This includes everything required to build a docker and corresponding singularity container to perform a minimal FreeSurfer T1 intensity normalization.
For docker:
sudo docker run --rm \
-v $(pwd)/INPUTS/:/INPUTS/ \
-v $(pwd)/OUTPUTS:/OUTPUTS/ \
-v <path to license.txt>:/extra/freesurfer/license.txt \
--user $(id -u):$(id -g) \
justinblaber/t1_normalization
For singularity:
singularity run -e \
-B INPUTS/:/INPUTS \
-B OUTPUTS/:/OUTPUTS \
-B <path to license.txt>:/extra/freesurfer/license.txt \
shub://justinblaber/t1_normalization_app