12, 300, 300), (12, 300, 300))

``` python
# test gridding recon results
np.allclose(ref_grid, my_grid)
```

    True

``` python
# test gridding recon results
np.array_equal(ref_grid, my_grid)
```

    False

``` python
print_metrics(np.abs(ref_grid[0]), np.abs(my_grid[0]))
```

    +---------+-----------+
    | Metrics |   Values  |
    +---------+-----------+
    |   MSE   | 1.472e-24 |
    |   NMSE  | 5.905e-15 |
    |   RMSE  | 1.213e-12 |
    |  NRMSE  | 7.684e-08 |
    |   PSNR  |   154.87  |
    |   SSIM  |    1.0    |
    +---------+-----------+

``` python
show_image_grid(my_grid, figsize=(10,10), rows=3, cols=4)
```

![](index_files/figure-commonmark/cell-20-output-1.png)

``` python
show_image_grid(rss_rec(my_grid), figsize=(10,10))
```

![](index_files/figure-commonmark/cell-21-output-1.png)

## Gradient Descent

``` python
guess = np.zeros((params['Data']['image_dim'],params['Data']['image_dim']))
SD_result, SD_residuals, SD_ref_res = steepest_descent(mriop, guess, 
                                            params['Data']['rawdata_density_cor'], 
                                            iters=50,
                                            ref=ref_cg)
```

    Residuum at iter 50 : 6.553379e-06

``` python
show_compared_images(np.abs(ref_cg), np.abs(SD_result), diff_fac=10, 
                     labels=['Reference', 'Steepest Descent', 'diff'])
```

![](index_files/figure-commonmark/cell-23-output-1.png)

``` python
np.allclose(ref_cg, SD_result)
```

    False

``` python
print_metrics(np.abs(ref_cg), np.abs(SD_result))
```

    +---------+-----------+
    | Metrics |   Values  |
    +---------+-----------+
    |   MSE   | 5.633e-14 |
    |   NMSE  | 7.888e-05 |
    |   RMSE  | 2.373e-07 |
    |  NRMSE  | 8.882e-03 |
    |   PSNR  |   55.242  |
    |   SSIM  |   0.9988  |
    +---------+-----------+

## CG’s Semi-Convergence Behavior

``` python
CG_result, CG_residuals, CG_ref_res = conjugate_gradient(mriop, guess, 
                                            params['Data']['rawdata_density_cor'], 
                                            iters=50,
                                            ref=ref_cg)
```

    Residuum at iter 50 : 2.993229e-06

``` python
plt.plot(np.log10(SD_ref_res),'*--', label='SD reference_norms');
plt.plot(np.log10(SD_residuals),'*--', label='SD residual_norms');
plt.plot(np.log10(CG_ref_res),'*--', label='CG reference_norms');
plt.plot(np.log10(CG_residuals),'*--', label='CG residual_norms');
plt.grid();
plt.xlabel("# iteration")
plt.ylabel("residuals (log10)")
plt.legend();
```

![](index_files/figure-commonmark/cell-27-output-1.png)

## Conjugate Gradient vs. REF

Based on the “semi-convergence” plot above, the optimal number of
iterations for CG and SD are around 10 and 28, respectively.

``` python
CG_result_vs_REF, _, _ = conjugate_gradient(mriop, guess, 
                                            params['Data']['rawdata_density_cor'], 
                                            iters=10,
                                            ref=ref_cg)
```

    Residuum at iter 10 : 1.826174e-05

``` python
show_compared_images(np.abs(ref_cg), np.abs(CG_result_vs_REF), diff_fac=200000, 
                     labels=['Reference', 'Conjugate Gradient', 'diff'])
```

![](index_files/figure-commonmark/cell-29-output-1.png)

``` python
np.allclose(ref_cg, CG_result_vs_REF)
```

    True

``` python
print_metrics(np.abs(ref_cg), np.abs(CG_result_vs_REF))
```

    +---------+-----------+
    | Metrics |   Values  |
    +---------+-----------+
    |   MSE   | 1.196e-22 |
    |   NMSE  | 1.675e-13 |
    |   RMSE  | 1.094e-11 |
    |  NRMSE  | 4.093e-07 |
    |   PSNR  |   141.97  |
    |   SSIM  |    1.0    |
    +---------+-----------+

# References

The list is not exhaustive so if you notice any missing references,
please [report an
issue](https://github.com/hdocmsu/cgsense2023/issues/new). I will
promptly correct it.

- [RRSG_Challenge_01](https://github.com/ISMRM/rrsg_challenge_01) github
  repository

- [fastMRI](https://github.com/facebookresearch/fastMRI) github
  repository

- [Original CG-SENSE Paper by Pruessmann et. al.,
  2001](https://onlinelibrary.wiley.com/doi/10.1002/mrm.1241)

- [CG-SENSE revisited: Results from the first ISMRM reproducibility
  challenge](https://onlinelibrary.wiley.com/doi/10.1002/mrm.28569)

- [Dwight Nishimura, (Published Jan 10, 2010), “Principles of Magnetic
  Resonance Imaging,” Stanford University, Palo Alto,
  CA](https://www.lulu.com/shop/dwight-nishimura/principles-of-magnetic-resonance-imaging/hardcover/product-1gvnv7yn.html?page=1&pageSize=4)

- [Prof. James V. Burke’s Lecture on “The Conjugate Gradient
  Algorithm”](https://sites.math.washington.edu/~burke/crs/408/lectures/L14-CG.pdf)

- [Magnetic Resonance Image Reconstruction: Theory, Methods, and
  Applications,
  (2022)](https://shop.elsevier.com/books/magnetic-resonance-image-reconstruction/akcakaya/978-0-12-822726-8)

- [sigPy github repo](https://github.com/mikgroup/sigpy)

# Citing this work

## DOI

[![](https://zenodo.org/badge/DOI/10.5281/zenodo.18526383.svg)](https://doi.org/10.5281/zenodo.18526383)

> Do, H. P. (2026). CG-SENSE Tutorial version 1.0.0 (1.0.0). Zenodo.
> https://doi.org/10.5281/zenodo.18526383