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.
- Ensure that you are in your home directory::
$ cd ~
- Install the github package:
$ git clone https://github.com/AlistairPerry/dwi2connectome.git
Fibre and connectome construction
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/
.