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README.md

intensity-normalization

Build Status Coverage Status Documentation Status Docker Automated Build Python Versions

This package contains various routines to normalize the intensity of various contrasts of magnetic resonance (MR) brain images; specifically, T1-weighted (T1-w), T2-weighted (T2-w), and FLuid-Attenuated Inversion Recovery (FLAIR). Intensity normalization is an important pre-processing step in many image processing applications regarding MR images since MR images do not have a consistent intensity scale. We implement various individual image-based and sample-based (i.e., a set of images of the same contrast taken from the same scanner) intensity normalization routines to help alleviate this issue.

Note that this package was developed to process adult human MR images; neonatal, pediatric, and animal MR images should also work (at least with some of the normalization schemes). But if there is a substantial difference in the contrast you are processing compared with the same contrast in an adult human, the normalization scheme may not work as expected. Please open an issue if you encounter such a problem.

Also note that when the package refers to any specific contrast image, it is referring to a non-contrast version unless otherwise stated. Using a contrast image as input to a method that assumes non-contrast will produce suboptimal results.

We implement the following normalization methods:

  • Z-score normalization
  • Fuzzy C-means (FCM)-segmentation-based white matter (WM) mean normalization
  • Least squares (LSQ) tissue mean normalization
  • Gaussian Mixture Model (GMM)-based WM mean normalization
  • Kernel Density Estimate WM Peak normalization
  • Piecewise Linear Histogram Matching [1,2]
  • WhiteStripe [3]
  • RAVEL [4]

We use this package to explore the impact of intensity normalization on a synthesis task (pre-print available here).

** Note that while this release was carefully inspected, there may be bugs. Please submit an issue if you encounter a problem. **

This package was developed by Jacob Reinhold and the other students and researchers of the Image Analysis and Communication Lab (IACL).

Link to main Gitlab Repository (The Github repo is a mirror of this Gitlab repo.)

Requirements

  • matplotlib
  • numpy
  • nibabel
  • scikit-fuzzy
  • scikit-learn
  • scipy
  • statsmodels

We have provided a script create_env.sh to create a conda environment with the necessary packages (run like: . ./create_env.sh, this package will be installed in the created environment)

Basic Usage

The easiest way to install the package is through the following command:

pip install git+git://github.com/jcreinhold/intensity-normalization.git

To install from the source directory, use

python setup.py install

or (if you actively want to make changes to the package)

python setup.py develop

and use the several provided command line scripts to interface with the package, e.g.,

fcm-normalize -i t1/ -m masks/ -o test_fcm -v

where t1/ is a directory full of N T1-w images and masks/ is a directory full of N corresponding brain masks, test_fcm is the output directory for the normalized images, and -v controls the verbosity of the output.

Note the package antspy is required for the RAVEL normalization routine, the preprocessing tool as well as the co-registration tool, but all other normalization and processing tools work without it. To also install the antspy package either append --antspy to your call to setup.py or create_env.sh.

To use the convenience pre-processing scripts, install the package with the following command:

python setup.py install --antspy --preprocess

or

python setup.py develop --antspy --preprocess

The command line interface is standard across all normalization routines (i.e., you should be able to run all normalization routines with the same call as in the above example); however, each has unique options and not all methods support single image processing.

Call any executable script with the -h flag to see more detailed instructions about the proper call.

Tutorial

5 minute Overview

In addition to the above small tutorial, there is consolidated documentation here.

Test Package

Unit tests can be run from the main directory as follows:

nosetests -v --with-coverage --cover-tests --cover-package=intensity_normalization tests

If you are using docker, then the equivalent command will be (depending on how the image was built):

docker run jcreinhold/intensity-normalization /bin/bash -c "pip install nose && nosetests -v tests/"

Singularity

You can build a singularity image from the docker image hosted on dockerhub via the following command:

singularity pull --name intensity_normalization.simg docker://jcreinhold/intensity-normalization

Citation

If you use the intensity-normalization package in an academic paper, please cite the corresponding paper:

@inproceedings{reinhold2019evaluating,
  title={Evaluating the impact of intensity normalization on {MR} image synthesis},
  author={Reinhold, Jacob C and Dewey, Blake E and Carass, Aaron and Prince, Jerry L},
  booktitle={Medical Imaging 2019: Image Processing},
  volume={10949},
  pages={109493H},
  year={2019},
  organization={International Society for Optics and Photonics}
}

References

[1] N. Laszlo G and J. K. Udupa, “On Standardizing the MR Image Intensity Scale,” Magn. Reson. Med., vol. 42, pp. 1072–1081, 1999.

[2] M. Shah, Y. Xiao, N. Subbanna, S. Francis, D. L. Arnold, D. L. Collins, and T. Arbel, “Evaluating intensity normalization on MRIs of human brain with multiple sclerosis,” Med. Image Anal., vol. 15, no. 2, pp. 267–282, 2011.

[3] R. T. Shinohara, E. M. Sweeney, J. Goldsmith, N. Shiee, F. J. Mateen, P. A. Calabresi, S. Jarso, D. L. Pham, D. S. Reich, and C. M. Crainiceanu, “Statistical normalization techniques for magnetic resonance imaging,” NeuroImage Clin., vol. 6, pp. 9–19, 2014.

[4] J. P. Fortin, E. M. Sweeney, J. Muschelli, C. M. Crainiceanu, and R. T. Shinohara, “Removing inter-subject technical variability in magnetic resonance imaging studies,” NeuroImage, vol. 132, pp. 198–212, 2016.

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