- You MUST read and agree to the license agreement and register with MGH before you use the software.
- Once you get your license you can edit the
manifest.jsonfile to include your license details before you build the container. Without a license the execution of the code will fail.
- This image is built with the Matlab MCRv80 included. The MCR is required to run the optional Hippocampal Subfields and Brainstem Structures processing (see
- The resulting image is ~12GB and builds in ~15min.
Configuration for running the algorithm (and adding the license) are defined within
manifest.json. The options available, along with their defaults, are described in the
If you would like to use specific options in a local run of this gear you can modify the
default key for each option, which will be used during the local run - executed when executed with Docker.
Example Local Usage
This Gear is designed to run within Flywheel, however you can run this Gear locally. To run
recon-all from this image you can do the following:
# Note that the `recon-all` command is omitted as it is called from the `Entrypoint`. docker run --rm -ti \ -v </path/to/input/data>:/input/flywheel/v0/input/anatomical \ -v </path/for/output/data>:/output \ scitran/freesurfer-recon-all:<version-tag>
- You must mount the directory (using the
-vflag) which contains your anatomical data (nifti or dicoms) in the container at
/input/flywheel/v0/input/anatomicaland also mount the directory where you want your output data stored at
/output, see the example above.
- Configuration options (including the license key) must be set in the
manifest.jsonfile before building the container.