flywheel/mri-deface repository overview

⁠flywheel/mri-deface

Build context for a Flywheel Gear⁠ which runs the MBIRN mri_deface tool⁠ (v1.22) from FreeSurfer.

• No other FreeSurfer tools are installed within this Docker image
• Unlike the full FreeSurfer software, a license file is not necessary to use this tool
• The resulting image is ~0.5GB

⁠Build the Image

To build the image:

git clone https://github.com/flywheel-apps/mri-deface
cd mri-deface
docker build -t flywheel/mri-deface .

⁠Example Local Usage

To run the mri_deface Gear your local instance with Docker, do the following:

docker run --rm -ti \
  -v </path/to/input/data>:/flywheel/v0/input/anatomical \
  -v </path/for/output/data>:/flywheel/v0/output \
  flywheel/mri-deface

Usage notes:

• You are mounting the directory (using the -v flag) which contains the input data in the container at /flywheel/v0/input/anatomical and mounting the directory where you want your output data within the container at /flywheel/v0/output
• The "input" directory (mounted within the container at /flywheel/v0/input/anatomical) should contain only the file you wish to 'deface'
• Only the first file found in the input directory will be run through the algorithm
• No input arguments are required for the container to be executed