def fallback_covariance(time_series):
from sklearn.ensemble import IsolationForest
from sklearn import covariance
# Remove gross outliers
model = IsolationForest(contamination=0.02)
model.fit(time_series)
outlier_mask = model.predict(time_series)
outlier_mask[outlier_mask == -1] = 0
time_series = time_series[outlier_mask.astype('bool')]
# Fall back to LedoitWolf
print('Matrix estimation failed with Lasso and shrinkage due to '
'ill conditions. Removing potential anomalies from the '
'time-series using IsolationForest...')
try:
print("Trying Ledoit-Wolf Estimator...")
conn_measure = ConnectivityMeasure(
cov_estimator=covariance.LedoitWolf(store_precision=True,
assume_centered=True),
kind=kind)
conn_matrix = conn_measure.fit_transform([time_series])[0]
except (np.linalg.linalg.LinAlgError, FloatingPointError):
print("Trying Oracle Approximating Shrinkage Estimator...")
conn_measure = ConnectivityMeasure(
cov_estimator=covariance.OAS(assume_centered=True), kind=kind)
try:
conn_matrix = conn_measure.fit_transform([time_series])[0]
except (np.linalg.linalg.LinAlgError, FloatingPointError):
raise ValueError('All covariance estimators failed to '
'converge...')
return conn_matrix
def precompute_flattened_fcm(subject_id=None):
""" Derives the correlation matrices for the parcellated timeseries data.
:param subject_id: subject ID if only one connectivity matrix needs to be precomputed
:return the flattened lower triangle of the correlation matrices for the parcellated timeseries data.
Saved as a binary numpy array with the name of patient ID in the preprocessed timeseries directory.
"""
conn_measure = ConnectivityMeasure(kind='correlation',
vectorize=True,
discard_diagonal=True)
suffix = '_ts_raw.txt'
if subject_id is not None:
print("Processing %s" % subject_id)
ts = np.loadtxt(os.path.join(data_timeseries, subject_id + suffix),
delimiter=',')
np.save(os.path.join(data_computed_fcms, subject_id),
conn_measure.fit_transform([np.transpose(ts)])[0])
else:
# Preompute all timeseries.
ts_filenames = [f for f in os.listdir(data_timeseries)]
suffix_length = len(suffix)
for ts_file in ts_filenames:
print("Processing %s" % ts_file)
ts = np.loadtxt(os.path.join(data_timeseries, ts_file),
delimiter=',')
np.save(os.path.join(data_computed_fcms, ts_file[:-suffix_length]),
conn_measure.fit_transform([np.transpose(ts)])[0])
def get_conn_matrix(time_series, conn_model, NETWORK, ID, dir_path, thr):
if conn_model == 'corr':
conn_measure = ConnectivityMeasure(kind='correlation')
conn_matrix = conn_measure.fit_transform([time_series])[0]
est_path = dir_path + '/' + ID + '_est_corr' + '_' + str(thr) + '.txt'
elif conn_model == 'corr_fast':
try:
conn_matrix = compute_correlation(time_series,time_series)
est_path = dir_path + '/' + ID + '_est_corr_fast' + '_' + str(thr) + '.txt'
except RuntimeError:
print('Cannot run accelerated correlation computation due to a missing dependency. You need brainiak installed!')
elif conn_model == 'partcorr':
conn_measure = ConnectivityMeasure(kind='partial correlation')
conn_matrix = conn_measure.fit_transform([time_series])[0]
est_path = dir_path + '/' + ID + '_est_part_corr' + '_' + str(thr) + '.txt'
elif conn_model == 'cov' or conn_model == 'sps':
##Fit estimator to matrix to get sparse matrix
estimator = GraphLassoCV()
try:
print("Fitting Lasso estimator...")
est = estimator.fit(time_series)
except RuntimeError:
print('Unstable Lasso estimation--Attempting to re-run by first applying shrinkage...')
#from sklearn.covariance import GraphLasso, empirical_covariance, shrunk_covariance
#emp_cov = empirical_covariance(time_series)
#for i in np.arange(0.8, 0.99, 0.01):
#shrunk_cov = shrunk_covariance(emp_cov, shrinkage=i)
#alphaRange = 10.0 ** np.arange(-8,0)
#for alpha in alphaRange:
#try:
#estimator_shrunk = GraphLasso(alpha)
#est=estimator_shrunk.fit(shrunk_cov)
#print("Calculated graph-lasso covariance matrix for alpha=%s"%alpha)
#break
#except FloatingPointError:
#print("Failed at alpha=%s"%alpha)
#if estimator_shrunk == None:
#pass
#else:
#break
print('Unstable Lasso estimation. Try again!')
