def test_joblib_cache():
from joblib import hash, Memory
mask = np.zeros((40, 40, 40))
mask[20, 20, 20] = 1
mask_img = Nifti1Image(mask, np.eye(4))
with testing.write_tmp_imgs(mask_img, create_files=True) as filename:
masker = NiftiMasker(mask_img=filename)
masker.fit()
mask_hash = hash(masker.mask_img_)
get_data(masker.mask_img_)
assert mask_hash == hash(masker.mask_img_)
# Test a tricky issue with memmapped joblib.memory that makes
# imgs return by inverse_transform impossible to save
cachedir = mkdtemp()
try:
masker.memory = Memory(location=cachedir, mmap_mode='r', verbose=0)
X = masker.transform(mask_img)
# inverse_transform a first time, so that the result is cached
out_img = masker.inverse_transform(X)
out_img = masker.inverse_transform(X)
out_img.to_filename(os.path.join(cachedir, 'test.nii'))
finally:
# enables to delete "filename" on windows
del masker
shutil.rmtree(cachedir, ignore_errors=True)
def test_masking_first_level_model():
"""
Checks that using NiftiMasker when instantiating
FirstLevelModel doesn't raise Error when calling
generate_report().
"""
with InTemporaryDirectory():
shapes, rk = ((7, 8, 7, 15), (7, 8, 7, 16)), 3
mask, fmri_data, design_matrices =\
write_fake_fmri_data_and_design(shapes, rk)
masker = NiftiMasker(mask_img=mask)
masker.fit(fmri_data)
flm = FirstLevelModel(mask_img=masker).fit(
fmri_data, design_matrices=design_matrices
)
contrast = np.eye(3)[1]
report_flm = flm.generate_report(
contrast, plot_type='glass', height_control=None,
min_distance=15, alpha=0.001, threshold=2.78
)
report_iframe = report_flm.get_iframe()
# So flake8 doesn't complain about not using variable (F841)
report_iframe
del mask, flm, fmri_data, masker
def test_overlaid_report(data_img_3d):
pytest.importorskip('matplotlib')
masker = NiftiMasker(target_affine=np.eye(3) * 8)
html = masker.generate_report()
assert "Please `fit` the object" in str(html)
masker.fit(data_img_3d)
html = masker.generate_report()
assert '<div class="overlay">' in str(html)
def test_with_files():
# Standard masking
data = np.zeros((40, 40, 40, 2))
data[20, 20, 20] = 1
data_img = Nifti1Image(data, np.eye(4))
with testing.write_tmp_imgs(data_img) as filename:
masker = NiftiMasker()
masker.fit(filename)
masker.transform(filename)
def test_mask_strategy_errors():
# Error with unknown mask_strategy
mask = NiftiMasker(mask_strategy='oops')
with pytest.raises(ValueError,
match="Unknown value of mask_strategy 'oops'"):
mask.fit()
# Warning with deprecated 'template' strategy
img = np.random.RandomState(42).uniform(size=(9, 9, 5))
img = Nifti1Image(img, np.eye(4))
mask = NiftiMasker(mask_strategy='template')
with pytest.warns(UserWarning,
match="Masking strategy 'template' is deprecated."):
mask.fit(img)
def test_5d():
mask = np.zeros((10, 10, 10))
mask[3:7, 3:7, 3:7] = 1
mask_img = Nifti1Image(mask, np.eye(4))
# Test that, in list of 4d images with last dimension=1, they are
# considered as 3d
rng = np.random.RandomState(42)
data_5d = [rng.random_sample((10, 10, 10, 3)) for i in range(5)]
data_5d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_5d]
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
with pytest.raises(DimensionError,
match="Input data has incompatible dimensionality: "
"Expected dimension is 4D and you provided "
"a list of 4D images \\(5D\\)."):
masker.transform(data_5d)
def test_4d_single_scan():
mask = np.zeros((10, 10, 10))
mask[3:7, 3:7, 3:7] = 1
mask_img = Nifti1Image(mask, np.eye(4))
# Test that, in list of 4d images with last dimension=1, they are
# considered as 3d
rng = np.random.RandomState(42)
data_5d = [rng.random_sample((10, 10, 10, 1)) for i in range(5)]
data_4d = [d[..., 0] for d in data_5d]
data_5d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_5d]
data_4d = [nibabel.Nifti1Image(d, np.eye(4)) for d in data_4d]
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
data_trans_5d = masker.transform(data_5d)
data_trans_4d = masker.transform(data_4d)
assert_array_equal(data_trans_4d, data_trans_5d)
def test_auto_mask():
# This mostly a smoke test
data = np.zeros((9, 9, 9))
data[3:-3, 3:-3, 3:-3] = 10
img = Nifti1Image(data, np.eye(4))
masker = NiftiMasker()
# Smoke test the fit
masker.fit(img)
# Smoke test the transform
# With a 4D img
masker.transform([
img,
])
# With a 3D img
masker.transform(img)
# check exception when transform() called without prior fit()
masker2 = NiftiMasker(mask_img=img)
with pytest.raises(ValueError, match='has not been fitted. '):
masker2.transform(img)
def test_nan():
data = np.ones((9, 9, 9))
data[0] = np.nan
data[:, 0] = np.nan
data[:, :, 0] = np.nan
data[-1] = np.nan
data[:, -1] = np.nan
data[:, :, -1] = np.nan
data[3:-3, 3:-3, 3:-3] = 10
img = Nifti1Image(data, np.eye(4))
masker = NiftiMasker(mask_args=dict(opening=0))
masker.fit(img)
mask = get_data(masker.mask_img_)
assert mask[1:-1, 1:-1, 1:-1].all()
assert not mask[0].any()
assert not mask[:, 0].any()
assert not mask[:, :, 0].any()
assert not mask[-1].any()
assert not mask[:, -1].any()
assert not mask[:, :, -1].any()
def test_high_level_glm_one_session():
shapes, rk = [(7, 8, 9, 15)], 3
mask, fmri_data, design_matrices =\
generate_fake_fmri_data_and_design(shapes, rk)
# Give an unfitted NiftiMasker as mask_img and check that we get an error
masker = NiftiMasker(mask)
with pytest.raises(ValueError,
match="It seems that NiftiMasker has not been fitted."):
FirstLevelModel(mask_img=masker).fit(
fmri_data[0], design_matrices=design_matrices[0])
# Give a fitted NiftiMasker with a None mask_img_ attribute
# and check that the masker parameters are overridden by the
# FirstLevelModel parameters
masker.fit()
masker.mask_img_ = None
with pytest.warns(UserWarning,
match="Parameter memory of the masker overridden"):
FirstLevelModel(mask_img=masker).fit(
fmri_data[0], design_matrices=design_matrices[0])
# Give a fitted NiftiMasker
masker = NiftiMasker(mask)
masker.fit()
single_session_model = FirstLevelModel(mask_img=masker).fit(
fmri_data[0], design_matrices=design_matrices[0])
assert single_session_model.masker_ == masker
# Call with verbose (improve coverage)
single_session_model = FirstLevelModel(mask_img=None, verbose=1).fit(
fmri_data[0], design_matrices=design_matrices[0])
single_session_model = FirstLevelModel(mask_img=None).fit(
fmri_data[0], design_matrices=design_matrices[0])
assert isinstance(single_session_model.masker_.mask_img_, Nifti1Image)
single_session_model = FirstLevelModel(mask_img=mask).fit(
fmri_data[0], design_matrices=design_matrices[0])
z1 = single_session_model.compute_contrast(np.eye(rk)[:1])
assert isinstance(z1, Nifti1Image)
def test_4d_reports(mask):
# Dummy 4D data
data = np.zeros((10, 10, 10, 3), dtype=int)
data[..., 0] = 1
data[..., 1] = 2
data[..., 2] = 3
data_img_4d = Nifti1Image(data, np.eye(4))
# test .fit method
masker = NiftiMasker(mask_strategy='epi')
masker.fit(data_img_4d)
assert masker._report_content['warning_message'] is None
html = masker.generate_report()
_check_html(html)
# test .fit_transform method
masker = NiftiMasker(mask_img=mask, standardize=True)
masker.fit_transform(data_img_4d)
assert masker._report_content['warning_message'] is None
html = masker.generate_report()
_check_html(html)
def test_matrix_orientation():
"""Test if processing is performed along the correct axis."""
