tasks.txt

0: Construct object
    input:
        voxel_coordinates.json
    output:
        Contacts object

1: Calculate transformations
    input:
        Contacts
        coregistration information
    output:
        Contacts.fs_mm
-- Surface (non-critical) --
2: Dykstra
    input:
        voxel_coordinates.json
        ['fs_mm']
        freesurfer pial surfaces
        get_pairs(voxel_coordinates) -> [['LAF1', 'LAF2'], ['LAF2', 'LAF3']]
    output:
        ['dyksra_mm']
        ['distance_from_vertex']
        ['displacement_from_original']
        ['average_deformation']
        ['anatomical_locations'] (dkt atlas)
-- Surface or depth --
3: Get atlas coordinates (for all atlases)
    inputs:
        ['dykstra_mm'] (surface)
        segmentations
    output:
        ['anatomical_locations'] (whole-brain, mtl, mni)
        Spheres for each modality
        ['dykstra_mm_native']

** SAVE 2 FILES:
- complete set of information
- contacts.json/pairs.json

-- Automated pipeline stop here --
4a: Build manual localization file (making excel file)
4b: Joel's localization
    inputs: 
         complete dictionary
         csv file (from excel)
    outputs:
        ['stein_localization'] ('comments', 'loc_tag')