sys.exit()
if NETWORK != None:
est_path = dir_path + '/' + ID + '_' + NETWORK + '_est%s'%('_sps_inv' if conn_model=='sps' else 'cov') + '_' + str(thr) + '.txt'
else:
est_path = dir_path + '/' + ID + '_est%s'%('_sps_inv' if conn_model=='sps' else 'cov') + '_' + str(thr) + '.txt'
if conn_model == 'sps':
try:
conn_matrix = -estimator.precision_
except:
conn_matrix = -estimator_shrunk.precision_
elif conn_model == 'cov':
try:
conn_matrix = estimator.covariance_
except:
conn_matrix = estimator_shrunk.covariance_
np.savetxt(est_path, conn_matrix, delimiter='\t')
return(conn_matrix, est_path)
def plot_connectome_mixture(data=None, index=None, metric="correlation", save_as=None, show=False, **kwargs):
# extract time series from all subjects and concatenate them
mm = data.X[index, :].copy()
time_series = [np.vstack(mm)]
# calculate correlation matrices across indexed frames in data
connectome_measure = ConnectivityMeasure(kind=metric)
connectome_measure.fit_transform(time_series)
connectivity = connectome_measure.mean_
np.fill_diagonal(connectivity, 0)
#connectivity[np.abs(connectivity) < 0.2] = 0.0
# grab center coordinates for atlas labels
atlas = kwargs.pop('atlas', data.atlas)
coords = plotting.find_parcellation_cut_coords(labels_img=atlas)
# assign node colors
cmap = kwargs.pop('cmap', 'jet')
node_cmap = plt.get_cmap('bone')
node_norm = mpl.colors.Normalize(vmin=-0.8, vmax=1.2)
node_colors = np.ravel([_[-1] for i,_ in enumerate(coords)])
node_colors = [_ / np.max(node_colors) for _ in node_colors]
node_colors = node_cmap(node_norm(node_colors))
# plot connectome matrix
fig = plt.figure(figsize=(12,5))
ax = plt.subplot2grid((1, 2), (0, 1), rowspan=1, colspan=1)
display = plotting.plot_matrix(
connectivity,
vmin=-.5, vmax=.5, colorbar=True, cmap=cmap,
axes=ax, #title='{} Matrix'.format(metric.title()),
)
# plot connectome with 99.7% edge strength in the connectivity
ax = plt.subplot2grid((1, 2), (0, 0), rowspan=1, colspan=1)
display = plotting.plot_connectome(
connectivity, coords,
edge_threshold="99.9%", display_mode='z',
node_color=node_colors, node_size=20, edge_kwargs=dict(lw=4),
edge_vmin=-.8, edge_vmax=.8, edge_cmap=cmap,
colorbar=False, black_bg=not True, alpha=0.5,
annotate=False,
axes=ax,
)
if show is True:
plt.show()
plt.subplots_adjust(left=0.05, right=0.95, bottom=0.05, top=0.95)
if save_as:
fig.savefig(save_as, transparent=True)#, facecolor='slategray', edgecolor='white')
plt.close(fig)
return display
def _run_interface(self, runtime):
fname = self.inputs.fmri_denoised
entities = parse_file_entities(fname)
bold_img = nb.load(fname)
parcellation_file = get_parcellation_file_path(entities['space'])
masker = NiftiLabelsMasker(labels_img=parcellation_file,
standardize=True)
time_series = masker.fit_transform(bold_img, confounds=None)
corr_measure = ConnectivityMeasure(kind='correlation')
corr_mat = corr_measure.fit_transform([time_series])[0]
entities['pipeline'] = extract_pipeline_from_path(fname)
conn_file = join(self.inputs.output_dir,
build_path(entities, self.conn_file_pattern, False))
carpet_plot_file = join(
self.inputs.output_dir,
build_path(entities, self.carpet_plot_pattern, False))
matrix_plot_file = join(
self.inputs.output_dir,
build_path(entities, self.matrix_plot_pattern, False))
make_carpetplot(time_series, carpet_plot_file)
mplot = plot_matrix(corr_mat, vmin=-1, vmax=1)
mplot.figure.savefig(matrix_plot_file)
np.save(conn_file, corr_mat)
self._results['corr_mat'] = conn_file
self._results['carpet_plot'] = carpet_plot_file
self._results['matrix_plot'] = matrix_plot_file
return runtime
def make_correlation_matrix(line, site, filename, bad_lst, good_lst):
seq_len = param.WINDOW_SIZE
time_series = []
good = bad = 0
n = len(line) - seq_len + 1
for j in range(n):
lst = []
for i in line[j:j + seq_len]:
lst.append(np.array(list(map(float, i.split()))))
time_series.append(np.array(lst))
correlation_measure = ConnectivityMeasure(kind='correlation')
correlation_matrix = correlation_measure.fit_transform(
[time_series[j]])[0]
fisher = np.arctanh(correlation_matrix)
np.fill_diagonal(fisher, 0)
# dd.io.save(folder + '/{}_correlation_matrix//{}_{}.h5'.format(site, filename, j), fisher)
# check whether there are lines all 0 in this subject
for i in range(num_region):
# column = correlation_matrix[i]
# tmp = column[i]
# np.delete(column, i)
# if np.all(column == 0) and tmp == 1:
if np.all(fisher[i] == 0):
bad += 1
bad_lst.append("{}".format(filename))
break
if i == (num_region - 1):
good += 1
good_lst.append("{}".format(filename))
def make_corr_matrix(ts_matrix):
"""
Make a symmetric pearson's r->z transforme correlation matrix.
Parameters
----------
ts_matrix : numpy.ndarray
2D numpy array with each column representing an atlas region
and each row representing a volume (time point)
Returns
-------
zcorr_matrix : numpy.ndarray
2D symmetric matrix measuring region-region correlations
main diagnal is all zeros
"""
from nilearn.connectome import ConnectivityMeasure
import numpy as np
def fisher_r_to_z(r):
import math
if r == 1.:
return 0.
else:
return math.log((1. + r) / (1. - r)) / 2.
correlation_measure = ConnectivityMeasure(kind='correlation')
corr_matrix = correlation_measure.fit_transform([ts_matrix])[0]
vfisher_r_to_z = np.vectorize(fisher_r_to_z)
# fisher's r to z
zcorr_matrix = vfisher_r_to_z(corr_matrix)
return zcorr_matrix
def postProcessing(nifti_file, subject_key, spheres_masker):
"""Perform post processing
param nifti_file: string. path to the nifty file
param subject_key: string. subject's key
return: dictionary raw.
key: subject's key .
