def compute_graph_lasso_covariance(subject_id,
group,
session='func1',
preprocessing_folder='pipeline_1',
plot=True,
save=True,
save_file=True,
msdl=False):
"""Returns graph lasso covariance for a subject_id
"""
# load timeseries
if msdl:
ts = load_dynacomp_msdl_timeseries(
subject_id,
session=session,
preprocessing_folder=preprocessing_folder)
roi_names, roi_coords = load_msdl_names_and_coords()
else:
ts = load_dynacomp_roi_timeseries(
subject_id,
session=session,
preprocessing_folder=preprocessing_folder)
# load rois
roi_names, roi_coords = load_roi_names_and_coords(subject_id)
# compute covariance
gl = covariance.GraphLassoCV(verbose=2)
gl.fit(ts)
if plot:
plot_connectivity_matrix(subject_id, group, gl.covariance_, roi_names,
'gl_covariance', session,
preprocessing_folder, save, msdl)
plot_connectivity_matrix(subject_id, group, gl.precision_, roi_names,
'gl_precision', session, preprocessing_folder,
save, msdl)
sparsity = (gl.precision_ == 0)
plot_connectivity_matrix(subject_id, group, sparsity, roi_names,
'gl_sparsity', session, preprocessing_folder,
save, msdl)
plot_connectivity_glassbrain(subject_id, group, gl.covariance_,
roi_coords, 'gl_covariance', session,
preprocessing_folder, save, msdl)
if save_file:
CONN_DIR = set_data_base_dir('Dynacomp/connectivity')
sparsity = (gl.precision_ == 0)
if not os.path.isdir(os.path.join(CONN_DIR, subject_id)):
os.mkdir(os.path.join(CONN_DIR, subject_id))
output_file = os.path.join(
CONN_DIR, subject_id, 'gl_' + session + '_' + preprocessing_folder)
if msdl:
output_file += '_msdl'
np.savez(output_file,
covariance=gl.covariance_,
precision=gl.precision_,
sparsity=sparsity,
roi_names=roi_names,
roi_coords=roi_coords)
return gl, roi_names, roi_coords
def compute_graph_lasso_covariance(subject_id, group, session='func1',
preprocessing_folder='pipeline_1',
plot=True, save=True, save_file=True,
msdl=False):
"""Returns graph lasso covariance for a subject_id
"""
# load timeseries
if msdl:
ts = load_dynacomp_msdl_timeseries(subject_id, session=session,
preprocessing_folder=preprocessing_folder)
roi_names, roi_coords = load_msdl_names_and_coords()
else:
ts = load_dynacomp_roi_timeseries(subject_id, session=session,
preprocessing_folder=preprocessing_folder)
# load rois
roi_names, roi_coords = load_roi_names_and_coords(subject_id)
# compute covariance
gl = covariance.GraphLassoCV(verbose=2)
gl.fit(ts)
if plot:
plot_connectivity_matrix(subject_id, group, gl.covariance_,
roi_names, 'gl_covariance', session,
preprocessing_folder, save, msdl)
plot_connectivity_matrix(subject_id, group, gl.precision_,
roi_names, 'gl_precision', session,
preprocessing_folder, save, msdl)
sparsity = (gl.precision_ == 0)
plot_connectivity_matrix(subject_id, group, sparsity,
roi_names, 'gl_sparsity', session,
preprocessing_folder, save, msdl)
plot_connectivity_glassbrain(subject_id, group, gl.covariance_,
roi_coords, 'gl_covariance', session,
preprocessing_folder, save, msdl)
if save_file:
CONN_DIR = set_data_base_dir('Dynacomp/connectivity')
sparsity = (gl.precision_ == 0)
if not os.path.isdir(os.path.join(CONN_DIR, subject_id)):
os.mkdir(os.path.join(CONN_DIR, subject_id))
output_file = os.path.join(CONN_DIR, subject_id,
'gl_' + session + '_' + preprocessing_folder)
if msdl:
