vistalab/recon-all repository overview

⁠vistalab/recon-all

This dockerfile will create a Freesurfer (v5.3.0) docker image that executes recon-all and compresses the outputs.

• You MUST read and agree to the license agreement and register with MGH before you use the software⁠.
• Once you get your license please edit the license file to reflect your license.
• You can also change build.sh to edit the tag for the image (default=vistalab/recon-all).
• The resulting image is ~8GB

⁠Build the Image

To build the image, either download the files from this repo or clone the repo:

git clone https://github.com/vistalab/docker
cd docker/freesurfer/recon-all/
./build.sh

⁠Entrypoint

An 'Entrypoint' has been configured for this image at /opt/run, which will do the following:

1. Look for inputs and show help as necessary
2. Run recon-all using the inputs provided
3. Compress (using zip) all the outputs generated
4. Remove the uncompressed outputs

⁠Example Usage

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 \
    -v </path/for/output/data>:/ouput \
    vistalab/recon-all -i /input/<t1_file.nii.gz> -subjid <subjectID> -all

• Note that you are mounting the directory (-v flag) which contains your data in the container at /input and mounting the directory where you want your output data within the container at /output.

• recon-all args (relative to the contianer) should be provided at the end of the docker run command, as shown above. Remember that if those inputs are files or other resources, they must also be mounted in the container and the full path to them (again, relative to the container) must be provided.