value: {"time_series" : matrix of time series (time_points,rois), "covariance" : covariance matrix of atlas rois (rois, rois),
"correlation" : correlation matrix of atlas rois (rois, rois)}
"""
try:
print("subject_key: " + subject_key)
print("Extract timeseries")
# Extract the time series
print(nifti_file)
timeseries = spheres_masker.fit_transform(nifti_file, confounds=None)
print("Extract covariance matrix")
cov_measure = ConnectivityMeasure(cov_estimator=LedoitWolf(
assume_centered=False, block_size=1000, store_precision=False),
kind='covariance')
cov = []
cor = []
cov = cov_measure.fit_transform([timeseries])[0, :, :]
print("Extract correlation matrix")
cor = nilearn.connectome.cov_to_corr(cov)
except:
raise Exception("subject_key: %s \n" % subject_key +
traceback.format_exc())
return (subject_key, {
"time_series": timeseries,
"covariance": cov,
"correlation": cor
})
def CrossValidation(model, measure, y, skf, atalas):
from sklearn.metrics import make_scorer
from sklearn.metrics import accuracy_score, recall_score
import numpy as np
scoring = {
'accuracy': make_scorer(accuracy_score),
'sensitivity': make_scorer(recall_score),
'specificity': make_scorer(recall_score, pos_label=0)
}
from nilearn.connectome import ConnectivityMeasure
from nilearn.connectome import sym_matrix_to_vec
conn_est = ConnectivityMeasure(kind=measure)
conn_matrices = conn_est.fit_transform(atalas)
X = sym_matrix_to_vec(conn_matrices)
from sklearn.model_selection import cross_validate
scores = cross_validate(model,
X,
y,
cv=skf,
scoring=scoring,
return_train_score=True)
return [X, scores]
def _run_interface(self, runtime):
from nilearn import datasets
from nilearn.input_data import NiftiLabelsMasker
import numpy as np
dataset = datasets.fetch_atlas_harvard_oxford(
self.inputs.atlas_identifier)
atlas_filename = dataset.maps
masker = NiftiLabelsMasker(labels_img=atlas_filename,
standardize=True,
detrend=True,
low_pass=0.1,
high_pass=0.01,
t_r=self.inputs.tr,
memory='nilearn_cache',
verbose=0)
#file_labels = open('/home/brainlab/Desktop/Rudas/Data/Parcellation/AAL from Freesourfer/fs_default.txt', 'r')
#labels = []
#for line in file_labels.readlines():
#labels.append(line)
#file_labels.close()
time_series = masker.fit_transform(
self.inputs.in_file, confounds=self.inputs.confounds_file)
np.savetxt(self.inputs.time_series_out_file,
time_series,
fmt='%10.2f',
delimiter=',')
if self.inputs.plot:
from nilearn import plotting
from nilearn.connectome import ConnectivityMeasure
import matplotlib
import matplotlib.pyplot as plt
fig, ax = matplotlib.pyplot.subplots()
font = {'family': 'normal', 'size': 5}
matplotlib.rc('font', **font)
correlation_measure = ConnectivityMeasure(kind='correlation')
correlation_matrix = correlation_measure.fit_transform(
[time_series])[0]
# Mask the main diagonal for visualization:
np.fill_diagonal(correlation_matrix, 0)
plotting.plot_matrix(correlation_matrix,
figure=fig,
labels=dataset.labels[1:],
vmax=0.8,
vmin=-0.8,
reorder=True)
fig.savefig(self.inputs.correlation_matrix_out_file, dpi=1200)
return runtime
def connectivity_data():
"""Fixture for connectivity tests."""
base_dir = os.path.abspath(pkg_resources.resource_filename(
"pynets", "../data/examples"))
func_file = f"{base_dir}/BIDS/sub-25659/ses-1/func/" \
f"sub-25659_ses-1_task-rest_space-T1w_desc-preproc_bold.nii.gz"
mask_file = f"{base_dir}/BIDS/sub-25659/ses-1/func/" \
f"sub-25659_ses-1_task-rest_space-T1w_desc-preproc_" \
f"bold_mask.nii.gz"
parcellation = pkg_resources.resource_filename(
"pynets", "templates/atlases/DesikanKlein2012.nii.gz"
)
masker = NiftiLabelsMasker(
labels_img=nib.load(parcellation), background_label=0,
resampling_target="labels", dtype="auto",
mask_img=nib.load(mask_file), standardize=True)
time_series = masker.fit_transform(func_file)
conn_measure = ConnectivityMeasure(
kind="correlation")
conn_matrix = conn_measure.fit_transform([time_series])[0]
[coords, _, _, label_intensities] = \
get_names_and_coords_of_parcels(parcellation)
labels = ['ROI_' + str(idx) for idx, val in enumerate(label_intensities)]
yield {'time_series': time_series, 'conn_matrix': conn_matrix,
'labels': labels, 'coords': coords, 'indices': label_intensities}
def connectomes_from_time_windows(time_windows_dict, kind, roi_names):
print("\n\n===Compute Connectomes from Time Windows===")
print("Connectivity Type: %s" % kind)
