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README.md

whitematteranalysis

Synopsis

WhiteMatterAnalysis (WMA) provides fiber clustering and tractography analysis tools.

WMA Installation

1. Install Python 3:

Miniconda is a nice option becuase it includes pip, setuptools, and all library dependencies (such as VTK and scipy).

2. Install whitematteranalysis with pip:

The following command will use pip to install whitematteranalysis from this source repository and all library dependencies:

  pip install git+https://github.com/SlicerDMRI/whitematteranalysis.git

(Note: On MacOS, to able to use pip, X-code needs to be installed using xcode-select --install.)

Run wm_quality_control_tractography.py --help to test if the installation is successful.

Documentation

References

Please cite the following papers:

O'Donnell, LJ., and Westin, CF. Automatic tractography segmentation
using a high-dimensional white matter atlas. Medical Imaging,
IEEE Transactions on 26.11 (2007): 1562-1575.

O’Donnell LJ, Wells III WM, Golby AJ, Westin CF. 
Unbiased groupwise registration of white matter tractography.
In MICCAI, 2012, pp. 123-130.

Zhang, F., Wu, Y., Norton, I., Rathi, Y., Makris, N., O'Donnell, LJ. 
An anatomically curated fiber clustering white matter atlas for consistent white matter tract parcellation across the lifespan. 
NeuroImage, 2018 (179): 429-447

For projects using Slicer and SlicerDMRI please also include the following text (or similar) and citations:

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White matter tractography clustering and more...

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