def mask_parcellation(mask_images, nb_parcel, threshold=0, output_image=None):
""" Performs the parcellation of a certain mask
Parameters
----------
mask_images: string or Nifti1Image or list of strings/Nifti1Images,
paths of mask image(s) that define(s) the common space.
nb_parcel: int,
number of desired parcels
threshold: float, optional,
level of intersection of the masks
output_image: string, optional
path of the output image
Returns
-------
wim: Nifti1Imagine instance, representing the resulting parcellation
"""
if isinstance(mask_images, basestring):
mask = mask_images
elif isinstance(mask_images, Nifti1Image):
mask = mask_images
else:
# mask_images should be a list
mask_data = intersect_masks(mask_images, threshold=0) > 0
mask = Nifti1Image(mask_data.astype('u8'),
load(mask_images[0]).get_affine())
domain = grid_domain_from_image(mask)
cent, labels, J = kmeans(domain.coord, nb_parcel)
sub_dom = SubDomains(domain, labels)
# get id (or labels) image
wim = sub_dom.to_image(fid='id', roi=True)
return wim
def mask_parcellation(mask_images, nb_parcel, threshold=0, output_image=None):
""" Performs the parcellation of a certain mask
Parameters
----------
mask_images: string or Nifti1Image or list of strings/Nifti1Images,
paths of mask image(s) that define(s) the common space.
nb_parcel: int,
number of desired parcels
threshold: float, optional,
level of intersection of the masks
output_image: string, optional
path of the output image
Returns
-------
wim: Nifti1Imagine instance, representing the resulting parcellation
"""
if isinstance(mask_images, basestring):
mask = mask_images
elif isinstance(mask_images, Nifti1Image):
mask = mask_images
else:
# mask_images should be a list
mask_data = intersect_masks(mask_images, threshold=0) > 0
mask = Nifti1Image(mask_data.astype('u8'),
get_affine(load(mask_images[0])))
domain = grid_domain_from_image(mask)
cent, labels, J = kmeans(domain.coord, nb_parcel)
sub_dom = SubDomains(domain, labels)
# get id (or labels) image
wim = sub_dom.to_image(fid='id', roi=True)
return wim
def fixed_parcellation(mask_image, betas, nbparcel, nn=6, method='ward',
write_dir=None, mu=10., verbose=0, fullpath=None):
""" Fixed parcellation of a given dataset
Parameters
----------
domain/mask_image
betas: list of paths to activation images from the subject
nbparcel, int : number fo desired parcels
nn=6: number of nearest neighbors to define the image topology
(6, 18 or 26)
method='ward': clustering method used, to be chosen among
'ward', 'gkm', 'ward_and-gkm'
'ward': Ward's clustering algorithm
'gkm': Geodesic k-means algorithm, random initialization
'gkm_and_ward': idem, initialized by Ward's clustering
write_di: string, topional, write directory.
If fullpath is None too, then no file output.
mu = 10., float: the relative weight of anatomical information
verbose=0: verbosity mode
fullpath=None, string,
path of the output image
If write_dir and fullpath are None then no file output.
If only fullpath is None then it is the write dir + a name
depending on the method.
Notes
-----
Ward's method takes time (about 6 minutes for a 60K voxels dataset)
Geodesic k-means is 'quick and dirty'
Ward's + GKM is expensive but quite good
To reduce CPU time, rather use nn=6 (especially with Ward)
"""
from nipy.algorithms.graph.field import field_from_coo_matrix_and_data
if method not in ['ward', 'gkm', 'ward_and_gkm', 'kmeans']:
raise ValueError('unknown method')
if nn not in [6, 18, 26]:
raise ValueError('nn should be 6,18 or 26')
# step 1: load the data ----------------------------
# 1.1 the domain
domain = grid_domain_from_image(mask_image, nn)
if method is not 'kmeans':
# 1.2 get the main cc of the graph
# to remove the small connected components
pass
coord = domain.coord
# 1.3 read the functional data
beta = np.array([domain.make_feature_from_image(b) for b in betas])
if len(beta.shape) > 2:
beta = np.squeeze(beta)
if beta.shape[0] != domain.size:
beta = beta.T
feature = np.hstack((beta, mu * coord / np.std(coord)))
#step 2: parcellate the data ---------------------------
if method is not 'kmeans':
g = field_from_coo_matrix_and_data(domain.topology, feature)
if method == 'kmeans':
_, u, _ = kmeans(feature, nbparcel)
if method == 'ward':
u, _ = g.ward(nbparcel)
if method == 'gkm':
seeds = np.argsort(np.random.rand(g.V))[:nbparcel]
_, u, _ = g.geodesic_kmeans(seeds)
if method == 'ward_and_gkm':
w, _ = g.ward(nbparcel)
_, u, _ = g.geodesic_kmeans(label=w)
lpa = SubDomains(domain, u)
if verbose:
var_beta = np.array(
[np.var(beta[lpa.label == k], 0).sum() for k in range(lpa.k)])
var_coord = np.array(
[np.var(coord[lpa.label == k], 0).sum() for k in range(lpa.k)])
size = lpa.get_size()
vf = np.dot(var_beta, size) / size.sum()
va = np.dot(var_coord, size) / size.sum()
print nbparcel, "functional variance", vf, "anatomical variance", va
# step3: write the resulting label image
if fullpath is not None:
label_image = fullpath
elif write_dir is not None:
label_image = os.path.join(write_dir, "parcel_%s.nii" % method)
else:
label_image = None
if label_image is not None:
lpa_img = lpa.to_image(
fid='id', roi=True, descrip='Intra-subject parcellation image')
save(lpa_img, label_image)
if verbose:
print "Wrote the parcellation images as %s" % label_image
return lpa
def _optim_hparcel(feature, domain, graphs, nb_parcel, lamb=1., dmax=10.,
niter=5, initial_mask=None, chunksize=1.e5, verbose=0):
""" Core function of the heirrachical parcellation procedure.
