Integration of multiple tractography and neural-fibers related tools and algorithms.
Project description
What is phybers?
Phybers is a library for Python that integrates multiple tractography and neural-fibers related algorithms. It includes the following modules:
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Segmentation: Fibers segmentation based on a multi-subject atlas. It's purpose is clasifying subject fibers in function of a multisubject-fascicle atlas.
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Hierarchichal Clustering: A hierarchichal clustering algorithm based on euclidean distance between pairs of fibers, originally applied between subjects, as part of an automatic method to identify short fiber fascicles that are reproducibles on a HARDI database.
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FFClust: A intra-subject clustering algorithm based on K-Means between fibers' points. It can be applied to the fibers of the whole brain's tractography. It's objective is creating similar groups of fibers, contingent on its position.
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Utils: The utils module is a compendium of tools used for both the pre-processing of a tractography as well as for evaluating the performance of the clustering and the segmentation. It includes:
- Tools for normalization to the MNI space for the HCP database.
- Sampling of the fibers to n equidistant points.
- The calculation of the intersection between fascicles.
- Tools to extract and filter statistics measures over the clustering or segmentation of fibers. Some of the measures extracted are: size, length and inter/intra distance over clusters or fascicles.
- Fibervis: A visualization tool for bundles and MRIs.
What do you need?
For now, phybers only works on Linux. It's currently being worked on for Windows cmd/PowerShell compatibilty.
What you'll need is:
- g++
- gcc
- python >= 3.8 (might work on previous versions, but for compatibility, >= 3.8.8 is recommended.)
New in version 0.0.6!
Now the utils module includes a visualization tool for bundles, MRIs and more!
FAQ
When running the utils' visualization submodule, i get: fatal error: GL/gl.h: No such file or directory
To fix this on LinuxFollow the Open GL Installation on Linux section on the following page: https://en.wikibooks.org/wiki/OpenGL_Programming/Installation/Linux
The utils' visualization submodule tool returns a PyQt5 error.
To solve this in Linux, you will need to upgrade your pip:
pip install --user --upgrade pip Then, manually install PyQt5: pip install PyQt5
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