vistalab/bet repository overview

⁠vistalab/bet

This dockerfile will create a FSL (v5.0) docker image that executes bet2

⁠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/fsl/bet
./build.sh

⁠Example Usage

To run bet2 from this image you can do the following:

docker run --rm -ti \
    -v </path/to/input/data>:/input \
    -v </path/to/output>:/output \
    vistalab/bet /input/<t1_file.nii.gz> /output/bet2_

• Note that the directory mounted at "/output" must be EMPTY for the algorithm to run.
• 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. You may wish to mount a single diretory and use it for both input and output.
• Note that the ENTRYPOINT is configured to be bet2, thus only the input arguments need be specified.