# the "step" kind generate heavyside-like signals for each voxel.
# all signals being identical, standardizing along the wrong axis
# would leave a null signal. Along the correct axis, the step remains.
fmri, mask = data_gen.generate_fake_fmri(shape=(40, 41, 42), kind="step")
masker = NiftiMasker(mask_img=mask, standardize=True, detrend=True)
timeseries = masker.fit_transform(fmri)
assert (timeseries.shape[0] == fmri.shape[3])
assert (timeseries.shape[1] == get_data(mask).sum())
std = timeseries.std(axis=0)
assert (std.shape[0] == timeseries.shape[1]) # paranoid
assert (not np.any(std < 0.1))
# Test inverse transform
masker = NiftiMasker(mask_img=mask, standardize=False, detrend=False)
masker.fit()
timeseries = masker.transform(fmri)
recovered = masker.inverse_transform(timeseries)
np.testing.assert_array_almost_equal(get_data(recovered), get_data(fmri))
def test_compute_epi_mask():
# Taken from test_masking.py, but used to test that the masker class
# is passing parameters appropriately.
mean_image = np.ones((9, 9, 3))
mean_image[3:-2, 3:-2, :] = 10
mean_image[5, 5, :] = 11
mean_image = Nifti1Image(mean_image.astype(float), np.eye(4))
masker = NiftiMasker(mask_strategy='epi', mask_args=dict(opening=False))
masker.fit(mean_image)
mask1 = masker.mask_img_
masker2 = NiftiMasker(mask_strategy='epi',
mask_args=dict(opening=False, exclude_zeros=True))
masker2.fit(mean_image)
mask2 = masker2.mask_img_
# With an array with no zeros, exclude_zeros should not make
# any difference
np.testing.assert_array_equal(get_data(mask1), get_data(mask2))
# Check that padding with zeros does not change the extracted mask
mean_image2 = np.zeros((30, 30, 3))
mean_image2[3:12, 3:12, :] = get_data(mean_image)
mean_image2 = Nifti1Image(mean_image2, np.eye(4))
masker3 = NiftiMasker(mask_strategy='epi',
mask_args=dict(opening=False, exclude_zeros=True))
masker3.fit(mean_image2)
mask3 = masker3.mask_img_
np.testing.assert_array_equal(get_data(mask1), get_data(mask3)[3:12, 3:12])
# However, without exclude_zeros, it does
masker4 = NiftiMasker(mask_strategy='epi', mask_args=dict(opening=False))
masker4.fit(mean_image2)
mask4 = masker4.mask_img_
assert not np.allclose(get_data(mask1), get_data(mask4)[3:12, 3:12])
def test_mask_4d():
# Dummy mask
mask = np.zeros((10, 10, 10), dtype=int)
mask[3:7, 3:7, 3:7] = 1
mask_bool = mask.astype(bool)
mask_img = Nifti1Image(mask, np.eye(4))
# Dummy data
data = np.zeros((10, 10, 10, 5), dtype=int)
data[..., 0] = 1
data[..., 1] = 2
data[..., 2] = 3
data_img_4d = Nifti1Image(data, np.eye(4))
data_imgs = [
index_img(data_img_4d, 0),
index_img(data_img_4d, 1),
index_img(data_img_4d, 2)
]
# check whether transform is indeed selecting niimgs subset
sample_mask = np.array([0, 2])
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
data_trans = masker.transform(data_imgs, sample_mask=sample_mask)
data_trans_img = index_img(data_img_4d, sample_mask)
data_trans_direct = get_data(data_trans_img)[mask_bool, :]
data_trans_direct = np.swapaxes(data_trans_direct, 0, 1)
assert_array_equal(data_trans, data_trans_direct)
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
data_trans2 = masker.transform(data_img_4d, sample_mask=sample_mask)
assert_array_equal(data_trans2, data_trans_direct)
diff_sample_mask = np.array([2, 4])
data_trans_img_diff = index_img(data_img_4d, diff_sample_mask)
data_trans_direct_diff = get_data(data_trans_img_diff)[mask_bool, :]
data_trans_direct_diff = np.swapaxes(data_trans_direct_diff, 0, 1)
masker = NiftiMasker(mask_img=mask_img)
masker.fit()
data_trans3 = masker.transform(data_img_4d, sample_mask=diff_sample_mask)
assert_array_equal(data_trans3, data_trans_direct_diff)
def non_parametric_inference(second_level_input,
confounds=None,
design_matrix=None,
second_level_contrast=None,
first_level_contrast=None,
mask=None,
smoothing_fwhm=None,
model_intercept=True,
n_perm=10000,
two_sided_test=False,
random_state=None,
n_jobs=1,
verbose=0):
"""Generate p-values corresponding to the contrasts provided
based on permutation testing. This function reuses the 'permuted_ols'
function Nilearn.
Parameters
----------
second_level_input : pandas DataFrame or list of Niimg-like objects.
If a pandas DataFrame, then they have to contain subject_label,
map_name and effects_map_path. It can contain multiple maps that
would be selected during contrast estimation with the argument
first_level_contrast of the compute_contrast function. The
DataFrame will be sorted based on the subject_label column to avoid
order inconsistencies when extracting the maps. So the rows of the
automatically computed design matrix, if not provided, will
correspond to the sorted subject_label column.
If list of Niimg-like objects then this is taken literally as Y
for the model fit and design_matrix must be provided.
confounds : pandas DataFrame, optional
Must contain a subject_label column. All other columns are
considered as confounds and included in the model. If
design_matrix is provided then this argument is ignored.
The resulting second level design matrix uses the same column
names as in the given DataFrame for confounds. At least two columns
are expected, "subject_label" and at least one confound.
design_matrix : pandas DataFrame, optional
Design matrix to fit the GLM. The number of rows
in the design matrix must agree with the number of maps derived
from second_level_input.
Ensure that the order of maps given by a second_level_input
list of Niimgs matches the order of the rows in the design matrix.
second_level_contrast : str or array of shape (n_col), optional
Where ``n_col`` is the number of columns of the design matrix.
The default (None) is accepted if the design matrix has a single
column, in which case the only possible contrast array((1)) is
applied; when the design matrix has multiple columns, an error is
raised.
first_level_contrast : str, optional
In case a pandas DataFrame was provided as second_level_input this
is the map name to extract from the pandas dataframe map_name column.
It has to be a 't' contrast.
.. versionadded:: 0.8.2
mask : Niimg-like, NiftiMasker or MultiNiftiMasker object, optional
Mask to be used on data. If an instance of masker is passed,
then its mask will be used. If no mask is given,
it will be computed automatically by a MultiNiftiMasker with default
parameters. Automatic mask computation assumes first level imgs have
already been masked.
%(smoothing_fwhm)s
model_intercept : bool, optional
If True, a constant column is added to the confounding variates
unless the tested variate is already the intercept.
Default=True.
n_perm : int, optional
Number of permutations to perform.
Permutations are costly but the more are performed, the more precision
one gets in the p-values estimation. Default=10000.
two_sided_test : boolean, optional
If True, performs an unsigned t-test. Both positive and negative
effects are considered; the null hypothesis is that the effect is zero.