Parameters
----------
feature: list of subject-related feature arrays
Pa : parcellation instance that is updated
graphs: graph that represents the topology of the parcellation
anat_coord: array of shape (nvox,3) space defining set of coordinates
nb_parcel: int
the number of desrired parcels
lamb=1.0: parameter to weight position
and feature impact on the algorithm
dmax = 10: locality parameter (in the space of anat_coord)
to limit surch volume (CPU save)
chunksize = int, optional
niter = 5: number of iterations in the algorithm
verbose=0: verbosity level
Returns
-------
U: list of arrays of length nsubj
subject-dependent parcellations
Proto_anat: array of shape (nvox) labelling of the common space
(template parcellation)
"""
nb_subj = len(feature)
# a1. perform a rough clustering of the data to make prototype
indiv_coord = np.array([domain.coord[initial_mask[:, s] > - 1]
for s in range(nb_subj)])
reduced_anat, reduced_feature = _reduce_and_concatenate(
indiv_coord, feature, chunksize)
_, labs, _ = kmeans(reduced_feature, nb_parcel, Labels=None, maxiter=10)
proto_anat = [np.mean(reduced_anat[labs == k], 0)
for k in range(nb_parcel)]
proto_anat = np.array(proto_anat)
proto = [np.mean(reduced_feature[labs == k], 0) for k in range(nb_parcel)]
proto = np.array(proto)
# a2. topological model of the parcellation
# group-level part
spatial_proto = Field(nb_parcel)
spatial_proto.set_field(proto_anat)
spatial_proto.voronoi_diagram(proto_anat, domain.coord)
spatial_proto.set_gaussian(proto_anat)
spatial_proto.normalize()
for git in range(niter):
LP = []
LPA = []
U = []
Energy = 0
for s in range(nb_subj):
# b.subject-specific instances of the model
# b.0 subject-specific information
Fs = feature[s]
lac = indiv_coord[s]
target = proto_anat.copy()
lseeds = np.zeros(nb_parcel, np.int)
aux = np.argsort(rand(nb_parcel))
toto = np.zeros(lac.shape[0])
for j in range(nb_parcel):
# b.1 speed-up :only take a small ball
i = aux[j]
dx = lac - target[i]
iz = np.nonzero(np.sum(dx ** 2, 1) < dmax ** 2)
iz = np.reshape(iz, np.size(iz))
if np.size(iz) == 0:
iz = np.array([np.argmin(np.sum(dx ** 2, 1))])
# b.2: anatomical constraints
lanat = np.reshape(lac[iz], (np.size(iz),
domain.coord.shape[1]))
pot = np.zeros(np.size(iz))
JM, rmin = _exclusion_map(i, spatial_proto, target, lanat)
pot[JM < 0] = np.inf
pot[JM >= 0] = - JM[JM >= 0]
# b.3: add feature discrepancy
df = Fs[iz] - proto[i]
df = np.reshape(df, (np.size(iz), proto.shape[1]))
pot += lamb * np.sum(df ** 2, 1)
# b.4: solution
if np.sum(np.isinf(pot)) == np.size(pot):
pot = np.sum(dx[iz] ** 2, 1)
sol = iz[np.argmin(pot)]
target[i] = lac[sol]
lseeds[i] = sol
toto[sol] = 1
if verbose > 1:
jm = _field_gradient_jac(spatial_proto, target)
print jm.min(), jm.max(), np.sum(toto > 0)
# c.subject-specific parcellation
g = graphs[s]
f = Field(g.V, g.edges, g.weights, Fs)
U.append(f.constrained_voronoi(lseeds))
Energy += np.sum((Fs - proto[U[-1]]) ** 2) / \
np.sum(initial_mask[:, s] > - 1)
# recompute the prototypes
# (average in subject s)
lproto = [np.mean(Fs[U[-1] == k], 0) for k in range(nb_parcel)]
lproto = np.array(lproto)
lproto_anat = np.array([np.mean(lac[U[-1] == k], 0)
for k in range(nb_parcel)])
LP.append(lproto)
LPA.append(lproto_anat)
# recompute the prototypes across subjects
proto_mem = proto.copy()
proto = np.mean(np.array(LP), 0)
proto_anat = np.mean(np.array(LPA), 0)
displ = np.sqrt(np.sum((proto_mem - proto) ** 2, 1).max())
if verbose:
print 'energy', Energy, 'displacement', displ
# recompute the topological model
spatial_proto.set_field(proto_anat)
