Major revision: Add non-cortex labels; replace FreeSurfer gray matter fill; remove protocol directory; fix transforms, clean up nipype workflow and directory tree, improve documentation,…

Non-cortex labels:
Use ANTS to transform labels in MNI152 to subject space and combine with cortical label volume. Currently building a (BrainCOLOR protocol) noncortical atlas.

Replace FreeSurfer gray matter fill:
Previously, surface labels were converted from .vtk to .label to .annot before using mri_aparc2aseg. Now we use the PropagateLabelsThroughMask function within ImageMath in the ANTS package. Mindboggle calls this within fill_volume_with_surface_labels() after placing the .vtk labels/scalars in a volume with transform_to_volume().

Remove protocol directory:
We have consolidated the label protocol information originally stored as .txt files in the labels/protocol directory as lists in a new label/protocol.py file.

Fix transforms:
The FreeSurfer mri_vol2vol command was not putting ugh data in subject space as expected, so replaced with mri_convert -rl…

Clean up nipype pipeline:
In addition to removing some FreeSurfer dependencies, all nodes exist within a single workflow and there are fewer nodes in the workflow. For example, the volume_per_label() function was altered so that it would not have to be called twice to construct the label volumes table.

Author:    Arno Klein <arno@binarybottle.com>
Merge branch 'master' of github.com:binarybottle/mindboggle