If False, only positive effects are considered as relevant. The null
hypothesis is that the effect is zero or negative.
Default=False.
random_state : int or None, optional
Seed for random number generator, to have the same permutations
in each computing units.
n_jobs : int, optional
Number of parallel workers.
If -1 is provided, all CPUs are used.
A negative number indicates that all the CPUs except (abs(n_jobs) - 1)
ones will be used. Default=1.
verbose : int, optional
Verbosity level (0 means no message). Default=0.
Returns
-------
neg_log_corrected_pvals_img : Nifti1Image
The image which contains negative logarithm of the
corrected p-values.
"""
_check_second_level_input(second_level_input,
design_matrix,
flm_object=False,
df_object=True)
_check_confounds(confounds)
_check_design_matrix(design_matrix)
if isinstance(second_level_input, pd.DataFrame):
second_level_input = _sort_input_dataframe(second_level_input)
sample_map, _ = _process_second_level_input(second_level_input)
# Report progress
t0 = time.time()
if verbose > 0:
sys.stderr.write("Fitting second level model...")
# Learn the mask. Assume the first level imgs have been masked.
if not isinstance(mask, NiftiMasker):
masker = NiftiMasker(mask_img=mask,
smoothing_fwhm=smoothing_fwhm,
memory=Memory(None),
verbose=max(0, verbose - 1),
memory_level=1)
else:
masker = clone(mask)
if smoothing_fwhm is not None:
if getattr(masker, 'smoothing_fwhm') is not None:
warn('Parameter smoothing_fwhm of the masker overridden')
setattr(masker, 'smoothing_fwhm', smoothing_fwhm)
masker.fit(sample_map)
# Report progress
if verbose > 0:
sys.stderr.write("\nComputation of second level model done in "
"%i seconds\n" % (time.time() - t0))
# Check and obtain the contrast
contrast = _get_contrast(second_level_contrast, design_matrix)
# Get effect_maps
effect_maps = _infer_effect_maps(second_level_input, first_level_contrast)
# Check design matrix and effect maps agree on number of rows
_check_effect_maps(effect_maps, design_matrix)
# Obtain tested_var
if contrast in design_matrix.columns.tolist():
tested_var = np.asarray(design_matrix[contrast])
# Mask data
target_vars = masker.transform(effect_maps)
# Perform massively univariate analysis with permuted OLS
neg_log_pvals_permuted_ols, _, _ = permuted_ols(
tested_var,
target_vars,
model_intercept=model_intercept,
n_perm=n_perm,
two_sided_test=two_sided_test,
random_state=random_state,
n_jobs=n_jobs,
verbose=max(0, verbose - 1))
neg_log_corrected_pvals_img = masker.inverse_transform(
np.ravel(neg_log_pvals_permuted_ols))
return neg_log_corrected_pvals_img
# print basic information on the dataset
print('First functional nifti image (4D) is at: %s' % func_filename)
###########################################################################
# Compute the mask
from nilearn.maskers import NiftiMasker
# As this is raw movie watching based EPI, the background is noisy and we
# cannot rely on the 'background' masking strategy. We need to use the 'epi'
# one
nifti_masker = NiftiMasker(standardize=True,
mask_strategy='epi',
memory="nilearn_cache",
memory_level=2,
smoothing_fwhm=8)
nifti_masker.fit(func_filename)
mask_img = nifti_masker.mask_img_
###########################################################################
# Visualize the mask using the plot_roi method
from nilearn.plotting import plot_roi
from nilearn.image.image import mean_img
# calculate mean image for the background
mean_func_img = mean_img(func_filename)
plot_roi(mask_img, mean_func_img, display_mode='y', cut_coords=4, title="Mask")
###########################################################################
# Visualize the mask using the 'generate_report' method
# This report can be displayed in a Jupyter Notebook,
class FirstLevelModel(BaseGLM):
""" Implementation of the General Linear Model
for single session fMRI data.
Parameters
----------
t_r : float
This parameter indicates repetition times of the experimental runs.
In seconds. It is necessary to correctly consider times in the design
matrix. This parameter is also passed to :func:`nilearn.signal.clean`.
Please see the related documentation for details.
slice_time_ref : float, optional
This parameter indicates the time of the reference slice used in the
slice timing preprocessing step of the experimental runs. It is
expressed as a percentage of the t_r (time repetition), so it can have
values between 0. and 1. Default=0.
%(hrf_model)s
Default='glover'.
drift_model : string, optional
This parameter specifies the desired drift model for the design
matrices. It can be 'polynomial', 'cosine' or None.
Default='cosine'.
high_pass : float, optional
This parameter specifies the cut frequency of the high-pass filter in
Hz for the design matrices. Used only if drift_model is 'cosine'.
Default=0.01.
drift_order : int, optional
This parameter specifies the order of the drift model (in case it is
polynomial) for the design matrices. Default=1.
fir_delays : array of shape(n_onsets) or list, optional
In case of FIR design, yields the array of delays used in the FIR
model, in scans. Default=[0].
min_onset : float, optional
This parameter specifies the minimal onset relative to the design
(in seconds). Events that start before (slice_time_ref * t_r +
min_onset) are not considered. Default=-24.
mask_img : Niimg-like, NiftiMasker object or False, optional
Mask to be used on data. If an instance of masker is passed,
then its mask will be used. If no mask is given,
it will be computed automatically by a NiftiMasker with default
parameters. If False is given then the data will not be masked.
target_affine : 3x3 or 4x4 matrix, optional
This parameter is passed to nilearn.image.resample_img.
Please see the related documentation for details.
target_shape : 3-tuple of integers, optional
This parameter is passed to nilearn.image.resample_img.
Please see the related documentation for details.
%(smoothing_fwhm)s
memory : string, optional
Path to the directory used to cache the masking process and the glm
fit. By default, no caching is done.
Creates instance of joblib.Memory.
memory_level : integer, optional
Rough estimator of the amount of memory used by caching. Higher value
means more memory for caching.
standardize : boolean, optional
If standardize is True, the time-series are centered and normed:
their variance is put to 1 in the time dimension. Default=False.
signal_scaling : False, int or (int, int), optional
If not False, fMRI signals are
scaled to the mean value of scaling_axis given,
which can be 0, 1 or (0, 1).
0 refers to mean scaling each voxel with respect to time,
1 refers to mean scaling each time point with respect to all voxels &
(0, 1) refers to scaling with respect to voxels and time,
which is known as grand mean scaling.
Incompatible with standardize (standardize=False is enforced when
signal_scaling is not False).
Default=0.
noise_model : {'ar1', 'ols'}, optional
The temporal variance model. Default='ar1'.
verbose : integer, optional
Indicate the level of verbosity. By default, nothing is printed.
If 0 prints nothing. If 1 prints progress by computation of
each run. If 2 prints timing details of masker and GLM. If 3
prints masker computation details. Default=0.
n_jobs : integer, optional
The number of CPUs to use to do the computation. -1 means
'all CPUs', -2 'all CPUs but one', and so on.
Default=1.
minimize_memory : boolean, optional
Gets rid of some variables on the model fit results that are not
necessary for contrast computation and would only be useful for
further inspection of model details. This has an important impact
on memory consumption. Default=True.
subject_label : string, optional
This id will be used to identify a `FirstLevelModel` when passed to
a `SecondLevelModel` object.
Attributes
----------
labels_ : array of shape (n_voxels,),
a map of values on voxels used to identify the corresponding model
results_ : dict,
with keys corresponding to the different labels values.
Values are SimpleRegressionResults corresponding to the voxels,
if minimize_memory is True,
RegressionResults if minimize_memory is False
Notes
-----
This class is experimental.
It may change in any future release of Nilearn.
