def test_find_parcel_centroids(cammoun_surf, scale, parcels, n_right, method):
lh, rh = cammoun_surf[scale]
coords, hemi = freesurfer.find_parcel_centroids(lhannot=lh, rhannot=rh,
method=method,
version='fsaverage5')
assert len(coords) == parcels
assert len(hemi) == parcels
assert np.sum(hemi) == n_right
def hungarian(y, parcellation, scale, fn=None):
y = np.asarray(y)
if USE_CACHED and fn is not None:
spins = simnulls.load_spins(fn, n_perm=N_PERM)
else:
annot = _get_annot(parcellation, scale)
coords, hemi = nnsurf.find_parcel_centroids(lhannot=annot.lh,
rhannot=annot.rh,
version='fsaverage5',
surf='sphere',
method='surface')
spins = nnstats.gen_spinsamples(coords, hemi, method='hungarian',
n_rotate=N_PERM, seed=SEED)
return y[spins]
def vazquez_rodriguez(y, parcellation, scale, fn=None):
y = np.asarray(y)
if USE_CACHED and fn is not None:
spins = simnulls.load_spins(fn, n_perm=N_PERM)
else:
if parcellation != 'vertex':
annot = _get_annot(parcellation, scale)
coords, hemi = nnsurf.find_parcel_centroids(lhannot=annot.lh,
rhannot=annot.rh,
version='fsaverage5',
surf='sphere',
method='surface')
else:
coords, hemi = nnsurf._get_fsaverage_coords(scale, 'sphere')
spins = nnstats.gen_spinsamples(coords, hemi, method='original',
n_rotate=N_PERM, seed=SEED)
return y[spins]
def generate_spins(parcel, lhannot, rhannot, order, info_path, hemi='',
k=10000):
'''
Function to generate spun permutation of a parcellation's parcels.
'''
# Generate the spins
coords, hemi_centroids = find_parcel_centroids(lhannot=lhannot,
rhannot=rhannot)
spins_LR = gen_spinsamples(coords, hemi_centroids, n_rotate=k)
# Get some info about hemispheres and subcortex
hemi_info = load_data._load_hemi_info(parcel, info_path)
sub_info = load_data._load_subcortex_info(parcel, info_path)
# Remove subcortex info from hemi_info (spins are only on the surface)
hemi_info = np.delete(hemi_info, sub_info)
R_id = np.where(hemi_info == 0)[0]
L_id = np.where(hemi_info == 1)[0]
n_R = len(R_id)
n_L = len(L_id)
# If order is RL, we must invert the order of the spun annotations
if order == 'RL':
spins = np.zeros((spins_LR.shape))
spins[R_id, :] = (spins_LR[np.where(hemi_centroids == 1)[0], :] - n_L)
spins[L_id, :] = (spins_LR[np.where(hemi_centroids == 0)[0], :] + n_R)
elif order == 'LR':
spins = spins_LR
# Only keep the information about the hemisphere we want
if hemi == "L":
if order == 'RL':
spins = spins[np.where(hemi_info == 1)[0], :] - n_R
elif order == 'LR':
spins = spins[np.where(hemi_info == 1)[0], :]
elif hemi == 'R':
if order == 'RL':
spins = spins[np.where(hemi_info == 0)[0], :]
elif order == 'LR':
spins = spins[np.where(hemi_info == 1)[0], :] - n_L
spins = spins.astype(int)
return spins
def generate_dist(annot):
"""
Parameters
----------
annot : (2,) namedtuple
With entries ('lh', 'rh') corresponding to annotation files for
specified hemisphere for `fsaverage5` resolution
Returns
-------
dist : (90, 90) np.ndarray
Distance matrix for resamplings from different null frameworks and
parcel centroid definition methods
"""
# generate spins for all the parcel-based rotation methods using
# three different methods for generating parcel centroid estimates
orig_spins, vasa_spins, hung_spins = [], [], []
for sptype, spins in zip(['original', 'vasa', 'hungarian'],
[orig_spins, vasa_spins, hung_spins]):
for method in ['average', 'surface', 'geodesic']:
# get parcel centroids using specified centroid method
coords, hemi = nnsurf.find_parcel_centroids(lhannot=annot.lh,
rhannot=annot.rh,
version='fsaverage5',
method=method)
# generate 10 spin resamples for specified spin method
out = nnstats.gen_spinsamples(coords,
hemi,
n_rotate=10,
method=sptype,
seed=1234)
spins.append(out)
# stack and transpose for easy distance calculation
all_spins = np.row_stack(
(np.column_stack(orig_spins).T, np.column_stack(vasa_spins).T,
np.column_stack(hung_spins).T))
all_dist = cdist(all_spins, all_spins, metric='hamming')
return all_dist
print('Generating naive permutations for fsaverage5 surface')
rs = np.random.default_rng(1234)
spins = np.column_stack([
rs.permutation(len(coords)) for f in range(10000)
])
putils.save_dir(fname, spins)
# now pre-generate the parcellation spins for five methods. we can't
# pre-generate the project-reduce-average method because that relies on the
# data itself, but we _can_ use the above vertex-level spins for that
for name, annotations in parcellations.items():
print(f'PARCELLATION: {name}')
for scale, annot in annotations.items():
coords, hemi = nnsurf.find_parcel_centroids(lhannot=annot.lh,
rhannot=annot.rh,
version='fsaverage5',
surf='sphere',
method='surface')
spin_fn = f'{scale}_spins.csv'
fname = SPINDIR / name / 'vazquez-rodriguez' / spin_fn
if not fname.exists():
print(f'Generating V-R spins for {scale}')
spins = nnstats.gen_spinsamples(coords, hemi, exact=False,
n_rotate=10000, verbose=True,
check_duplicates=False,
seed=1234)
putils.save_dir(fname, spins)
fname = SPINDIR / name / 'vasa' / spin_fn
if not fname.exists():