# Initialize an empty dictionary to store connectome 3D Arrays
connectomes_dict = {}
# If Coherence, set the sampling interval, lower, and upper bounds of frequencies we are interested in.
# Then for each set of timewindows, compute coherence.
if kind == "coherence":
TR = .720
f_lb = 0.02
f_ub = 0.15
for timeseries_name, time_windows in time_windows_dict.items():
connectomes_dict[timeseries_name] = compute_coherence(
time_windows, TR, f_lb, f_ub, roi_names)
# If kind is not coherence, do regular Connectivity (i.e. correlation)
else:
connectivity = ConnectivityMeasure(kind=kind)
# For each scan's 3D array of time windows, compute their connectomes
for timeseries_name, time_windows in time_windows_dict.items():
connectomes_dict[timeseries_name] = connectivity.fit_transform(
time_windows)
return (connectomes_dict)
def _run_interface(self, runtime):
fname = self.inputs.fmri_denoised
bold_img = nb.load(fname)
masker = NiftiLabelsMasker(labels_img=self.inputs.parcellation,
standardize=True)
time_series = masker.fit_transform(bold_img, confounds=None)
corr_measure = ConnectivityMeasure(kind='correlation')
corr_mat = corr_measure.fit_transform([time_series])[0]
_, base, _ = split_filename(fname)
conn_file = f'{self.inputs.output_dir}/{base}_conn_mat.npy'
carpet_plot_file = join(self.inputs.output_dir,
f'{base}_carpet_plot.png')
matrix_plot_file = join(self.inputs.output_dir,
f'{base}_matrix_plot.png')
create_carpetplot(time_series, carpet_plot_file)
mplot = plot_matrix(corr_mat, vmin=-1, vmax=1)
mplot.figure.savefig(matrix_plot_file)
np.save(conn_file, corr_mat)
self._results['corr_mat'] = conn_file
self._results['carpet_plot'] = carpet_plot_file
self._results['matrix_plot'] = matrix_plot_file
return runtime
def plot_sliding_window(series, width, step):
'''
Plot a sliding-window graph
Parameters
----------
series: time-series, array , 3-D
width: window width
step: window step size, in samples. If not provided, window and step size are equal.
'''
from nilearn import plotting
import numpy as np
from nilearn.connectome import sym_matrix_to_vec
from nilearn.connectome import ConnectivityMeasure
cut = sliding_window_2d(series, width, step)
cut_matrix = np.zeros((cut.shape[0], cut.shape[2], cut.shape[2]))
correlation_measure = ConnectivityMeasure(kind='correlation')
for i in range(cut.shape[0]):
matrix = correlation_measure.fit_transform([cut[i]])[0]
cut_matrix[i, :, :] = matrix
vectors = np.zeros(
(cut_matrix.shape[0], sym_matrix_to_vec(cut_matrix[1]).shape[0]))
for i in range(cut_matrix.shape[0]):
vec = sym_matrix_to_vec(cut_matrix[i])
vectors[i, :] = vec
ax = np.corrcoef(vectors)
plotting.plot_matrix(ax, title="width={} step={}".format(width, step))
def compute_correlations(time_series, kind='partial correlation'):
correlation_measure = ConnectivityMeasure(kind=kind)
print("Fit-transforming time series...")
timer("tic")
correlation_matrices = correlation_measure.fit_transform(time_series)
timer("toc", name="fitting all time series")
return correlation_measure, correlation_matrices
def get_nilearn_adhd_data(n_subjects, nilearn_download_dir):
# Load the functional datasets
datasets.get_data_dirs(data_dir=nilearn_download_dir)
adhd_data = datasets.fetch_adhd(n_subjects=n_subjects,
data_dir=nilearn_download_dir)
msdl_data = datasets.fetch_atlas_msdl(data_dir=nilearn_download_dir)
masker = input_data.NiftiMapsMasker(msdl_data.maps,
resampling_target="data",
t_r=2.5,
detrend=True,
low_pass=.1,
high_pass=.01,
memory='nilearn_cache',
memory_level=1)
pooled_subjects = []
adhd_labels = [] # 1 if ADHD, 0 if control
age = []
for func_file, confound_file, phenotypic in zip(adhd_data.func,
adhd_data.confounds,
adhd_data.phenotypic):
time_series = masker.fit_transform(func_file, confounds=confound_file)
pooled_subjects.append(time_series)
adhd_labels.append(phenotypic['adhd'])
age.append(phenotypic['age'])
correlation_measure = ConnectivityMeasure(kind='correlation')
corr_mat = correlation_measure.fit_transform(pooled_subjects)
print('Correlations are stacked in an array of shape {0}'.format(
corr_mat.shape))
beh = np.zeros((n_subjects, 2))
beh[:, 0] = adhd_labels
beh[:, 1] = age
return corr_mat, beh
def plot_corr(time_series, labels):
'''
Parameters
----------
time_series : array
Time series of the signal in each region .
labels : list
Labels of all the regions in parcellation.
Returns
-------
None.
