Update README file about iusm-connpipe

[echumin]

Some points to update:

• in the code main_conn_pipeline.sh is named sample_main.sh, need to make names consistent between code and documentation.
• Should clarify things like 'module' in the readme are specific to the IU supercomputing system and are not general instructions.
• is pip install dipy --user necessary? the text only describes two packages that are needed.
• maybe add the clarification that the config script must be pointed to in the main script if it is copied elsewhere and/or renamed.
• Add a clarification that main.sh must have executable permissions (which can go away if the file is copied elsewhere).
• Clearly state that the main script must stay in and be executed from the pipeline directory. The config file I think can be moved as long as its accurately pointed to in the main (line47) script.

[echumin]

README will be redone as the bidsywork branch becomes master.