spatial_proto.voronoi_diagram(proto_anat, domain.coord)
spatial_proto.set_gaussian(proto_anat)
spatial_proto.normalize()
if displ < 1.e-4 * dmax:
break
return U, proto_anat
def fixed_parcellation(mask_image, betas, nbparcel, nn=6, method='ward',
write_dir=None, mu=10., verbose=0, fullpath=None):
""" Fixed parcellation of a given dataset
Parameters
----------
domain/mask_image
betas: list of paths to activation images from the subject
nbparcel, int : number fo desired parcels
nn=6: number of nearest neighbors to define the image topology
(6, 18 or 26)
method='ward': clustering method used, to be chosen among
'ward', 'gkm', 'ward_and-gkm'
'ward': Ward's clustering algorithm
'gkm': Geodesic k-means algorithm, random initialization
'gkm_and_ward': idem, initialized by Ward's clustering
write_di: string, topional, write directory.
If fullpath is None too, then no file output.
mu = 10., float: the relative weight of anatomical information
verbose=0: verbosity mode
fullpath=None, string,
path of the output image
If write_dir and fullpath are None then no file output.
If only fullpath is None then it is the write dir + a name
depending on the method.
Notes
-----
Ward's method takes time (about 6 minutes for a 60K voxels dataset)
Geodesic k-means is 'quick and dirty'
Ward's + GKM is expensive but quite good
To reduce CPU time, rather use nn=6 (especially with Ward)
"""
from nipy.algorithms.graph.field import field_from_coo_matrix_and_data
if method not in ['ward', 'gkm', 'ward_and_gkm', 'kmeans']:
raise ValueError('unknown method')
if nn not in [6, 18, 26]:
raise ValueError('nn should be 6,18 or 26')
# step 1: load the data ----------------------------
# 1.1 the domain
domain = grid_domain_from_image(mask_image, nn)
if method is not 'kmeans':
# 1.2 get the main cc of the graph
# to remove the small connected components
pass
coord = domain.coord
# 1.3 read the functional data
beta = np.array([domain.make_feature_from_image(b) for b in betas])
if len(beta.shape) > 2:
beta = np.squeeze(beta)
if beta.shape[0] != domain.size:
beta = beta.T
feature = np.hstack((beta, mu * coord / np.std(coord)))
#step 2: parcellate the data ---------------------------
if method is not 'kmeans':
g = field_from_coo_matrix_and_data(domain.topology, feature)
if method == 'kmeans':
_, u, _ = kmeans(feature, nbparcel)
if method == 'ward':
u, _ = g.ward(nbparcel)
if method == 'gkm':
seeds = np.argsort(np.random.rand(g.V))[:nbparcel]
_, u, _ = g.geodesic_kmeans(seeds)
if method == 'ward_and_gkm':
w, _ = g.ward(nbparcel)
_, u, _ = g.geodesic_kmeans(label=w)
lpa = SubDomains(domain, u)
if verbose:
var_beta = np.array(
[np.var(beta[lpa.label == k], 0).sum() for k in range(lpa.k)])
var_coord = np.array(
[np.var(coord[lpa.label == k], 0).sum() for k in range(lpa.k)])
size = lpa.get_size()
vf = np.dot(var_beta, size) / size.sum()
va = np.dot(var_coord, size) / size.sum()
print nbparcel, "functional variance", vf, "anatomical variance", va
# step3: write the resulting label image
if fullpath is not None:
label_image = fullpath
elif write_dir is not None:
label_image = os.path.join(write_dir, "parcel_%s.nii" % method)
else:
label_image = None
if label_image is not None:
lpa_img = lpa.to_image(
fid='id', roi=True, descrip='Intra-subject parcellation image')
save(lpa_img, label_image)
if verbose:
print "Wrote the parcellation images as %s" % label_image
return lpa
def _optim_hparcel(feature,
domain,
graphs,
nb_parcel,
lamb=1.,
dmax=10.,
niter=5,
initial_mask=None,
chunksize=1.e5,
verbose=0):
""" Core function of the heirrachical parcellation procedure.