'''
correlation_measure = ConnectivityMeasure(kind='correlation')
correlation_matrix = correlation_measure.fit_transform([time_series])[0]
# Mask the main diagonal for visualization:
np.fill_diagonal(correlation_matrix, 0)
# The labels we have start with the background (0), hence we skip the first label
plotting.plot_matrix(correlation_matrix,
figure=(10, 8),
labels=labels[1:],
vmax=0.8,
vmin=-0.8,
reorder=True)
def connectivity_matrix(timeseries, kind='partial correlation'):
# timeseries: as output by load_timeseries
correlation_measure = ConnectivityMeasure(kind=kind,
vectorize=True,
discard_diagonal=True)
correlation_matrix = correlation_measure.fit_transform(timeseries)
return correlation_matrix, correlation_measure
def correlation_matrix(ts,atlas, confounds=None, mask=None, loud=False, structure_names=[], save_as='', low_pass=0.25, high_pass=0.004, smoothing_fwhm=.3, ): """Return a CSV file containing correlations between ROIs. Parameters ---------- ts : str Path to the 4D NIfTI timeseries file on which to perform the connectivity analysis. confounds : 2D array OR path to CSV file Array/CSV file containing confounding time-series to be regressed out before FC analysis. atlas : str, optional Path to a 3D NIfTI-like binary label file designating ROIs. structure_names : list, optional Ordered list of all structure names in atlas (length N). save_as : str Path under which to save the Pandas DataFrame conttaining the NxN correlation matrix. """ ts = path.abspath(path.expanduser(ts)) if isinstance(atlas,str): atlas = path.abspath(path.expanduser(atlas)) if mask: mask = path.abspath(path.expanduser(mask)) tr = nib.load(ts).header['pixdim'][0] labels_masker = NiftiLabelsMasker( labels_img=atlas, mask_img=mask, standardize=True, memory='nilearn_cache', verbose=5, low_pass=low_pass, high_pass = high_pass, smoothing_fwhm=smoothing_fwhm, t_r=tr, ) #TODO: test confounds with physiological signals if(confounds): confounds = path.abspath(path.expanduser(confounds)) timeseries = labels_masker.fit_transform(ts, confounds=confounds) else: timeseries = labels_masker.fit_transform(ts) correlation_measure = ConnectivityMeasure(kind='correlation') correlation_matrix = correlation_measure.fit_transform([timeseries])[0] if structure_names: df = pd.DataFrame(columns=structure_names, index=structure_names, data=correlation_matrix) else: df = pd.DataFrame(data=correlation_matrix) if save_as: save_dir = path.dirname(save_as) if not path.exists(save_dir): makedirs(save_dir) df.to_csv(save_as)
def generate_connectivity_matrix(time_series, kind='correlation'):
"""
Generate a connectivity matrix from a collection of time series.
param :kind: Any kind accepted by nilearn ConnectivityMeasure
"""
connectivity_measure = ConnectivityMeasure(kind=kind)
connectivity_matrix = connectivity_measure.fit_transform([time_series])[0]
return connectivity_matrix
def prepare_data(data_dir, output_dir, pipeline = "cpac", quality_checked = True):
# get dataset
print("Loading dataset...")
abide = datasets.fetch_abide_pcp(data_dir = data_dir,
pipeline = pipeline,
quality_checked = quality_checked)
# make list of filenames
fmri_filenames = abide.func_preproc
# load atlas
multiscale = datasets.fetch_atlas_basc_multiscale_2015()
atlas_filename = multiscale.scale064
# initialize masker object
masker = NiftiLabelsMasker(labels_img=atlas_filename,
standardize=True,
memory='nilearn_cache',
verbose=0)
# initialize correlation measure
correlation_measure = ConnectivityMeasure(kind='correlation', vectorize=True,
discard_diagonal=True)
try: # check if feature file already exists
# load features
feat_file = os.path.join(output_dir, 'ABIDE_BASC064_features.npz')
X_features = np.load(feat_file)['a']
print("Feature file found.")
except: # if not, extract features
X_features = [] # To contain upper half of matrix as 1d array
print("No feature file found. Extracting features...")
for i,sub in enumerate(fmri_filenames):
# extract the timeseries from the ROIs in the atlas
time_series = masker.fit_transform(sub)
# create a region x region correlation matrix
correlation_matrix = correlation_measure.fit_transform([time_series])[0]
# add to our container
X_features.append(correlation_matrix)
# keep track of status
print('finished extracting %s of %s'%(i+1,len(fmri_filenames)))
# Save features
np.savez_compressed(os.path.join(output_dir, 'ABIDE_BASC064_features'),
a = X_features)
# Dimensionality reduction of features with PCA
print("Running PCA...")
pca = PCA(0.99).fit(X_features) # keeping 99% of variance
X_features_pca = pca.transform(X_features)
# Transform phenotypic data into dataframe
abide_pheno = pd.DataFrame(abide.phenotypic)
# Get the target vector
y_target = abide_pheno['DX_GROUP']
return(X_features_pca, y_target)
def _run_interface(self, runtime):
from nilearn.input_data import NiftiLabelsMasker
from nilearn.connectome import ConnectivityMeasure
from sklearn.covariance import EmpiricalCovariance
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from mne.viz import plot_connectivity_circle
import re
plt.switch_backend('Agg')
# extract timeseries from every label
masker = NiftiLabelsMasker(labels_img=self.inputs.atlas_file,
standardize=True, verbose=1)
timeseries = masker.fit_transform(self.inputs.timeseries_file)
# create correlation matrix
correlation_measure = ConnectivityMeasure(cov_estimator=EmpiricalCovariance(),
kind="correlation")
correlation_matrix = correlation_measure.fit_transform([timeseries])[0]
np.fill_diagonal(correlation_matrix, np.NaN)
# add the atlas labels to the matrix
atlas_lut_df = pd.read_csv(self.inputs.atlas_lut, sep='\t')
regions = atlas_lut_df['regions'].values
correlation_matrix_df = pd.DataFrame(correlation_matrix, index=regions, columns=regions)
# do a fisher's r -> z transform
fisher_z_matrix_df = correlation_matrix_df.apply(lambda x: (np.log(1 + x) - np.log(1 - x)) * 0.5)
