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,…

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.