These are generic image analysis scripts that I have written, collected, and otherwise given cobbled-together life to through much trial and error during my time at MUSC in the BRIDGE Lab. Versions of these scripts can be found in various studies' "STUDY_code" BIDS folders. These are here as a log/reference do the most basic, generic forms of these scripts, not modified for any particular study's analysis pipeline.

www.bridge-lab.org
www.bridgelab.info

Docker Setup

Step 1: Install Docker

• macOS / Windows: Download Docker Desktop
• Linux: Install Docker Engine via your package manager (apt, yum, etc.)

Step 2: Check Installation

• Verify installation by running:

docker --version

Freesurfer 6.0 Docker Container

Step 1: Download Freesurfer Docker Package

svn checkout https://github.com/ryn-thorn/Image_Analysis_Scripts/trunk/Preprocessing/freesurfer-6.0-docker

cd /path/to/freesurfer-6.0-docker
docker build -t freesurfer:6.0 .