"""
def __init__(self, t_r=None, slice_time_ref=0., hrf_model='glover',
drift_model='cosine', high_pass=.01, drift_order=1,
fir_delays=[0], min_onset=-24, mask_img=None,
target_affine=None, target_shape=None, smoothing_fwhm=None,
memory=Memory(None), memory_level=1, standardize=False,
signal_scaling=0, noise_model='ar1', verbose=0, n_jobs=1,
minimize_memory=True, subject_label=None):
# design matrix parameters
self.t_r = t_r
self.slice_time_ref = slice_time_ref
self.hrf_model = hrf_model
self.drift_model = drift_model
self.high_pass = high_pass
self.drift_order = drift_order
self.fir_delays = fir_delays
self.min_onset = min_onset
# glm parameters
self.mask_img = mask_img
self.target_affine = target_affine
self.target_shape = target_shape
self.smoothing_fwhm = smoothing_fwhm
if isinstance(memory, str):
self.memory = Memory(memory)
else:
self.memory = memory
self.memory_level = memory_level
self.standardize = standardize
if signal_scaling is False:
self.signal_scaling = signal_scaling
elif signal_scaling in [0, 1, (0, 1)]:
self.signal_scaling = signal_scaling
self.standardize = False
else:
raise ValueError('signal_scaling must be "False", "0", "1"'
' or "(0, 1)"')
self.noise_model = noise_model
self.verbose = verbose
self.n_jobs = n_jobs
self.minimize_memory = minimize_memory
# attributes
self.labels_ = None
self.results_ = None
self.subject_label = subject_label
@property
def scaling_axis(self):
warn(DeprecationWarning(
"Deprecated. `scaling_axis` will be removed in 0.11.0. "
"Please use `signal_scaling` instead."
))
return self.signal_scaling
def fit(self, run_imgs, events=None, confounds=None, sample_masks=None,
design_matrices=None, bins=100):
"""Fit the GLM
For each run:
1. create design matrix X
2. do a masker job: fMRI_data -> Y
3. fit regression to (Y, X)
Parameters
----------
run_imgs : Niimg-like object or list of Niimg-like objects,
Data on which the GLM will be fitted. If this is a list,
the affine is considered the same for all.
events : pandas Dataframe or string or list of pandas DataFrames \
or strings, optional
fMRI events used to build design matrices. One events object
expected per run_img. Ignored in case designs is not None.
If string, then a path to a csv file is expected.
confounds : pandas Dataframe, numpy array or string or
list of pandas DataFrames, numpy arrays or strings, optional
Each column in a DataFrame corresponds to a confound variable
to be included in the regression model of the respective run_img.
The number of rows must match the number of volumes in the
respective run_img. Ignored in case designs is not None.
If string, then a path to a csv file is expected.
sample_masks : array_like, or list of array_like, optional
shape of array: (number of scans - number of volumes removed, )
Indices of retained volumes. Masks the niimgs along time/fourth
dimension to perform scrubbing (remove volumes with high motion)
and/or remove non-steady-state volumes.
Default=None.
.. versionadded:: 0.9.2.dev
design_matrices : pandas DataFrame or \
list of pandas DataFrames, optional
Design matrices that will be used to fit the GLM. If given it
takes precedence over events and confounds.
bins : int, optional
Maximum number of discrete bins for the AR coef histogram.
If an autoregressive model with order greater than one is specified
then adaptive quantification is performed and the coefficients
will be clustered via K-means with `bins` number of clusters.
Default=100.
"""
# Initialize masker_ to None such that attribute exists
self.masker_ = None
# Raise a warning if both design_matrices and confounds are provided
if design_matrices is not None and \
(confounds is not None or events is not None):
warn(
'If design matrices are supplied, '
'confounds and events will be ignored.'
)
# Local import to prevent circular imports
from nilearn.maskers import NiftiMasker # noqa
# Check arguments
# Check imgs type
if events is not None:
_check_events_file_uses_tab_separators(events_files=events)
if not isinstance(run_imgs, (list, tuple)):
run_imgs = [run_imgs]
if design_matrices is None:
if events is None:
raise ValueError('events or design matrices must be provided')
if self.t_r is None:
raise ValueError('t_r not given to FirstLevelModel object'
' to compute design from events')
else:
design_matrices = _check_run_tables(run_imgs, design_matrices,
'design_matrices')
# Check that number of events and confound files match number of runs
# Also check that events and confound files can be loaded as DataFrame
if events is not None:
events = _check_run_tables(run_imgs, events, 'events')
if confounds is not None:
confounds = _check_run_tables(run_imgs, confounds, 'confounds')
if sample_masks is not None:
sample_masks = _check_run_sample_masks(len(run_imgs), sample_masks)
# Learn the mask
if self.mask_img is False:
# We create a dummy mask to preserve functionality of api
ref_img = check_niimg(run_imgs[0])
self.mask_img = Nifti1Image(np.ones(ref_img.shape[:3]),
ref_img.affine)
if not isinstance(self.mask_img, NiftiMasker):
self.masker_ = NiftiMasker(mask_img=self.mask_img,
smoothing_fwhm=self.smoothing_fwhm,
target_affine=self.target_affine,
standardize=self.standardize,
mask_strategy='epi',
t_r=self.t_r,
memory=self.memory,
verbose=max(0, self.verbose - 2),
target_shape=self.target_shape,
memory_level=self.memory_level
)
self.masker_.fit(run_imgs[0])
else:
# Make sure masker has been fitted otherwise no attribute mask_img_
self.mask_img._check_fitted()
if self.mask_img.mask_img_ is None and self.masker_ is None:
self.masker_ = clone(self.mask_img)
for param_name in ['target_affine', 'target_shape',
'smoothing_fwhm', 't_r', 'memory',
'memory_level']:
our_param = getattr(self, param_name)
if our_param is None:
continue
if getattr(self.masker_, param_name) is not None:
warn('Parameter %s of the masker'
' overridden' % param_name)
setattr(self.masker_, param_name, our_param)
self.masker_.fit(run_imgs[0])
else:
self.masker_ = self.mask_img
# For each run fit the model and keep only the regression results.
self.labels_, self.results_, self.design_matrices_ = [], [], []
n_runs = len(run_imgs)
t0 = time.time()
for run_idx, run_img in enumerate(run_imgs):
# Report progress
if self.verbose > 0:
percent = float(run_idx) / n_runs
percent = round(percent * 100, 2)
dt = time.time() - t0
# We use a max to avoid a division by zero
if run_idx == 0:
remaining = 'go take a coffee, a big one'
else:
remaining = (100. - percent) / max(0.01, percent) * dt
remaining = '%i seconds remaining' % remaining
sys.stderr.write(
"Computing run %d out of %d runs (%s)\n"
% (run_idx + 1, n_runs, remaining))
# Build the experimental design for the glm
run_img = check_niimg(run_img, ensure_ndim=4)
if design_matrices is None:
n_scans = get_data(run_img).shape[3]
if confounds is not None:
confounds_matrix = confounds[run_idx].values
if confounds_matrix.shape[0] != n_scans:
raise ValueError('Rows in confounds does not match'
'n_scans in run_img at index %d'
% (run_idx,))
confounds_names = confounds[run_idx].columns.tolist()
else:
confounds_matrix = None
confounds_names = None
start_time = self.slice_time_ref * self.t_r
end_time = (n_scans - 1 + self.slice_time_ref) * self.t_r
frame_times = np.linspace(start_time, end_time, n_scans)
design = make_first_level_design_matrix(frame_times,
events[run_idx],
self.hrf_model,
self.drift_model,
self.high_pass,
self.drift_order,
self.fir_delays,
confounds_matrix,
confounds_names,
self.min_onset
)
else:
design = design_matrices[run_idx]
if sample_masks is not None:
sample_mask = sample_masks[run_idx]
design = design.iloc[sample_mask, :]
else:
sample_mask = None
self.design_matrices_.append(design)
# Mask and prepare data for GLM
if self.verbose > 1:
t_masking = time.time()
sys.stderr.write('Starting masker computation \r')
Y = self.masker_.transform(run_img, sample_mask=sample_mask)
del run_img # Delete unmasked image to save memory
if self.verbose > 1:
t_masking = time.time() - t_masking
sys.stderr.write('Masker took %d seconds \n'
% t_masking)
if self.signal_scaling is not False: # noqa
Y, _ = mean_scaling(Y, self.signal_scaling)
if self.memory:
mem_glm = self.memory.cache(run_glm, ignore=['n_jobs'])
else:
mem_glm = run_glm
# compute GLM
if self.verbose > 1:
t_glm = time.time()
sys.stderr.write('Performing GLM computation\r')
labels, results = mem_glm(Y, design.values,
noise_model=self.noise_model,
bins=bins, n_jobs=self.n_jobs)
if self.verbose > 1:
t_glm = time.time() - t_glm
sys.stderr.write('GLM took %d seconds \n' % t_glm)
self.labels_.append(labels)
# We save memory if inspecting model details is not necessary
if self.minimize_memory:
for key in results:
results[key] = SimpleRegressionResults(results[key])
self.results_.append(results)
del Y
# Report progress
if self.verbose > 0:
sys.stderr.write("\nComputation of %d runs done in %i seconds\n\n"
% (n_runs, time.time() - t0))
return self
def compute_contrast(self, contrast_def, stat_type=None,
output_type='z_score'):
"""Generate different outputs corresponding to
the contrasts provided e.g. z_map, t_map, effects and variance.