# write out the file.
out_file = os.path.join(runtime.cwd, 'fisher_z_correlation.tsv')
fisher_z_matrix_df.to_csv(out_file, sep='\t', na_rep='n/a')
# save the filename in the outputs
self._results['correlation_matrix'] = out_file
# visualizations with mne
connmat = fisher_z_matrix_df.values
labels = list(fisher_z_matrix_df.index)
# define title and outfile names:
trial_regex = re.compile(r'.*trialtype-(?P<trial>[A-Za-z0-9]+)')
title = re.search(trial_regex, self.inputs.timeseries_file).groupdict()['trial']
outfile = os.path.join(runtime.cwd, ".".join([title, "svg"]))
n_lines = int(np.sum(connmat > 0) / 2)
fig = plt.figure(figsize=(5, 5))
plot_connectivity_circle(connmat, labels, n_lines=n_lines, fig=fig, title=title, fontsize_title=10,
facecolor='white', textcolor='black', colormap='jet', colorbar=1,
node_colors=['black'], node_edgecolor=['white'], show=False, interactive=False)
fig.savefig(outfile, dpi=300)
self._results['correlation_fig'] = outfile
return runtime
def estimate_connectivity(time_series, measure_type="correlation"):
"""
Main function to estimate connectivity from atlas regions
"""
correlation_measure = ConnectivityMeasure(kind=measure_type)
correlation_matrix = correlation_measure.fit_transform([time_series])[0]
return ((correlation_measure, correlation_matrix))
def _compute_correlation_matrix(df_nc, df_sz):
corr_kind = 'correlation'
# NC correlation
nc_measure = ConnectivityMeasure(kind=corr_kind)
nc_correlation_array = nc_measure.fit_transform(df_nc['ts_array'].values)
for i in range(nc_correlation_array.shape[0]):
np.fill_diagonal(nc_correlation_array[i], 0)
df_nc = df_nc.assign(corr_matrix=[nc_correlation_array[i] for i in range(nc_correlation_array.shape[0])])
# SZ correlation
sz_measure = ConnectivityMeasure(kind=corr_kind)
sz_correlation_array = sz_measure.fit_transform(df_sz['ts_array'].values)
for i in range(sz_correlation_array.shape[0]):
np.fill_diagonal(sz_correlation_array[i], 0)
df_sz = df_sz.assign(corr_matrix=[sz_correlation_array[i] for i in range(sz_correlation_array.shape[0])])
return df_nc, df_sz
def process(self):
# Read data into huge `Data` list.
data_list: list[Data] = []
filtered_people = np.load(UKB_IDS_PATH)
main_covars = pd.read_csv(UKB_PHENOTYPE_PATH).set_index('ID')
conn_measure = ConnectivityMeasure(kind='correlation', vectorize=False)
for person in filtered_people:
if person in [1663368, 3443644]:
# No information in Covars file
continue
if self.target_var == 'bmi' and person in UKB_WITHOUT_BMI:
continue
if self.connectivity_type == ConnType.FMRI:
ts = np.loadtxt(
f'{UKB_TIMESERIES_PATH}/UKB{person}_ts_raw.txt',
delimiter=',')
if ts.shape[0] < 84:
continue
elif ts.shape[1] == 523:
ts = ts[:, :490]
assert ts.shape == (84, 490)
# Getting only the last 68 cortical regions
ts = ts[-68:, :]
# For normalisation part and connectivity
ts = ts.T
corr_arr = conn_measure.fit_transform([ts])
assert corr_arr.shape == (1, 68, 68)
corr_arr = corr_arr[0]
G = create_thresholded_graph(corr_arr,
threshold=self.threshold,
num_nodes=self.num_nodes)
edge_index = torch.tensor(np.array(G.edges()),
dtype=torch.long).t().contiguous()
if self.include_edge_weights:
edge_attr = torch.tensor(list(
nx.get_edge_attributes(G, 'weight').values()),
dtype=torch.float).unsqueeze(1)
else:
edge_attr = None
data = self.__create_data_object(person=person,
ts=ts,
edge_index=edge_index,
edge_attr=edge_attr,
covars=main_covars)
data_list.append(data)
data, slices = self.collate(data_list)
torch.save((data, slices), self.processed_paths[0])
def createCorMat(time_series):
from nilearn.connectome import ConnectivityMeasure
correlation_measure = ConnectivityMeasure(
kind='correlation') # can choose partial - it might be better
# create correlation matrix for each subject
fullMatrix = []
for time_s in time_series:
correlation_matrix = correlation_measure.fit_transform([time_s])[0]
fullMatrix.append(correlation_matrix)
return fullMatrix
def make_connectivity_biomarkers(kind, labels, adhd200, pooled_subjects):
"""
This function takes the masked fMRI volumes and the corresponding phenotypic information (age, gender and dexterity)
and turns them into a 2D array for doing ML classification. If there is no phenotypic information available,
we exlude it from the dataset.
