Introduction
The TVB - UK Biobank Pipeline project is a multi-modal MRI processing pipeline written in Python, bash, MATLAB, and R. It uses FSL as the basic building blocks and is heavily based on the UK Biobank Pipeline, developed by the FMRIB Analysis Group, University of Oxford.
The TVB implementation includes the addition of a user-provided parcellation for 1) computing ROI-based timeseries and functional connectivity (Pearson correlations) using resting-state fMRI; and 2) connectome construction using diffusion-weighted imaging tractography.
TheVirtualBrain (TVB) is an open source software platform for simulating brain dynamics. The outputs from the TVB-UKBB MRI pipeline can be directly inputted into TVB for connectome-based modelling.
The TVB-UKBB Pipeline works out-of-the-box with the Cam-CAN and ADNI3. It is also likely to continue to work with the UK Biobank dataset, but this remains untested. Datasets that use similar imaging protocols as one of our supported datasets is likely to work with few modifications.
Currently, gradient distortion correction, TOPUP distortion correction, NODDI, AUTOPTX, task fMRI and susceptibility-weighted imaging processing from the original UKBiobank pipeline are either not implemented or remain untested.
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.
See here for the paper preprint: https://doi.org/10.1101/2022.02.24.481836
The original UK_biobank_pipeline is explained in detail in the paper Image Processing and Quality Control for the first 10,000 Brain Imaging Datasets from UK Biobank.
Tractography for connectome construction is based on methods validated using tracer data in macaques (see Shen et al. 2019 https://doi.org/10.1016/j.neuroimage.2019.02.018).