Update the use of Paths in files

Change to ensure that paths are both:

1. stored in a OS agnostic way 
2. relative

As well, in this release, inplane and functional files are now copied into standard directories in the session path. These files will become Inplane/InplaneNifti.nii.gz and Inplane/Original/TSeries/TSeriesScan{1}.nii.gz

These changes will be reflected in session that are initialized from now on.