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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

Searching the Wiki

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>

Need help?

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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