### Perform massively univariate analysis with permuted OLS ###################
tested_var = np.ones((n_samples, 1), dtype=float) # intercept
neg_log_pvals, all_scores, h0 = permuted_ols(
tested_var, fmri_masked, model_intercept=False,
n_perm=5000, # 5,000 for the sake of time. 10,000 is recommended
two_sided_test=False, # RPBI does not perform a two-sided test
n_jobs=1) # can be changed to use more CPUs
neg_log_pvals_unmasked = nifti_masker.inverse_transform(
np.ravel(neg_log_pvals))
### Randomized Parcellation Based Inference ###################################
neg_log_pvals_rpbi, _, _ = randomized_parcellation_based_inference(
tested_var, fmri_masked,
np.asarray(nifti_masker.mask_img_.get_data()).astype(bool),
n_parcellations=30, # 30 for the sake of time, 100 is recommended
n_parcels=1000,
threshold='auto',
n_perm=5000, # 5,000 for the sake of time. 10,000 is recommended
random_state=0, memory='nilearn_cache', n_jobs=1, verbose=True)
neg_log_pvals_rpbi_unmasked = nifti_masker.inverse_transform(
neg_log_pvals_rpbi)
### Visualization #############################################################
import matplotlib.pyplot as plt
from nilearn.plotting import plot_stat_map
# Here, we should use a structural image as a background, when available.
# Various plotting parameters
z_slice = 39 # plotted slice
from nilearn.image.resampling import coord_transform
n_detections = (neg_log_pvals_slice_data > threshold).sum()
title = ('Negative $\log_{10}$ p-values'
'\n(Non-parametric + max-type correction)'
'\n%d detections') % n_detections
display.title(title, y=1.2)
### Randomized Parcellation Based Inference ###################################
from nilearn_sandbox.mass_univariate.rpbi import randomized_parcellation_based_inference
print "Randomized Parcellation Based Inference"
neg_log_pvals_rpbi, _, _ = randomized_parcellation_based_inference(
age,
gm_maps_masked, # + intercept as a covariate by default
np.asarray(nifti_masker.mask_img_.get_data()).astype(bool),
n_parcellations=30, # 30 for the sake of time, 100 is recommended
n_parcels=1000,
threshold='auto',
n_perm=1000, # 1,000 for the sake of time. 10,000 is recommended
random_state=0,
memory='nilearn_cache',
n_jobs=1,
verbose=True)
neg_log_pvals_rpbi_unmasked = nifti_masker.inverse_transform(
np.ravel(neg_log_pvals_rpbi))
### Show results
fig = plt.figure(figsize=(5.5, 7.5), facecolor='k')
display = plot_stat_map(neg_log_pvals_rpbi_unmasked,
bg_img=bg_filename,
threshold=threshold,
cmap=plt.cm.RdBu_r,
tested_var,
fmri_masked,
model_intercept=False,
n_perm=5000, # 5,000 for the sake of time. 10,000 is recommended
two_sided_test=False, # RPBI does not perform a two-sided test
n_jobs=1) # can be changed to use more CPUs
neg_log_pvals_unmasked = nifti_masker.inverse_transform(
np.ravel(neg_log_pvals))
### Randomized Parcellation Based Inference ###################################
neg_log_pvals_rpbi, _, _ = randomized_parcellation_based_inference(
tested_var,
fmri_masked,
np.asarray(nifti_masker.mask_img_.get_data()).astype(bool),
n_parcellations=30, # 30 for the sake of time, 100 is recommended
n_parcels=1000,
threshold='auto',
n_perm=5000, # 5,000 for the sake of time. 10,000 is recommended
random_state=0,
memory='nilearn_cache',
n_jobs=1,
verbose=True)
neg_log_pvals_rpbi_unmasked = nifti_masker.inverse_transform(
neg_log_pvals_rpbi)
### Visualization #############################################################
import matplotlib.pyplot as plt
from nilearn.plotting import plot_stat_map
# Here, we should use a structural image as a background, when available.
# Various plotting parameters
def test_randomized_parcellation_based_inference(random_state=1):
"""Test RPBI API.
"""
# check random state
rng = check_random_state(random_state)
# Generate toy data
# define data structure
shape = (5, 5, 5)
n_voxels = np.prod(shape)
mask = np.ones(shape, dtype=bool)
# data generation
data = np.zeros(shape)
data[1:3, 1:3, 1:3] = 1.
data = data.reshape((1, -1))
data = np.repeat(data, 8, 0)
# add noise to avoid constant columns
data += 0.1 * rng.randn(data.shape[0], data.shape[1])
# Randomized Parcellation Based Inference
n_parcellations = 2
n_parcels = 3
neg_log_pvals, counting_statistic_original_data, h0 = (
randomized_parcellation_based_inference(
np.ones(8), data, mask, confounding_vars=None,
model_intercept=True,
n_parcellations=n_parcellations, n_parcels=n_parcels,
threshold=0.05 / n_parcels, n_perm=9, random_state=rng,
verbose=True))
# check pvalues
expected_neg_log_pvals = np.zeros(shape)
expected_neg_log_pvals[1:3, 1:3, 1:3] = 1.