In multi-session case, outputs the fixed effects map.
Parameters
----------
contrast_def : str or array of shape (n_col) or list of (string or
array of shape (n_col))
where ``n_col`` is the number of columns of the design matrix,
(one array per run). If only one array is provided when there
are several runs, it will be assumed that the same contrast is
desired for all runs. The string can be a formula compatible with
`pandas.DataFrame.eval`. Basically one can use the name of the
conditions as they appear in the design matrix of the fitted model
combined with operators +- and combined with numbers
with operators +-`*`/.
stat_type : {'t', 'F'}, optional
Type of the contrast.
output_type : str, optional
Type of the output map. Can be 'z_score', 'stat', 'p_value',
'effect_size', 'effect_variance' or 'all'.
Default='z_score'.
Returns
-------
output : Nifti1Image or dict
The desired output image(s). If ``output_type == 'all'``, then
the output is a dictionary of images, keyed by the type of image.
"""
if self.labels_ is None or self.results_ is None:
raise ValueError('The model has not been fit yet')
if isinstance(contrast_def, (np.ndarray, str)):
con_vals = [contrast_def]
elif isinstance(contrast_def, (list, tuple)):
con_vals = contrast_def
else:
raise ValueError('contrast_def must be an array or str or list of'
' (array or str)')
n_runs = len(self.labels_)
n_contrasts = len(con_vals)
if n_contrasts == 1 and n_runs > 1:
warn('One contrast given, assuming it for all %d runs' % n_runs)
con_vals = con_vals * n_runs
elif n_contrasts != n_runs:
raise ValueError('%d contrasts given, while there are %d runs' %
(n_contrasts, n_runs))
# Translate formulas to vectors
for cidx, (con, design_mat) in enumerate(zip(con_vals,
self.design_matrices_)
):
design_columns = design_mat.columns.tolist()
if isinstance(con, str):
con_vals[cidx] = expression_to_contrast_vector(
con, design_columns)
valid_types = ['z_score', 'stat', 'p_value', 'effect_size',
'effect_variance']
valid_types.append('all') # ensuring 'all' is the final entry.
if output_type not in valid_types:
raise ValueError(
'output_type must be one of {}'.format(valid_types))
contrast = _compute_fixed_effect_contrast(self.labels_, self.results_,
con_vals, stat_type)
output_types = (valid_types[:-1]
if output_type == 'all' else [output_type])
outputs = {}
for output_type_ in output_types:
estimate_ = getattr(contrast, output_type_)()
# Prepare the returned images
output = self.masker_.inverse_transform(estimate_)
contrast_name = str(con_vals)
output.header['descrip'] = (
'%s of contrast %s' % (output_type_, contrast_name))
outputs[output_type_] = output
return outputs if output_type == 'all' else output
def _get_voxelwise_model_attribute(self, attribute,
result_as_time_series):
"""Transform RegressionResults instances within a dictionary
(whose keys represent the autoregressive coefficient under the 'ar1'
noise model or only 0.0 under 'ols' noise_model and values are the
RegressionResults instances) into input nifti space.
Parameters
----------
attribute : str
an attribute of a RegressionResults instance.
possible values include: residuals, normalized_residuals,
predicted, SSE, r_square, MSE.
result_as_time_series : bool
whether the RegressionResult attribute has a value
per timepoint of the input nifti image.
Returns
-------
output : list
A list of Nifti1Image(s).
"""
# check if valid attribute is being accessed.
all_attributes = dict(vars(RegressionResults)).keys()
possible_attributes = [prop
for prop in all_attributes
if '__' not in prop
]
if attribute not in possible_attributes:
msg = ("attribute must be one of: "
"{attr}".format(attr=possible_attributes)
)
raise ValueError(msg)
if self.minimize_memory:
raise ValueError(
'To access voxelwise attributes like '
'R-squared, residuals, and predictions, '
'the `FirstLevelModel`-object needs to store '
'there attributes. '
'To do so, set `minimize_memory` to `False` '
'when initializing the `FirstLevelModel`-object.')
if self.labels_ is None or self.results_ is None:
raise ValueError('The model has not been fit yet')
output = []
for design_matrix, labels, results in zip(self.design_matrices_,
self.labels_,
self.results_
):
if result_as_time_series:
voxelwise_attribute = np.zeros((design_matrix.shape[0],
len(labels))
)
else:
voxelwise_attribute = np.zeros((1, len(labels)))
for label_ in results:
label_mask = labels == label_
voxelwise_attribute[:, label_mask] = getattr(results[label_],
attribute)
output.append(self.masker_.inverse_transform(voxelwise_attribute))
return output
def non_parametric_inference(
second_level_input,
confounds=None,
design_matrix=None,
second_level_contrast=None,
first_level_contrast=None,
mask=None,
smoothing_fwhm=None,
model_intercept=True,
n_perm=10000,
two_sided_test=False,
random_state=None,
n_jobs=1,
verbose=0,
threshold=None,
):
"""Generate p-values corresponding to the contrasts provided
based on permutation testing.
This function is a light wrapper around
:func:`~nilearn.mass_univariate.permuted_ols`, with additional steps to
ensure compatibility with the :mod:`~nilearn.glm.second_level` module.
Parameters
----------
second_level_input : :obj:`pandas.DataFrame` or :obj:`list` of Niimg-like \
objects
If a pandas DataFrame, then they have to contain subject_label,
map_name and effects_map_path. It can contain multiple maps that
would be selected during contrast estimation with the argument
first_level_contrast of the compute_contrast function. The
DataFrame will be sorted based on the subject_label column to avoid
order inconsistencies when extracting the maps. So the rows of the
automatically computed design matrix, if not provided, will
correspond to the sorted subject_label column.
If list of Niimg-like objects then this is taken literally as Y
for the model fit and design_matrix must be provided.
confounds : :obj:`pandas.DataFrame`, optional
Must contain a subject_label column. All other columns are
considered as confounds and included in the model. If
design_matrix is provided then this argument is ignored.