:param kind: (str) The type of functional connnectity we extract
:param labels: (list) The truth values for the ADHD200 dataset
:param adhd200: (ADHD200) The ADHD200 object
:param pooled_subjects: (list) The masked fMRI volumes
:return: (list) features, (list) labels
"""
new_labels = [] # Initialize a new list for containing the new labels (only labels for fMRI volumes that
# have corresponding phenotypic information
temp_features = [] # Initialize a new list for containing the new labels (only labels for fMRI volumes that
# have corresponding phenotypic information
conn_measure = ConnectivityMeasure(kind=kind, vectorize=True, discard_diagonal=True) # Generate the functional
# connectivity using the biomarker specified
connectivity = conn_measure.fit_transform(pooled_subjects) # Apply it to all of the masked fMRI scans
bar = ProgressBar(max_value=len(adhd200.func)) # Instantiate a new progressbar
ops = 0 # Set the default value of the bar to 0
for index in range(len(adhd200.func)):
phenotypic_information = Helpers.get_params(adhd200, adhd200.func[
index]) # Retrieve the corresponding phenotypic information for each fMRI
ops += 1 # Increment the bar by one
bar.update(ops) # Update the progressbar to the value of the variable "ops"
if phenotypic_information is not None: # If we found phenotypic information for that fMRI
new_labels.append(labels[index]) # Add it to the "approved" labels list
generated_features = np.array(
[Helpers.conform_1d(phenotypic_information, connectivity[index].shape[0]), connectivity[index]])
# Add the phenotypic information and the functional connectivity as a matrix. We have to
# surround the phenotypic information by 0s to make it the same shape as the connectivity (conform 1d)
temp_features.append(generated_features) # add it to the temp features
else:
continue # Skip that fMRI scan from the dataset
d3_dataset = np.array(temp_features) # Convert the 3D temp_features array to a numpy array
nsamples, nx, ny = d3_dataset.shape # Extract the dimensionality of the data
d2_functional_connectivity = d3_dataset.reshape((nsamples, nx * ny)) # Convert it to 2 dimensions
with open('pickles/features.pkl',
'wb') as features_file: # Cache the features so that we don't have to run this
# function again
dump(d2_functional_connectivity, features_file) # Dump them to the pickle file
with open('pickles/adhd_labels.pkl', 'wb') as labels_file: # Cache the biomarkers so that we don't have to run this
# function again
dump(new_labels, labels_file) # Dump them to the pickle file
return d2_functional_connectivity, new_labels # Return them
def cal_connectome(fmri_ff,
confound_ff,
atlas_ff,
outputjpg_ff,
metric='correlation',
labelrange=None,
label_or_map=0):
if label_or_map == 0:
# “correlation”, “partial correlation”, “tangent”, “covariance”, “precision”
masker = NiftiLabelsMasker(labels_img=atlas_ff,
standardize=True,
verbose=0)
else:
masker = NiftiMapsMasker(maps_img=atlas_ff,
standardize=True,
verbose=0)
time_series_0 = masker.fit_transform(fmri_ff, confounds=confound_ff)
if labelrange is None:
labelrange = np.arange(time_series_0.shape[1])
time_series = time_series_0[:, labelrange]
if metric == 'sparse inverse covariance':
try:
estimator = GraphLassoCV()
estimator.fit(time_series)
correlation_matrix = -estimator.precision_
except:
correlation_matrix = np.zeros(
(time_series.shape[1], time_series.shape[1]))
else:
correlation_measure = ConnectivityMeasure(kind=metric)
correlation_matrix = correlation_measure.fit_transform([time_series
])[0]
# Plot the correlation matrix
fig = plt.figure(figsize=(6, 5), dpi=100)
plt.clf()
# Mask the main diagonal for visualization:
np.fill_diagonal(correlation_matrix, 0)
plt.imshow(correlation_matrix,
interpolation="nearest",
cmap="RdBu_r",
vmax=0.8,
vmin=-0.8)
plt.gca().yaxis.tick_right()
plt.axis('off')
plt.colorbar()
plt.title(metric.title(), fontsize=12)
plt.tight_layout()
fig.savefig(outputjpg_ff, bbox_inches='tight')
plt.close()
return correlation_matrix
def correlation(self, estimator="maximum_likelihood", assume_centered=False):
if estimator=="maximum_likelihood":
correlation_measure = ConnectivityMeasure(kind="correlation", cov_estimator=EmpiricalCovariance(assume_centered=assume_centered))
elif estimator=="ledoit_wolf":
correlation_measure = ConnectivityMeasure(kind="correlation", cov_estimator=LedoitWolf(assume_centered=assume_centered))
else:
raise ValueError("Estimator should be 'maximum_likelihood' or 'ledoit_wolf'")
R = np.nan_to_num(correlation_measure.fit_transform(self.ts))
return R
def get_correlation_matrix(region_timeseries_list):
"""
Compute correlation matrix for a list of timeseries
"""
correlation_matrices = []
correlation_measure = ConnectivityMeasure(kind='correlation')
for item in region_timeseries_list:
matrix = correlation_measure.fit_transform([item])[0]
correlation_matrices.append(matrix)
return np.array(correlation_matrices)
def compute_correlation(time_series, method):
data = np.genfromtxt(time_series).T
if method == 'PearsonCorr':
method = 'correlation'
elif method == 'PartialCorr':
method = 'partial correlation'
connectivity_measure = ConnectivityMeasure(kind=method)
connectome = connectivity_measure.fit_transform([data])[0]
file = os.path.abspath('./%s_connectome.npy' % (method.replace(" ", "-")))
np.save(file, connectome)
return file
connectome_measure = ConnectivityMeasure(kind='correlation')
# useful for plotting connectivity interactions on glass brain
from nilearn import plotting
# create masker to extract functional data within atlas parcels
masker = NiftiLabelsMasker(labels_img=yeo['thick_17'], standardize=True,
memory='nilearn_cache')
# extract time series from all subjects and concatenate them
time_series = []
for func, confounds in zip(data.func, data.confounds):
time_series.append(masker.fit_transform(func, confounds=confounds))
# calculate correlation matrices across subjects and display
correlation_matrices = connectome_measure.fit_transform(time_series)
# Mean correlation matrix across 10 subjects can be grabbed like this,
# using connectome measure object
mean_correlation_matrix = connectome_measure.mean_
# grab center coordinates for atlas labels
coordinates = plotting.find_parcellation_cut_coords(labels_img=yeo['thick_17'])
# plot connectome with 80% edge strength in the connectivity
plotting.plot_connectome(mean_correlation_matrix, coordinates,
edge_threshold="80%",
title='Yeo Atlas 17 thick (func)')