output_file += '_msdl'
np.savez(output_file, covariance=gl.covariance_,
precision=gl.precision_, sparsity=sparsity,
roi_names=roi_names, roi_coords=roi_coords)
return gl, roi_names, roi_coords
def compute_pearson_connectivity(subject_id,
group,
session='func1',
preprocessing_folder='pipeline_1',
plot=True,
save=True,
save_file=True,
msdl=False):
"""Returns Pearson correlation coefficient for a subject_id
"""
# load timeseries
if msdl:
ts = load_dynacomp_msdl_timeseries(
subject_id,
session=session,
preprocessing_folder=preprocessing_folder)
roi_names, roi_coords = load_msdl_names_and_coords()
else:
ts = load_dynacomp_roi_timeseries(
subject_id,
session=session,
preprocessing_folder=preprocessing_folder)
# load rois
roi_names, roi_coords = load_roi_names_and_coords(subject_id)
# pearson correlation
pc = np.corrcoef(ts.T)
if plot:
print session
plot_connectivity_matrix(subject_id, group, pc, roi_names, 'pc',
session, preprocessing_folder, save, msdl)
plot_connectivity_glassbrain(subject_id, group, pc, roi_coords, 'pc',
session, preprocessing_folder, save, msdl)
if save_file:
CONN_DIR = set_data_base_dir('Dynacomp/connectivity')
if not os.path.isdir(os.path.join(CONN_DIR, subject_id)):
os.mkdir(os.path.join(CONN_DIR, subject_id))
output_file = os.path.join(
CONN_DIR, subject_id, 'pc_' + session + '_' + preprocessing_folder)
if msdl:
output_file += '_msdl'
np.savez(output_file,
correlation=pc,
roi_names=roi_names,
roi_coords=roi_coords)
return pc, roi_names, roi_coords
def compute_pearson_connectivity(subject_id, group, session='func1',
preprocessing_folder='pipeline_1',
plot=True, save=True, save_file=True,
msdl=False):
"""Returns Pearson correlation coefficient for a subject_id
"""
# load timeseries
if msdl:
ts = load_dynacomp_msdl_timeseries(subject_id, session=session,
preprocessing_folder=preprocessing_folder)
roi_names, roi_coords = load_msdl_names_and_coords()
else:
ts = load_dynacomp_roi_timeseries(subject_id, session=session,
preprocessing_folder=preprocessing_folder)
# load rois
roi_names, roi_coords = load_roi_names_and_coords(subject_id)
# pearson correlation
pc = np.corrcoef(ts.T)
if plot:
print session
plot_connectivity_matrix(subject_id, group, pc,
roi_names, 'pc',
session,
preprocessing_folder, save, msdl)
plot_connectivity_glassbrain(subject_id, group, pc,
roi_coords, 'pc', session,
preprocessing_folder, save, msdl)
if save_file:
CONN_DIR = set_data_base_dir('Dynacomp/connectivity')
if not os.path.isdir(os.path.join(CONN_DIR, subject_id)):
os.mkdir(os.path.join(CONN_DIR, subject_id))
output_file = os.path.join(CONN_DIR, subject_id,
'pc_' + session + '_' + preprocessing_folder)
if msdl:
output_file += '_msdl'
np.savez(output_file, correlation=pc,
roi_names=roi_names, roi_coords=roi_coords)
return pc, roi_names, roi_coords
def compute_group_sparse_covariance(dataset, session='func1',
preprocessing_folder='pipeline_1',
plot=True, save=True, save_file=True,
msdl=False):
"""Returns Group sparse covariance for all subjects
"""
ts = []
# load timeseries
if msdl:
for subject_id in dataset.subjects:
ts.append(load_dynacomp_msdl_timeseries(subject_id,\
session=session, preprocessing_folder=preprocessing_folder))
roi_names, roi_coords = load_msdl_names_and_coords()
else:
