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Installation

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Steven Meisler edited this page Oct 24, 2023 · 5 revisions

Install from GitHub

(Currently the only working method) We recommend installing the fsub_extractor and dependencies in a dedicated virtual environment (e.g., Anaconda)

# Clone the master branch
git clone https://github.com/smeisler/fsub-extractor.git
cd fsub-extractor
pip install -e .   # for end user
# You may remove the original source code if you are an end user:
cd ../
rm -r fsub-extractor`

If you are a developer, and if there is any update in the source code locally, you may update the installation with:

# Suppose you're in root directory of fsub-extractor source code:
pip install -e .    # for developer to update

Dependencies

Dependencies include (code might work with other later or earlier versions, but has not been extensively tested):

  • Python >= 3.9.0
  • MRTrix >= 3.0.3
  • DIPY >= 1.5.0
  • vtk >= 9.1.0
  • Fury >= 0.8.0
  • FreeSurfer >= 7.2.0

Install from PyPi

We will update this when have a version distributed on PyPi. Dependencies should be installed as part of the pip install process.

Containerized Distribution

We are working on making a Docker container (currently focusing on minimizing the image size - please reach out if you have experience with this!). All dependencies will be included in the container.

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