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WMA Flow reimplements python scripts from the WMA github repository for tractogram bundling. See https://github.com/SlicerDMRI/whitematteranalysis.
Export path/to/bin to PATH
Create a virtual environment with python3.7 and pip install the wma github repository:
pip install git+https://github.com/SlicerDMRI/whitematteranalysis.git
pip install git+https://github.com/scilus/scilpy.git
Run wm_quality_control_tractography.py --help to test if the installation is successful.
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Install 3D Slicer
3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization.
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Install SlicerDMRI
SlicerDMRI is an open-source project to improve and extend diffusion magnetic resonance imaging software in 3D Slicer.
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Install whitematteranalysis (WMA)
WMA is an open source software package for data-driven fiber clustering white matter parcellation.
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ANTs
- Download the tutorial data package (WMA_tutorial_data.zip, ~2.5GB)
- All files must be in TRK format
- A weird hack is done in the preprocessing process. We flip P-A to A-P while still being in RAS. The atlas is flipped for some unknown reasons
- All output files are in VTP. We are currently looking to convert VTP format to TRK. Slicer is a great software to read the VTP format !
- Nextflow
- Python 3.7
- Slicer
- ANTs
See USAGE or run nextflow run main.nf --help
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
O'Donnell LJ, Wells III WM, Golby AJ, Westin CF.
Unbiased groupwise registration of white matter tractography.
In MICCAI, 2012, pp. 123-130.
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.