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.

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.

Conversion to NiFTI for T1

Conversion to MIF for DWI

FreeSurfer preprocessing

Advanced preprocessing

Segmentation and parcellation

Fibre and connectome construction

Custom parcellations

Fixel processing pipeline

Quality checking of images

Bugs and errors

FAQs

Fixel-based analysis

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/.