alerokhin/freesurfer6 repository overview

⁠FreeSurfer v6.0 Docker image

This is a minimal FreeSurver image that can perform full recon-all computation.

⁠Requirements

License should be acquired in order to make the tool operational. For more information please see: FreeSurfer License⁠. Store acquired license file in a dedicated folder on your local machine (in examples /home/user/license folder is specified).

⁠Usage

⁠Pull the latest image from the hub

docker pull alerokhin/freesurfer6

⁠Start in interactive mode

Note the -v option mounting license file folder to /usr/local/freesurfer/license inside a container

docker run -it -v "/home/user/license":"/usr/local/freesurfer/license" alerokhin/freesurfer6 bash

Most likely you'd need to mount more than one volume in order to supply input data and get output data to the host. For example:

docker run -it -v "/home/user/sources":"/usr/local/freesurfer/sources" -v \
 "/home/user/freesurfer/license":"/usr/local/freesurfer/license" alerokhin/freesurfer6 bash

⁠Limitations

The main goal of this image was to make FreeSurfer distribution as small as possible keeping full functionality of recon-all script.

If you are experiencing some issues please send your feedback to: [email protected]⁠ .