Pipeline v3

Running PYB pipeline on bash/zsh

Pre-requisites

You need to have these installed on your computer:

• Freesurfer
• ANTs
• FSL

Running pipeline

1. Download pyb.sh and config.sh from here.

2. Download a brain template for brain extraction on ANTs (available here).

   You can experiment with different templates and see which works best for your data.

3. Set up variables in config.sh.

4. Open terminal. Set freesurfer environment variable [Mac / Linux]

5. Go to the directory containing the scripts. Run pyb.sh

./pyb.sh

If you encounter a permission error (typical with zsh) zsh: permission denied: ./pyb.sh, run this instead:

bash ./pyb.sh

Recommended folder structure

.
├── pyb.sh
├── config.sh
├── data
│   └── <subject_name>
│       └── <T1_name>.nii
└── templates
    └── <template_name>
        ├── <brainCerebellumProbabilityMask.nii>
        └── <brainTemplate.nii>