The resulting second level design matrix uses the same column
names as in the given DataFrame for confounds. At least two columns
are expected, "subject_label" and at least one confound.
design_matrix : :obj:`pandas.DataFrame`, optional
Design matrix to fit the GLM. The number of rows
in the design matrix must agree with the number of maps derived
from second_level_input.
Ensure that the order of maps given by a second_level_input
list of Niimgs matches the order of the rows in the design matrix.
second_level_contrast : :obj:`str` or array of shape (n_col), optional
Where ``n_col`` is the number of columns of the design matrix.
The default (None) is accepted if the design matrix has a single
column, in which case the only possible contrast array((1)) is
applied; when the design matrix has multiple columns, an error is
raised.
first_level_contrast : :obj:`str`, optional
In case a pandas DataFrame was provided as second_level_input this
is the map name to extract from the pandas dataframe map_name column.
It has to be a 't' contrast.
.. versionadded:: 0.9.0
mask : Niimg-like, :obj:`~nilearn.maskers.NiftiMasker` or \
:obj:`~nilearn.maskers.MultiNiftiMasker` object, optional
Mask to be used on data. If an instance of masker is passed,
then its mask will be used. If no mask is given,
it will be computed automatically by a MultiNiftiMasker with default
parameters. Automatic mask computation assumes first level imgs have
already been masked.
%(smoothing_fwhm)s
model_intercept : :obj:`bool`, optional
If True, a constant column is added to the confounding variates
unless the tested variate is already the intercept.
Default=True.
n_perm : :obj:`int`, optional
Number of permutations to perform.
Permutations are costly but the more are performed, the more precision
one gets in the p-values estimation. Default=10000.
two_sided_test : :obj:`bool`, optional
If True, performs an unsigned t-test. Both positive and negative
effects are considered; the null hypothesis is that the effect is zero.
If False, only positive effects are considered as relevant. The null
hypothesis is that the effect is zero or negative.
Default=False.
random_state : :obj:`int` or None, optional
Seed for random number generator, to have the same permutations
in each computing units.
n_jobs : :obj:`int`, optional
Number of parallel workers.
If -1 is provided, all CPUs are used.
A negative number indicates that all the CPUs except (abs(n_jobs) - 1)
ones will be used. Default=1.
verbose : :obj:`int`, optional
Verbosity level (0 means no message). Default=0.
threshold : None or :obj:`float`, optional
Cluster-forming threshold in p-scale.
This is only used for cluster-level inference.
If None, no cluster-level inference will be performed.
Default=None.
.. warning::
Performing cluster-level inference will increase the computation
time of the permutation procedure.
.. versionadded:: 0.9.2.dev
Returns
-------
neg_log10_vfwe_pvals_img : :class:`~nibabel.nifti1.Nifti1Image`
The image which contains negative logarithm of the
voxel-level FWER-corrected p-values.
.. note::
This is returned if ``threshold`` is None (the default).
outputs : :obj:`dict`
Output images, organized in a dictionary.
Each image is 3D/4D, with the potential fourth dimension corresponding
to the regressors.
.. note::
This is returned if ``threshold`` is not None.
.. versionadded:: 0.9.2.dev
Here are the keys:
=============== =======================================================
key description
=============== =======================================================
t T-statistics associated with the significance test of
the n_regressors explanatory variates against the
n_descriptors target variates.
logp_max_t Negative log10 family-wise error rate-corrected
p-values corrected based on the distribution of maximum
t-statistics from permutations.
logp_max_size Negative log10 family-wise error rate-corrected
p-values corrected based on the distribution of maximum
cluster sizes from permutations.
This map is generated through cluster-level methods, so
the values in the map describe the significance of
clusters, rather than individual voxels.
Returned only if ``threshold`` is not None.
logp_max_mass Negative log10 family-wise error rate-corrected
p-values corrected based on the distribution of maximum
cluster masses from permutations.
This map is generated through cluster-level methods, so
the values in the map describe the significance of
clusters, rather than individual voxels.
Returned only if ``threshold`` is not None.
============= =======================================================
"""
_check_second_level_input(second_level_input,
design_matrix,
flm_object=False,
df_object=True)
_check_confounds(confounds)
_check_design_matrix(design_matrix)
if isinstance(second_level_input, pd.DataFrame):
second_level_input = _sort_input_dataframe(second_level_input)
sample_map, _ = _process_second_level_input(second_level_input)
# Report progress
t0 = time.time()
if verbose > 0:
sys.stderr.write("Fitting second level model...")
# Learn the mask. Assume the first level imgs have been masked.
if not isinstance(mask, NiftiMasker):
masker = NiftiMasker(mask_img=mask,
smoothing_fwhm=smoothing_fwhm,
memory=Memory(None),
verbose=max(0, verbose - 1),
memory_level=1)
else:
masker = clone(mask)
if smoothing_fwhm is not None:
if getattr(masker, 'smoothing_fwhm') is not None:
warn('Parameter smoothing_fwhm of the masker overridden')
setattr(masker, 'smoothing_fwhm', smoothing_fwhm)
masker.fit(sample_map)
# Report progress
if verbose > 0:
sys.stderr.write("\nComputation of second level model done in "
"%i seconds\n" % (time.time() - t0))
# Check and obtain the contrast
contrast = _get_contrast(second_level_contrast, design_matrix)
# Get effect_maps
effect_maps = _infer_effect_maps(second_level_input, first_level_contrast)
# Check design matrix and effect maps agree on number of rows
_check_effect_maps(effect_maps, design_matrix)
# Obtain tested_var
if contrast in design_matrix.columns.tolist():
tested_var = np.asarray(design_matrix[contrast])
# Mask data
target_vars = masker.transform(effect_maps)
# Perform massively univariate analysis with permuted OLS
outputs = permuted_ols(
tested_var,
target_vars,
model_intercept=model_intercept,
n_perm=n_perm,
two_sided_test=two_sided_test,
random_state=random_state,
n_jobs=n_jobs,
verbose=max(0, verbose - 1),
masker=masker,
threshold=threshold,
output_type='dict',
)
neg_log10_vfwe_pvals = outputs['logp_max_t']
neg_log10_vfwe_pvals_img = masker.inverse_transform(
np.ravel(neg_log10_vfwe_pvals), )
if threshold is not None:
# Original t-statistics
t_img = masker.inverse_transform(np.ravel(outputs['t']))
# Cluster size-based p-values
neg_log10_csfwe_pvals_img = masker.inverse_transform(
np.ravel(outputs['logp_max_size']), )
# Cluster mass-based p-values
neg_log10_cmfwe_pvals_img = masker.inverse_transform(
np.ravel(outputs['logp_max_mass']), )
out = {
't': t_img,
'logp_max_t': neg_log10_vfwe_pvals_img,
'logp_max_size': neg_log10_csfwe_pvals_img,
'logp_max_mass': neg_log10_cmfwe_pvals_img,
}
return out
else:
return neg_log10_vfwe_pvals_img
class SecondLevelModel(BaseGLM):
""" Implementation of the General Linear Model for multiple subject
fMRI data
Parameters
----------
mask_img : Niimg-like, NiftiMasker or MultiNiftiMasker object, optional
Mask to be used on data. If an instance of masker is passed,
then its mask will be used. If no mask is given,
it will be computed automatically by a MultiNiftiMasker with default
parameters. Automatic mask computation assumes first level imgs have
already been masked.
target_affine : 3x3 or 4x4 matrix, optional
This parameter is passed to :func:`nilearn.image.resample_img`.
Please see the related documentation for details.
target_shape : 3-tuple of integers, optional
This parameter is passed to :func:`nilearn.image.resample_img`.
Please see the related documentation for details.
