Yes, thought so the docker container is isolated.
Well, sourcing fsl.sh in docker like you suggest, and then start the segment pipeline works. However, there seems to be non-correct usage description in the scripts/segmentation/pipeline.sh, since it should take more arguments. I can successfully run the segmentation step as:
$ docker run --rm -t -u $(id -u):$(id -g) -v $PWD:/data --entrypoint /bin/bash biomedia/dhcp-structural-pipeline:latest -c ". /etc/fsl/fsl.sh && /usr/src/structural-pipeline/scripts/segmentation/pipeline.sh 3dt2_bias_in_meanb0.nii.gz pk323-mri 40 -t 1