Cascade: Reproducible Segmentation of White Matter Changes using Strict Statistical Definition

This is the Cascade, academic version. Cascade-academic depends on FSL so you need acknowledge FSL terms of use before using this software.

Content

• Introduction
• Installation
• Citation
• Copyright
• License

Introduction

Cascade, Classification of White Matter Changes, is a fully automated tool for quantification of White Matter Changes. Cascade is designed to be as flexible as possible and can work with all sort of input sequences. It can work without any manually delineated samples as reference. Cascade is designed to work alongside other workflows such as FreeSurfer, SPM and FSL; and not as stand alone software; i.e. Cascade should be run as an extension to existing pipeline to add the capacity to analyse white matter changes. Using Cascade as stand alone software (with its pre-processing) is for demonstration only and should not be used in real research setting.

Please report any issue at https://github.com/Damangir/Cascade/issues.

Install

In order to install the software you need to have the following application installed on your computer.

• Modern C++ compiler (gcc is recommended)
• make
• cmake 2.8+ (cmake.org)
• Insight Toolkit 4.0+ (itk.org)

For the script generator and premade scripts you may use:

• Bash 3+

You can check availability of these packages on your computer (on Unix-like computers e.g. Mac and Ubuntu). Please note the last command might take a few minutes to run.

~$ echo -ne "C++ compiler: "; command -v cc||  command -v gcc||  command -v clang||  command -v c++||  echo "No C++ compiler found"
~$ make --version
~$ cmake --version
~$ bash --version
~$ find / -name "ITKConfigVersion.cmake" -print -exec head -n1 {} \; 2>/dev/null

Once you obtain the Cascade, you can install it via:

~$ cd Cascade
Cascade$ mkdir build
Cascade$ cd build
build$ cmake ../src
build$ make

Before using the scripts you should export some envirnment variables:

export CASCADE_BIN=Cascade/build
export CASCADE_DATA=Cascade/data

You can use script generators located at src/Shell to generate scripts for your studies. There are some ready to use scripts which can import the results of freesurfer or volbrain and runs the Cascade based on their results. It is recommended to import the results of your GM analysis. Otherwise use the script generator to generate a script which handles GM analysis internally (This is for demonstration purpose only and not recommended).

An example usage of the softwares are:

$ RADIUS=1.5 FREESURFER_DIR=/path/to/FS_Subject FLAIR=/path/to/FLAIR OUTPUT_DIR=/path/to/cascade/output  modelfree.freesurfer.sh

or

$ RADIUS=1.5 VOLBRAIN_DIR=/path/to/volbrain_Subject FLAIR=/path/to/FLAIR OUTPUT_DIR=/path/to/cascade/output  modelfree.volbrain.sh

These scripts will generate a p-value mape ( 1-pvalue ) for being WML. You can use report script should you need to convert it to binary mask.

Citation

If you are using this software in your research, you should refer to:

Damangir, S., Westman, E., Simmons, A., Vrenken, H., Wahlund, L. O., & Spulber, G. (2017). Reproducible segmentation of white matter hyperintensities using a new statistical definition. Magnetic Resonance Materials in Physics, Biology and Medicine, 30(3), 227-237.

Damangir, S., Manzouri, A., Oppedal, K., Carlsson, S., Firbank, M. J., Sonnesyn, H., Tysnes O. B., O'Brien J. T., Beyer M. K., Westman E., Aarsland D., Wahlund L. O., Spulber G. (2012). Multispectral MRI segmentation of age related white matter changes using a cascade of support vector machines. Journal of the neurological sciences, 322(1), 211-216.

Copyright

Copyright (C) 2013-2017 Soheil Damangir - All Rights Reserved

License

Cascade by Soheil Damangir is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/.