Welcome to SNG Diffusion Pipeline's 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.

Setup Information

1. Ensure that you are in your home directory on the avalon cluster::

$ cd ~

2. Install the github package:

$ git clone https://github.com/breakspear/diffusion-pipeline.git

3. Make sure your bash environment is setup correctly:

$ cp ~/diffusion-pipeline/.bashrc ~/.

You will need to restart your terminal session:

$ bash

for these changes to take effect. You may also wish to copy the contents of the .bashrc file into an existing .bashrc file in your home directory.

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

Post-processing and Fixel-based analysis

Custom parcellations

Fixel processing pipeline

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/.