This adds a dockerfile based on the dev setup listed here
I'm not sure your familiarity with Docker, but here are the commands to build and get a shell inside the environment.
Change into a local copy of the freesurfer repo, and checkout the correct branch, then run docker build:
cd /path/to/freesurfer
git checkout nf-gems2-python-port
docker build -t python-samseg .
Mount directories containing data to process and the SAMSEG_DATA_DIR (note that the mount path for the SAMSEG_DATA_DIR must be /data/samseg_data, but the other data can be mounted wherever you want)
This adds a dockerfile based on the dev setup listed here
I'm not sure your familiarity with Docker, but here are the commands to build and get a shell inside the environment.
Change into a local copy of the
freesurfer
repo, and checkout the correct branch, then run docker build:Mount directories containing data to process and the
SAMSEG_DATA_DIR
(note that the mount path for theSAMSEG_DATA_DIR
must be/data/samseg_data
, but the other data can be mounted wherever you want)Inside the container, run this command to process subject
008
:(This is currently running now and seems to be working!)