%(smoothing_fwhm)s
memory : string, optional
Path to the directory used to cache the masking process and the glm
fit. By default, no caching is done. Creates instance of joblib.Memory.
memory_level : integer, optional
Rough estimator of the amount of memory used by caching. Higher value
means more memory for caching. Default=1.
verbose : integer, optional
Indicate the level of verbosity. By default, nothing is printed.
If 0 prints nothing. If 1 prints final computation time.
If 2 prints masker computation details. Default=0.
n_jobs : integer, optional
The number of CPUs to use to do the computation. -1 means
'all CPUs', -2 'all CPUs but one', and so on.
Default=1.
minimize_memory : boolean, optional
Gets rid of some variables on the model fit results that are not
necessary for contrast computation and would only be useful for
further inspection of model details. This has an important impact
on memory consumption. Default=True.
Notes
-----
This class is experimental.
It may change in any future release of Nilearn.
"""
def __init__(self,
mask_img=None,
target_affine=None,
target_shape=None,
smoothing_fwhm=None,
memory=Memory(None),
memory_level=1,
verbose=0,
n_jobs=1,
minimize_memory=True):
self.mask_img = mask_img
self.target_affine = target_affine
self.target_shape = target_shape
self.smoothing_fwhm = smoothing_fwhm
if isinstance(memory, str):
self.memory = Memory(memory)
else:
self.memory = memory
self.memory_level = memory_level
self.verbose = verbose
self.n_jobs = n_jobs
self.minimize_memory = minimize_memory
self.second_level_input_ = None
self.confounds_ = None
self.labels_ = None
self.results_ = None
def fit(self, second_level_input, confounds=None, design_matrix=None):
""" Fit the second-level GLM
1. create design matrix
2. do a masker job: fMRI_data -> Y
3. fit regression to (Y, X)
Parameters
----------
second_level_input: list of `FirstLevelModel` objects or pandas
DataFrame or list of Niimg-like objects.
Giving FirstLevelModel objects will allow to easily compute
the second level contrast of arbitrary first level contrasts thanks
to the first_level_contrast argument of the compute_contrast
method. Effect size images will be computed for each model to
contrast at the second level.
If a pandas DataFrame, then they have to contain subject_label,
map_name and effects_map_path. It can contain multiple maps that
would be selected during contrast estimation with the argument
first_level_contrast of the compute_contrast function. The
DataFrame will be sorted based on the subject_label column to avoid
order inconsistencies when extracting the maps. So the rows of the
automatically computed design matrix, if not provided, will
correspond to the sorted subject_label column.
If list of Niimg-like objects then this is taken literally as Y
for the model fit and design_matrix must be provided.
confounds : pandas DataFrame, optional
Must contain a subject_label column. All other columns are
considered as confounds and included in the model. If
design_matrix is provided then this argument is ignored.
The resulting second level design matrix uses the same column
names as in the given DataFrame for confounds. At least two columns
are expected, "subject_label" and at least one confound.
design_matrix : pandas DataFrame, optional
Design matrix to fit the GLM. The number of rows
in the design matrix must agree with the number of maps derived
from second_level_input.
Ensure that the order of maps given by a second_level_input
list of Niimgs matches the order of the rows in the design matrix.
"""
# check second_level_input
_check_second_level_input(second_level_input,
design_matrix,
confounds=confounds)
# check confounds
_check_confounds(confounds)
# check design matrix
_check_design_matrix(design_matrix)
if isinstance(second_level_input, pd.DataFrame):
second_level_input = _sort_input_dataframe(second_level_input)
self.second_level_input_ = second_level_input
self.confounds_ = confounds
sample_map, subjects_label = _process_second_level_input(
second_level_input)
# Report progress
t0 = time.time()
if self.verbose > 0:
sys.stderr.write("Fitting second level model. "
"Take a deep breath\r")
# Create and set design matrix, if not given
if design_matrix is None:
design_matrix = make_second_level_design_matrix(
subjects_label, confounds)
self.design_matrix_ = design_matrix
# Learn the mask. Assume the first level imgs have been masked.
if not isinstance(self.mask_img, NiftiMasker):
self.masker_ = NiftiMasker(mask_img=self.mask_img,
target_affine=self.target_affine,
target_shape=self.target_shape,
smoothing_fwhm=self.smoothing_fwhm,
memory=self.memory,
verbose=max(0, self.verbose - 1),
memory_level=self.memory_level)
else:
self.masker_ = clone(self.mask_img)
for param_name in ['smoothing_fwhm', 'memory', 'memory_level']:
our_param = getattr(self, param_name)
if our_param is None:
continue
if getattr(self.masker_, param_name) is not None:
warn('Parameter %s of the masker overridden' % param_name)
setattr(self.masker_, param_name, our_param)
self.masker_.fit(sample_map)
# Report progress
if self.verbose > 0:
sys.stderr.write("\nComputation of second level model done in "
"%i seconds\n" % (time.time() - t0))
return self
def compute_contrast(self,
second_level_contrast=None,
first_level_contrast=None,
second_level_stat_type=None,
output_type='z_score'):
"""Generate different outputs corresponding to
the contrasts provided e.g. z_map, t_map, effects and variance.
Parameters
----------
second_level_contrast : str or array of shape (n_col), optional
Where ``n_col`` is the number of columns of the design matrix. The
string can be a formula compatible with `pandas.DataFrame.eval`.
Basically one can use the name of the conditions as they appear in
the design matrix of the fitted model combined with operators +-
and combined with numbers with operators +-`*`/. The default (None)
is accepted if the design matrix has a single column, in which case
the only possible contrast array((1)) is applied; when the design
matrix has multiple columns, an error is raised.
first_level_contrast : str or array of shape (n_col) with respect to
FirstLevelModel, optional
In case a list of FirstLevelModel was provided as
second_level_input, we have to provide a contrast to apply to
the first level models to get the corresponding list of images
desired, that would be tested at the second level. In case a
pandas DataFrame was provided as second_level_input this is the
map name to extract from the pandas dataframe map_name column.
It has to be a 't' contrast.
second_level_stat_type : {'t', 'F'}, optional
Type of the second level contrast
output_type : str, optional
Type of the output map. Can be 'z_score', 'stat', 'p_value',
'effect_size', 'effect_variance' or 'all'.
Default='z-score'.
Returns
-------
output_image : Nifti1Image
The desired output image(s). If ``output_type == 'all'``, then
the output is a dictionary of images, keyed by the type of image.
"""
if self.second_level_input_ is None:
raise ValueError('The model has not been fit yet')
# check first_level_contrast
_check_first_level_contrast(self.second_level_input_,
first_level_contrast)
# check contrast and obtain con_val
con_val = _get_con_val(second_level_contrast, self.design_matrix_)
# check output type
# 'all' is assumed to be the final entry;
# if adding more, place before 'all'
valid_types = [
'z_score', 'stat', 'p_value', 'effect_size', 'effect_variance',
'all'
]
_check_output_type(output_type, valid_types)
# Get effect_maps appropriate for chosen contrast
effect_maps = _infer_effect_maps(self.second_level_input_,
first_level_contrast)
# Check design matrix X and effect maps Y agree on number of rows
_check_effect_maps(effect_maps, self.design_matrix_)
# Fit an Ordinary Least Squares regression for parametric statistics
Y = self.masker_.transform(effect_maps)
if self.memory:
mem_glm = self.memory.cache(run_glm, ignore=['n_jobs'])
else:
mem_glm = run_glm
labels, results = mem_glm(Y,
self.design_matrix_.values,
n_jobs=self.n_jobs,
noise_model='ols')
# We save memory if inspecting model details is not necessary
if self.minimize_memory:
for key in results:
results[key] = SimpleRegressionResults(results[key])
self.labels_ = labels
self.results_ = results
# We compute contrast object
if self.memory:
mem_contrast = self.memory.cache(compute_contrast)
else:
mem_contrast = compute_contrast
contrast = mem_contrast(self.labels_, self.results_, con_val,
second_level_stat_type)
output_types = \
valid_types[:-1] if output_type == 'all' else [output_type]
outputs = {}
for output_type_ in output_types:
# We get desired output from contrast object
estimate_ = getattr(contrast, output_type_)()
# Prepare the returned images
output = self.masker_.inverse_transform(estimate_)
contrast_name = str(con_val)
output.header['descrip'] = ('%s of contrast %s' %
(output_type, contrast_name))
outputs[output_type_] = output
return outputs if output_type == 'all' else output
def _get_voxelwise_model_attribute(self, attribute, result_as_time_series):
"""Transform RegressionResults instances within a dictionary
(whose keys represent the autoregressive coefficient under the 'ar1'
noise model or only 0.0 under 'ols' noise_model and values are the
RegressionResults instances) into input nifti space.