for subject_id in dataset.subjects:
ts.append(load_dynacomp_roi_timeseries(subject_id, session=session,\
preprocessing_folder=preprocessing_folder))
# load rois
roi_names, roi_coords = load_roi_names_and_coords(subject_id)
gsc = GroupSparseCovarianceCV(verbose=2)
gsc.fit(ts)
if plot:
for i in range(len(dataset.subjects)):
if not msdl:
# load rois
roi_names,\
roi_coords = load_roi_names_and_coords(dataset.subjects[i])
plot_connectivity_matrix(dataset.subjects[i], dataset.group[i],
gsc.covariances_[..., i],
roi_names, 'gsc_covariance', session,
preprocessing_folder, save, msdl)
plot_connectivity_matrix(dataset.subjects[i], dataset.group[i],
gsc.precisions_[..., i],
roi_names, 'gsc_precision', session,
preprocessing_folder, save, msdl)
sparsity = (gsc.precisions_[..., i] == 0)
plot_connectivity_matrix(dataset.subjects[i], dataset.group[i],
sparsity,
roi_names, 'gsc_sparsity', session,
preprocessing_folder, save, msdl)
plot_connectivity_glassbrain(dataset.subjects[i], dataset.group[i],
gsc.covariances_[..., i],
roi_coords, 'gsc_covariance', session,
preprocessing_folder, save, msdl)
for i in range(len(dataset.subjects)):
if not msdl:
# load rois
roi_names,\
roi_coords = load_roi_names_and_coords(dataset.subjects[i])
sparsity = (gsc.precisions_[..., i] == 0)
CONN_DIR = set_data_base_dir('Dynacomp/connectivity')
subject_id = dataset.subjects[i]
if not os.path.isdir(os.path.join(CONN_DIR, subject_id)):
os.mkdir(os.path.join(CONN_DIR, subject_id))
output_file = os.path.join(CONN_DIR, subject_id,
'gsc_' + session + '_' + preprocessing_folder)
if msdl:
output_file += '_msdl'
np.savez(output_file, covariance=gsc.covariances_[..., i],
precision=gsc.precisions_[..., i], sparsity=sparsity,
roi_names=roi_names, roi_coords=roi_coords)
return gsc, roi_names, roi_coords
dataset = load_dynacomp()
func = dataset.func1
n_components = 20
canica = CanICA(n_components=n_components,
mask=dataset.mask,
smoothing_fwhm=None,
do_cca=True,
threshold=3.,
n_init=10,
standardize=True,
random_state=42,
n_jobs=2,
verbose=2)
CANICA_PATH = set_data_base_dir('Dynacomp/canica')
output_file = os.path.join(CANICA_PATH,
'canica_' + str(n_components) + '.nii.gz')
if not os.path.isfile(output_file):
canica.fit(func)
components_img = canica.masker_.inverse_transform(canica.components_)
components_img.to_filename(output_file)
else:
components_img = output_file
FIG_PATH = set_figure_base_dir('canica')
for i, cur_img in enumerate(iter_img(components_img)):
output_file = os.path.join(FIG_PATH,
'canica_' + str(n_components) + '_IC%d' % i)
from loader import load_dynacomp, set_data_base_dir, set_figure_base_dir
from nilearn.decomposition import CanICA
from nilearn.plotting import plot_stat_map
from nilearn.image import iter_img
dataset = load_dynacomp()
func = dataset.func1
n_components = 20
canica = CanICA(n_components=n_components, mask=dataset.mask,
smoothing_fwhm=None, do_cca=True, threshold=3.,
n_init=10, standardize=True, random_state=42,
n_jobs=2, verbose=2)
CANICA_PATH = set_data_base_dir('Dynacomp/canica')
output_file = os.path.join(CANICA_PATH,
'canica_' + str(n_components) + '.nii.gz')
if not os.path.isfile(output_file):
canica.fit(func)
components_img = canica.masker_.inverse_transform(canica.components_)
components_img.to_filename(output_file)