expected_neg_log_pvals = np.ravel(expected_neg_log_pvals)
assert_equal(neg_log_pvals.shape, (n_voxels,))
assert_array_almost_equal(neg_log_pvals, expected_neg_log_pvals)
# check counting statistic
assert_equal(counting_statistic_original_data.shape, (n_voxels,))
assert_array_almost_equal(counting_statistic_original_data,
2 * expected_neg_log_pvals)
# h0
assert_equal(h0.shape, (9,))
assert_array_almost_equal(h0, np.zeros(9))
### Same test with 1-dimensional tested_vars
# check random state
rng = check_random_state(random_state)
rng.randn(data.shape[0], data.shape[1])
# Randomized Parcellation Based Inference
n_parcellations = 2
n_parcels = 3
neg_log_pvals, counting_statistic_original_data, h0 = (
randomized_parcellation_based_inference(
np.ones(8), data, mask, confounding_vars=None,
model_intercept=True,
n_parcellations=n_parcellations, n_parcels=n_parcels,
threshold=0.05 / n_parcels, n_perm=9, random_state=rng,
verbose=True))
# check pvalues
expected_neg_log_pvals = np.zeros(shape)
expected_neg_log_pvals[1:3, 1:3, 1:3] = 1.
expected_neg_log_pvals = np.ravel(expected_neg_log_pvals)
assert_equal(neg_log_pvals.shape, (n_voxels,))
assert_array_almost_equal(neg_log_pvals, expected_neg_log_pvals)
# check counting statistic
assert_equal(counting_statistic_original_data.shape, (n_voxels,))
assert_array_almost_equal(counting_statistic_original_data,
2 * expected_neg_log_pvals)
# h0
assert_equal(h0.shape, (9,))
assert_array_almost_equal(h0, np.zeros(9))
def test_randomized_parcellation_based_inference(random_state=1):
"""Test RPBI API.
"""
# check random state
rng = check_random_state(random_state)
# Generate toy data
# define data structure
shape = (5, 5, 5)
n_voxels = np.prod(shape)
mask = np.ones(shape, dtype=bool)
# data generation
data = np.zeros(shape)
data[1:3, 1:3, 1:3] = 1.
data = data.reshape((1, -1))
data = np.repeat(data, 8, 0)
# add noise to avoid constant columns
data += 0.1 * rng.randn(data.shape[0], data.shape[1])
# Randomized Parcellation Based Inference
n_parcellations = 2
n_parcels = 3
neg_log_pvals, counting_statistic_original_data, h0 = (
randomized_parcellation_based_inference(
np.ones(8),
data,
mask,
confounding_vars=None,
model_intercept=True,
n_parcellations=n_parcellations,
n_parcels=n_parcels,
threshold=0.05 / n_parcels,
n_perm=9,
random_state=rng,
verbose=True))
# check pvalues
expected_neg_log_pvals = np.zeros(shape)
expected_neg_log_pvals[1:3, 1:3, 1:3] = 1.
expected_neg_log_pvals = np.ravel(expected_neg_log_pvals)
assert_equal(neg_log_pvals.shape, (n_voxels, ))
assert_array_almost_equal(neg_log_pvals, expected_neg_log_pvals)
# check counting statistic
assert_equal(counting_statistic_original_data.shape, (n_voxels, ))
assert_array_almost_equal(counting_statistic_original_data,
2 * expected_neg_log_pvals)
# h0
assert_equal(h0.shape, (9, ))
assert_array_almost_equal(h0, np.zeros(9))
### Same test with 1-dimensional tested_vars
# check random state
rng = check_random_state(random_state)
rng.randn(data.shape[0], data.shape[1])
# Randomized Parcellation Based Inference
n_parcellations = 2
n_parcels = 3
neg_log_pvals, counting_statistic_original_data, h0 = (
randomized_parcellation_based_inference(
np.ones(8),
data,
mask,
confounding_vars=None,
model_intercept=True,
n_parcellations=n_parcellations,
n_parcels=n_parcels,
threshold=0.05 / n_parcels,
n_perm=9,
random_state=rng,
verbose=True))
# check pvalues
expected_neg_log_pvals = np.zeros(shape)
expected_neg_log_pvals[1:3, 1:3, 1:3] = 1.
expected_neg_log_pvals = np.ravel(expected_neg_log_pvals)
assert_equal(neg_log_pvals.shape, (n_voxels, ))
assert_array_almost_equal(neg_log_pvals, expected_neg_log_pvals)
# check counting statistic
assert_equal(counting_statistic_original_data.shape, (n_voxels, ))
assert_array_almost_equal(counting_statistic_original_data,
2 * expected_neg_log_pvals)
# h0
assert_equal(h0.shape, (9, ))
assert_array_almost_equal(h0, np.zeros(9))
# effect sign to add it back at the end and thus observe the signed effect
neg_log_pvals, t_scores_original_data, _ = permuted_ols(
grouped_conditions_encoded, grouped_fmri_masked,
# + intercept as a covariate by default
n_perm=5000, # 5,000 for the sake of time. 10,000 is recommended
two_sided_test=False, # RPBI does not perform a two-sided test
n_jobs=1) # can be changed to use more CPUs
neg_log_pvals_unmasked = nifti_masker.inverse_transform(
neg_log_pvals)
### Randomized Parcellation Based Inference ###################################
neg_log_pvals_rpbi, _, _ = randomized_parcellation_based_inference(
grouped_conditions_encoded, grouped_fmri_masked,
# + intercept as a covariate by default
nifti_masker.mask_img_.get_data().astype(bool),
n_parcellations=30, # 30 for the sake of time, 100 is recommended
n_parcels=1000,
threshold='auto',
n_perm=5000, # 5,000 for the sake of time. 10,000 is recommended
random_state=0, memory='nilearn_cache',
n_jobs=1, verbose=True)
neg_log_pvals_rpbi_unmasked = nifti_masker.inverse_transform(
neg_log_pvals_rpbi)
### Visualization #############################################################
import matplotlib.pyplot as plt
from nilearn.plotting import plot_stat_map
# Use the fMRI mean image as a surrogate of anatomical data
from nilearn import image
mean_fmri_img = image.mean_img(haxby_dataset.func)