##########################################################################
# Load probabilistic atlases - extracting coordinates on brain maps
# First we need to do subjects timeseries signals extraction and then estimating
# correlation matrices on those signals.
# To extract timeseries signals, we call transform() from RegionExtractor object
# onto each subject functional data stored in func_filenames.
# To estimate correlation matrices we import connectome utilities from nilearn
from nilearn.connectome import ConnectivityMeasure
correlations = []
# Initializing ConnectivityMeasure object with kind='correlation'
connectome_measure = ConnectivityMeasure(kind='correlation')
for filename, confound in zip(func_filenames, confounds):
# call transform from RegionExtractor object to extract timeseries signals
timeseries_each_subject = extractor.transform(filename, confounds=confound)
# call fit_transform from ConnectivityMeasure object
correlation = connectome_measure.fit_transform([timeseries_each_subject])
# saving each subject correlation to correlations
correlations.append(correlation)
# Mean of all correlations
import numpy as np
mean_correlations = np.mean(correlations, axis=0).reshape(n_regions_extracted,
n_regions_extracted)
###############################################################################
# Plot resulting connectomes
# ----------------------------
title = 'Correlation between %d regions' % n_regions_extracted
# First plot the matrix
masker = NiftiMapsMasker(maps_img=atlas_filename, standardize=True,
memory='nilearn_cache', verbose=5)
time_series = masker.fit_transform(data.func[0],
confounds=data.confounds)
############################################################################
# `time_series` is now a 2D matrix, of shape (number of time points x
# number of regions)
print(time_series.shape)
############################################################################
# Build and display a correlation matrix
from nilearn.connectome import ConnectivityMeasure
correlation_measure = ConnectivityMeasure(kind='correlation')
correlation_matrix = correlation_measure.fit_transform([time_series])[0]
# Display the correlation matrix
import numpy as np
from matplotlib import pyplot as plt
plt.figure(figsize=(10, 10))
# Mask out the major diagonal
np.fill_diagonal(correlation_matrix, 0)
plt.imshow(correlation_matrix, interpolation="nearest", cmap="RdBu_r",
vmax=0.8, vmin=-0.8)
plt.colorbar()
# And display the labels
x_ticks = plt.xticks(range(len(labels)), labels, rotation=90)
y_ticks = plt.yticks(range(len(labels)), labels)
############################################################################
plt.title('Default Mode Network Time Series')
plt.xlabel('Scan number')
plt.ylabel('Normalized signal')
plt.legend()
plt.tight_layout()
##########################################################################
# Compute partial correlation matrix
# -----------------------------------
# Using object :class:`nilearn.connectome.ConnectivityMeasure`: Its
# default covariance estimator is Ledoit-Wolf, allowing to obtain accurate
# partial correlations.
from nilearn.connectome import ConnectivityMeasure
connectivity_measure = ConnectivityMeasure(kind='partial correlation')
partial_correlation_matrix = connectivity_measure.fit_transform(
[time_series])[0]
##########################################################################
# Display connectome
# -------------------
from nilearn import plotting
plotting.plot_connectome(partial_correlation_matrix, dmn_coords,
title="Default Mode Network Connectivity")
##########################################################################
# Display connectome with hemispheric projections.
# Notice (0, -52, 18) is included in both hemispheres since x == 0.
plotting.plot_connectome(partial_correlation_matrix, dmn_coords,
title="Connectivity projected on hemispheres",
display_mode='lyrz')
# Compute connectivity metrics
individual_connectivity_matrices = {}
mean_connectivity_matrix = {}
p_ind = 0.
for func_type in func_type_list:
subjects_connectivity = {}
mean_connectivity = {}
for kind in kinds:
try:
conn_measure = ConnectivityMeasure(cov_estimator = estimator, kind = kind)
#conn_measure = nilearn.connectivity.ConnectivityMeasure(cov_estimator =estimator, kind=kind)
t_s=np.asarray(all_time_series_r[func_type])
subjects_connectivity[kind] = conn_measure.fit_transform(t_s)
if kind == 'tangent':
mean_connectivity[kind] = conn_measure.mean_
else:
mean_connectivity[kind] = \
subjects_connectivity[kind].mean(axis=0)
except:
print('estimation failed for '+ kind + ' in group ' + func_type)
pass
p_ind = p_ind + 1.
progress = str(100*p_ind/(len(kinds)*len(func_type_list)))
print(str(progress) + '% done in computing metrics ('+kind+' '+func_type+')')
individual_connectivity_matrices[func_type] = subjects_connectivity
mean_connectivity_matrix[func_type] = mean_connectivity
print('Data has {0} ADHD subjects.'.format(len(adhd_subjects)))
###############################################################################
# ROI-to-ROI correlations of ADHD patients
# ----------------------------------------
# The simpler and most commonly used kind of connectivity is correlation. It
# models the full (marginal) connectivity between pairwise ROIs. We can
# estimate it using :class:`nilearn.connectome.ConnectivityMeasure`.
from nilearn.connectome import ConnectivityMeasure
correlation_measure = ConnectivityMeasure(kind='correlation')
###############################################################################
# From the list of ROIs time-series for ADHD subjects, the
# `correlation_measure` computes individual correlation matrices.
correlation_matrices = correlation_measure.fit_transform(adhd_subjects)
# All individual coefficients are stacked in a unique 2D matrix.
print('Correlations of ADHD patients are stacked in an array of shape {0}'
.format(correlation_matrices.shape))
###############################################################################
# as well as the average correlation across all fitted subjects.
mean_correlation_matrix = correlation_measure.mean_
print('Mean correlation has shape {0}.'.format(mean_correlation_matrix.shape))
###############################################################################
# We display the connectomes of the first 3 ADHD subjects and the mean
# correlation matrix over all ADHD patients.
from nilearn import plotting