else:
components_img = output_file
FIG_PATH = set_figure_base_dir('canica')
for i, cur_img in enumerate(iter_img(components_img)):
output_file = os.path.join(FIG_PATH,
'canica_'+ str(n_components) +'_IC%d' % i )
# -*- coding: utf-8 -*-
"""
Created on Wed Apr 1 14:37:52 2015
@author: mr243268
"""
import os
import numpy as np
from loader import load_dynacomp, set_data_base_dir,\
load_msdl_names_and_coords, load_dynacomp_fc
from nilearn.plotting import plot_connectome
import seaborn as sns
import matplotlib.pyplot as plt
STAT_DIR = set_data_base_dir('Dynacomp/stat')
def read_test(metric, group, session):
"""Returns test data
"""
filename = '_'.join(['ttest_connectome', session, group, metric, 'msdl' ])
path = os.path.join(STAT_DIR, filename + '.npy')
return np.load(path)
def read_test2(metric, groups, session):
"""Returns test data
"""
filename = '_'.join(['ttest2_connectome', session, groups[0], groups[1], metric, 'msdl' ])
path = os.path.join(STAT_DIR, filename + '.npy')
return np.load(path)
def compute_group_sparse_covariance(dataset,
session='func1',
preprocessing_folder='pipeline_1',
plot=True,
save=True,
save_file=True,
msdl=False):
"""Returns Group sparse covariance for all subjects
"""
ts = []
# load timeseries
if msdl:
for subject_id in dataset.subjects:
ts.append(load_dynacomp_msdl_timeseries(subject_id,\
session=session, preprocessing_folder=preprocessing_folder))
roi_names, roi_coords = load_msdl_names_and_coords()
else:
for subject_id in dataset.subjects:
ts.append(load_dynacomp_roi_timeseries(subject_id, session=session,\
preprocessing_folder=preprocessing_folder))
# load rois
roi_names, roi_coords = load_roi_names_and_coords(subject_id)
gsc = GroupSparseCovarianceCV(verbose=2)
gsc.fit(ts)
if plot:
for i in range(len(dataset.subjects)):
if not msdl:
# load rois
roi_names,\
roi_coords = load_roi_names_and_coords(dataset.subjects[i])
plot_connectivity_matrix(dataset.subjects[i], dataset.group[i],
gsc.covariances_[..., i], roi_names,
'gsc_covariance', session,
preprocessing_folder, save, msdl)
plot_connectivity_matrix(dataset.subjects[i], dataset.group[i],
gsc.precisions_[..., i], roi_names,
'gsc_precision', session,
preprocessing_folder, save, msdl)
sparsity = (gsc.precisions_[..., i] == 0)
plot_connectivity_matrix(dataset.subjects[i], dataset.group[i],
sparsity, roi_names, 'gsc_sparsity',
session, preprocessing_folder, save, msdl)
plot_connectivity_glassbrain(dataset.subjects[i], dataset.group[i],
gsc.covariances_[..., i], roi_coords,
'gsc_covariance', session,
preprocessing_folder, save, msdl)
for i in range(len(dataset.subjects)):
if not msdl:
# load rois
roi_names,\
roi_coords = load_roi_names_and_coords(dataset.subjects[i])
sparsity = (gsc.precisions_[..., i] == 0)
CONN_DIR = set_data_base_dir('Dynacomp/connectivity')
subject_id = dataset.subjects[i]
if not os.path.isdir(os.path.join(CONN_DIR, subject_id)):
os.mkdir(os.path.join(CONN_DIR, subject_id))
output_file = os.path.join(
CONN_DIR, subject_id,
'gsc_' + session + '_' + preprocessing_folder)
if msdl:
output_file += '_msdl'
np.savez(output_file,
covariance=gsc.covariances_[..., i],
precision=gsc.precisions_[..., i],
sparsity=sparsity,
roi_names=roi_names,
roi_coords=roi_coords)
return gsc, roi_names, roi_coords