Parameters
----------
attribute : str
an attribute of a RegressionResults instance.
possible values include: 'residuals', 'normalized_residuals',
'predicted', SSE, r_square, MSE.
result_as_time_series : bool
whether the RegressionResult attribute has a value
per timepoint of the input nifti image.
Returns
-------
output : list
A list of Nifti1Image(s).
"""
# check if valid attribute is being accessed.
all_attributes = dict(vars(RegressionResults)).keys()
possible_attributes = [
prop for prop in all_attributes if '__' not in prop
]
if attribute not in possible_attributes:
msg = ("attribute must be one of: "
"{attr}".format(attr=possible_attributes))
raise ValueError(msg)
if self.minimize_memory:
raise ValueError(
'To access voxelwise attributes like '
'R-squared, residuals, and predictions, '
'the `SecondLevelModel`-object needs to store '
'there attributes. '
'To do so, set `minimize_memory` to `False` '
'when initializing the `SecondLevelModel`-object.')
if self.labels_ is None or self.results_ is None:
raise ValueError("The model has no results. This could be "
"because the model has not been fitted yet "
"or because no contrast has been computed "
"already.")
if result_as_time_series:
voxelwise_attribute = np.zeros(
(self.design_matrix_.shape[0], len(self.labels_)))
else:
voxelwise_attribute = np.zeros((1, len(self.labels_)))
for label_ in self.results_:
label_mask = self.labels_ == label_
voxelwise_attribute[:,
label_mask] = getattr(self.results_[label_],
attribute)
return self.masker_.inverse_transform(voxelwise_attribute)
######################################################################
# Reshape and mask images
# -----------------------
print("\nReshaping and masking images.\n")
with warnings.catch_warnings():
warnings.simplefilter('ignore', UserWarning)
warnings.simplefilter('ignore', DeprecationWarning)
mask_img = load_mni152_brain_mask()
masker = NiftiMasker(
mask_img=mask_img, memory='nilearn_cache', memory_level=1)
masker = masker.fit()
# Images may fail to be transformed, and are of different shapes,
# so we need to transform one-by-one and keep track of failures.
X = []
is_usable = np.ones((len(images),), dtype=bool)
for index, image_path in enumerate(images):
# load image and remove nan and inf values.
# applying smooth_img to an image with fwhm=None simply cleans up
# non-finite values but otherwise doesn't modify the image.
image = smooth_img(image_path, fwhm=None)
try:
X.append(masker.transform(image))
except Exception as e:
meta = nv_data['images_meta'][index]
# Load Miyawaki dataset
from nilearn import datasets
miyawaki_dataset = datasets.fetch_miyawaki2008()
# print basic information on the dataset
print('First functional nifti image (4D) is located at: %s' %
miyawaki_dataset.func[0]) # 4D data
miyawaki_filename = miyawaki_dataset.func[0]
miyawaki_mean_img = image.mean_img(miyawaki_filename)
plot_epi(miyawaki_mean_img, title='Mean EPI image')
###############################################################################
# A NiftiMasker with the default strategy
masker = NiftiMasker()
masker.fit(miyawaki_filename)
# Plot the generated mask using the mask_img_ attribute
plot_roi(masker.mask_img_,
miyawaki_mean_img,
title="Mask from already masked data")
###############################################################################
# Plot the generated mask using the .generate_report method
report = masker.generate_report()
report
###############################################################################
# Computing a mask from raw EPI data
###############################################################################
#
def test_cluster_level_parameters_smoke(random_state=0):
"""Test combinations of parameters related to cluster-level inference."""
import nibabel as nib
from nilearn.maskers import NiftiMasker
# create design
target_var1 = np.arange(0, 10).reshape((-1, 1)) # positive effect
target_var = np.hstack(( # corresponds to 3 x 3 x 3 x 10 niimg
target_var1, # voxel 1 has positive effect
-target_var1, # voxel 2 has negative effect
np.random.random((10, 25)), # 25 remaining voxels
))
tested_var = np.arange(0, 20, 2)
mask_img = nib.Nifti1Image(np.ones((3, 3, 3)), np.eye(4))
masker = NiftiMasker(mask_img)
masker.fit(mask_img)
# threshold is defined, indicating cluster-level inference should be done,
# but masker is not defined.
with pytest.raises(ValueError):
permuted_ols(
tested_var,
target_var,
model_intercept=False,
two_sided_test=False,
n_perm=100,
random_state=random_state,
threshold=0.001,
masker=None,
)
# masker is defined, but threshold is not.
# no cluster-level inference is performed, but there's a warning.
with pytest.warns():
out = permuted_ols(
tested_var,
target_var,
model_intercept=False,
two_sided_test=False,
n_perm=100,
random_state=random_state,
threshold=None,
masker=masker,
output_type="legacy",
)
assert isinstance(out, tuple)
# threshold is defined, but output_type is "legacy".
# raise a warning, and get a dictionary.
with pytest.warns():
out = permuted_ols(
tested_var,
target_var,
model_intercept=False,
two_sided_test=False,
n_perm=0,
random_state=random_state,
threshold=0.001,
masker=masker,
output_type="legacy",
)
assert isinstance(out, dict)
# output_type is "legacy".
# raise a deprecation warning, but get the standard output.
with pytest.warns(DeprecationWarning):
out = permuted_ols(
tested_var,
target_var,
model_intercept=False,
two_sided_test=False,
n_perm=100,
random_state=random_state,
threshold=None,
masker=None,
output_type="legacy",
)
assert isinstance(out, tuple)
# no permutations and output_type is "dict", so check for "t" map
out = permuted_ols(
tested_var,
target_var,
model_intercept=False,
two_sided_test=False,
n_perm=0,
random_state=random_state,
threshold=None,
masker=None,
output_type="dict",
)
assert isinstance(out, dict)
assert "t" in out.keys()
# permutations, threshold, and masker are defined,
# so check for cluster-level maps
n_perm = 10
out = permuted_ols(
tested_var,
target_var,
model_intercept=False,
two_sided_test=True,
n_perm=n_perm,
random_state=random_state,
threshold=0.001,
masker=masker,
output_type="dict",
)
assert isinstance(out, dict)
assert "t" in out.keys()
assert "logp_max_t" in out.keys()
assert "logp_max_size" in out.keys()
assert "logp_max_mass" in out.keys()
assert "h0_max_t" in out.keys()
assert "h0_max_size" in out.keys()
assert "h0_max_mass" in out.keys()
assert out["h0_max_t"].size == n_perm
assert out["h0_max_size"].size == n_perm
assert out["h0_max_mass"].size == n_perm
def test_compute_brain_mask(strategy, mask_args, expected_mask):
# Check masker for template masking strategy
img = _get_random_img((9, 9, 5))
masker = NiftiMasker(mask_strategy=strategy, mask_args=mask_args)
masker.fit(img)
np.testing.assert_array_equal(get_data(masker.mask_img_), expected_mask)