Merge remote-tracking branch 'origin/master'

Author: akeshavan

README.md

@@ -27,16 +27,18 @@ To pull the docker image from Docker Hub, do
 docker pull bids/mindboggle
 ```
 
-To run the docker, do
+To run the docker, do:
 
 ```
- docker run -ti -v /path/to/bids_dir:/root/data bids/mindboggle /root/input /root/output/ participant
+docker run -ti -v $PWD/ds114_test1:/home/jovyan/work/data bids/mindboggle /home/jovyan/work/data /home/jovyan/work/data/derivatives/ participant
 ```
 
+Its important to mount to a directory in `/home/jovyan/` because you are not root in this Docker image.
+
 To use bash:
 
 ```
- docker run -ti -v /Users/keshavan/Downloads/mindboggle_input_example/bids:/root/data --entrypoint /bin/bash bids/mindboggle 
+ docker run -ti -v /Users/keshavan/Downloads/mindboggle_input_example/bids:/home/jovyan/work/data --entrypoint /bin/bash bids/mindboggle 
 ```
 
 For developers, you can make changes to the Dockerfile, and build the docker image, by running