Home - McIntosh-Lab/tvb-ukbb GitHub Wiki

Welcome

Welcome to the tvb-ukbb wiki! This is the knowledge base for the TVB-UKBB Pipeline.

This code supports the submitted paper "A robust modular automated neuroimaging pipeline for model inputs to TheVirtualBrain" by Noah Frazier-Logue, Justin Wang, Zheng Wang, Devin Sodums, Anisha Khosla, Alexandria Samson, Anthony R. McIntosh, and Kelly Shen.

Paper

The paper has a full overview of the methods for the overall pipeline and each sub-pipeline (i.e. structural, functional, diffusion, QC). See here for the paper: A robust modular automated neuroimaging pipeline for model inputs to TheVirtualBrain

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To search for content in our codebase, wiki, or discussions, enter the following in the GitHub search bar:

repo:McIntosh-Lab/tvb-ukbb <content_keywords>

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Check out the FAQ or Discussions Page if you need help.

Wiki Outline

• Home
• Introduction
• User Guide
  • Installation
    • Installation on a General HPC/non-HPC System
    • Installing on Digital Research Alliance of Canada's infrastructure
    • Installing on SGE (legacy)
  • Basic Usage
    • Running Subjects on a General HPC/non-HPC system
    • Running Subjects on Digital Research Alliance of Canada's infrastructure
    • Running Subjects on SGE (legacy)
  • Customizing the pipeline to your dataset
    • Modifying init_vars
    • Supported Features
    • Modifying bb_file_manager.py to capture input files
    • Modifying FEAT, ICA, FIX
    • Modifying IDP Generation
    • Modifying QC Generation
  • Inputs
  • Outputs
  • Running a sample subject
  • Miscellaneous Tools
    • Reparcellation Tool
• FAQ

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