Parameters
----------
feature: list of subject-related feature arrays
Pa : parcellation instance that is updated
graphs: graph that represents the topology of the parcellation
anat_coord: array of shape (nvox,3) space defining set of coordinates
nb_parcel: int
the number of desrired parcels
lamb=1.0: parameter to weight position
and feature impact on the algorithm
dmax = 10: locality parameter (in the space of anat_coord)
to limit surch volume (CPU save)
chunksize = int, optional
niter = 5: number of iterations in the algorithm
verbose=0: verbosity level
Returns
-------
U: list of arrays of length nsubj
subject-dependent parcellations
Proto_anat: array of shape (nvox) labelling of the common space
(template parcellation)
"""
nb_subj = len(feature)
# a1. perform a rough clustering of the data to make prototype
indiv_coord = np.array(
[domain.coord[initial_mask[:, s] > -1] for s in range(nb_subj)])
reduced_anat, reduced_feature = _reduce_and_concatenate(
indiv_coord, feature, chunksize)
_, labs, _ = kmeans(reduced_feature, nb_parcel, Labels=None, maxiter=10)
proto_anat = [
np.mean(reduced_anat[labs == k], 0) for k in range(nb_parcel)
]
proto_anat = np.array(proto_anat)
proto = [np.mean(reduced_feature[labs == k], 0) for k in range(nb_parcel)]
proto = np.array(proto)
# a2. topological model of the parcellation
# group-level part
spatial_proto = Field(nb_parcel)
spatial_proto.set_field(proto_anat)
spatial_proto.voronoi_diagram(proto_anat, domain.coord)
spatial_proto.set_gaussian(proto_anat)
spatial_proto.normalize()
for git in range(niter):
LP = []
LPA = []
U = []
Energy = 0
for s in range(nb_subj):
# b.subject-specific instances of the model
# b.0 subject-specific information
Fs = feature[s]
lac = indiv_coord[s]
target = proto_anat.copy()
lseeds = np.zeros(nb_parcel, np.int)
aux = np.argsort(rand(nb_parcel))
toto = np.zeros(lac.shape[0])
for j in range(nb_parcel):
# b.1 speed-up :only take a small ball
i = aux[j]
dx = lac - target[i]
iz = np.nonzero(np.sum(dx**2, 1) < dmax**2)
iz = np.reshape(iz, np.size(iz))
if np.size(iz) == 0:
iz = np.array([np.argmin(np.sum(dx**2, 1))])
# b.2: anatomical constraints
lanat = np.reshape(lac[iz],
(np.size(iz), domain.coord.shape[1]))
pot = np.zeros(np.size(iz))
JM, rmin = _exclusion_map(i, spatial_proto, target, lanat)
pot[JM < 0] = np.inf
pot[JM >= 0] = -JM[JM >= 0]
# b.3: add feature discrepancy
df = Fs[iz] - proto[i]
df = np.reshape(df, (np.size(iz), proto.shape[1]))
pot += lamb * np.sum(df**2, 1)
# b.4: solution
if np.sum(np.isinf(pot)) == np.size(pot):
pot = np.sum(dx[iz]**2, 1)
sol = iz[np.argmin(pot)]
target[i] = lac[sol]
lseeds[i] = sol
toto[sol] = 1
if verbose > 1:
jm = _field_gradient_jac(spatial_proto, target)
print jm.min(), jm.max(), np.sum(toto > 0)
# c.subject-specific parcellation
g = graphs[s]
f = Field(g.V, g.edges, g.weights, Fs)
U.append(f.constrained_voronoi(lseeds))
Energy += np.sum((Fs - proto[U[-1]]) ** 2) / \
np.sum(initial_mask[:, s] > - 1)
# recompute the prototypes
# (average in subject s)
lproto = [np.mean(Fs[U[-1] == k], 0) for k in range(nb_parcel)]
lproto = np.array(lproto)
lproto_anat = np.array(
[np.mean(lac[U[-1] == k], 0) for k in range(nb_parcel)])
LP.append(lproto)
LPA.append(lproto_anat)
# recompute the prototypes across subjects
proto_mem = proto.copy()
proto = np.mean(np.array(LP), 0)
proto_anat = np.mean(np.array(LPA), 0)
displ = np.sqrt(np.sum((proto_mem - proto)**2, 1).max())
if verbose:
print 'energy', Energy, 'displacement', displ
# recompute the topological model
spatial_proto.set_field(proto_anat)
spatial_proto.voronoi_diagram(proto_anat, domain.coord)
spatial_proto.set_gaussian(proto_anat)
spatial_proto.normalize()
if displ < 1.e-4 * dmax:
break
return U, proto_anat