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Welcome to the DWI2Connectome user documentation!

This pipeline provides a streamlined way of processing diffusion weighted images (and as a side effect, structural images) through the MRtrix, FSL and FreeSurfer packages. Note that this currently only works on the Avalon cluster at QIMR. If you would like to adapt the scripts to your own HPC cluster please feel free to fork the repository.

Setup Information

  1. Ensure that you are in your home directory::

$ cd ~

  1. Install the github package:

$ git clone https://github.com/AlistairPerry/dwi2connectome.git

Getting started

Conversion to NiFTI for T1

Conversion to MIF for DWI

Structural image preprocessing

FreeSurfer preprocessing

Diffusion image preprocessing

Advanced preprocessing

Segmentation and parcellation

Fibre and connectome construction

Fixel-based analysis

Fixel processing pipeline

Fixel statistics

Quality checking

Quality checking of images

Troubleshooting

Bugs and errors

FAQs

Fixel-based analysis

Tips and Tricks

Bash commands

Interactive sessions on Avalon

All processed files (images, matrices, text files) can be found in:

/working/your_lab_here/your_working_dir/Diff/your_sub/preproc/.

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