def extract_data(images, masks):
""" given a set of brain images and a set of masks, extract the average signal inside each mask for each brain image.
Returns a dataframe with 3 columns: image, mask, value.
"""
masker = NiftiMapsMasker(masks)
values = masker.fit_transform(images)
nimgs, nmasks = values.shape
cp = op.commonpath(images)
labelsimages = [i.replace(cp, '') for i in images]
print(cp)
print(labelsimages)
cpmask = op.commonprefix(masks)
labelsrois = [i.replace(cpmask, '').replace('.nii.gz', '') for i in masks]
print(cpmask)
print(labelsrois)
df = pd.DataFrame(columns=['image', 'mask', 'value'])
row = 0
for iimg in range(nimgs):
for iroi in range(nmasks):
df.loc[row] = pd.Series({
'image': labelsimages[iimg],
'mask': labelsrois[iroi],
'value': values[iimg, iroi]
})
row = row + 1
return df
def extract_from_masker(dataset_like,dataset_mask, funci, timer =True):
tic = time.clock()
maps_img = dict_to_list(dataset_like)
#add mask, smoothing, filter and detrending
print 'Nifti'
masker = NiftiMapsMasker(maps_img=maps_img,
mask_img = dataset_mask,
low_pass = .1,
high_pass = .01,
smoothing_fwhm =6.,
t_r = 1.05,
detrend = True,
standardize = False,
resampling_target ='data',
memory_level = 0,
verbose=5)
#extract signal to x
print 'masker'
x = masker.fit_transform(funci)
if timer:
print time.clock() - tic
return x
def extract_rois_signals(preprocessing_folder ='pipeline_2', prefix= 'resampled_wr'):
dataset = load_dynacomp(preprocessing_folder = preprocessing_folder,prefix = prefix)
for idx, func in enumerate([dataset.func1, dataset.func2]):
for i in range(len(dataset.subjects)):
tic = time.clock()
print func[i]
output_path, _ = os.path.split(func[i])
print dataset.subjects[i]
maps_img = dict_to_list(dataset.rois[i])
#add mask, smoothing, filter and detrending
print 'Nifti'
masker = NiftiMapsMasker(maps_img=maps_img,
mask_img = dataset.mask,
low_pass = .1,
high_pass = .01,
smoothing_fwhm =6.,
t_r = 1.05,
detrend = True,
standardize = False,
resampling_target ='data',
memory_level = 0,
verbose=5)
#extract signal to x
print 'masker'
x = masker.fit_transform(func[i])
print x
np.save(os.path.join(PATH_TO_SAVE_DATA,'output' + str(i+1) +'_rois_filter'),x)
print time.clock() - tic
return x
def extract_one_signal(dataset):
for idx, func in enumerate([dataset.func1, dataset.func2]):
for i in range(len(dataset.subjects)):
tic = time.clock()
#maps_img = dict_to_list(func)
#add mask, smoothing, filter and detrending
maps_img = dict_to_list(dataset.rois[i])
masker = NiftiMapsMasker(maps_img=maps_img,
mask_img = dataset.mask,
low_pass = .1,
high_pass = .01,
smoothing_fwhm =6.,
t_r = 1.05,
detrend = True,
standardize = False,
resampling_target ='data',
memory_level = 0,
verbose=5)
#extract signal to x
x = masker.fit_transform(func[i])
print "loading time : "+ str(time.clock() - tic)
return x,maps_img
def get_data_in_roi(path_roi, data_file):
"""Using of the NiftiMapsMasker """
masker = NiftiMapsMasker([path_roi])
array_datas = np.zeros((len(data_file), 177))
for e, d in enumerate(data_file):
nifti_obj = nibabel.load(d)
data = masker.fit_transform(d)
array_datas[e-1] = data.ravel()
return array_datas
def get_data_in_roi(path_roi, data_file):
"""Using of the NiftiMapsMasker """
masker = NiftiMapsMasker([path_roi])
array_datas = np.zeros((len(data_file), 177))
for e, d in enumerate(data_file):
nifti_obj = nibabel.load(d)
data = masker.fit_transform(d)
array_datas[e - 1] = data.ravel()
return array_datas
def extract_parcellation_time_series(in_data, parcellation_name,
parcellations_dict, bp_freqs, tr):
'''
Depending on parcellation['is_probabilistic'] this function chooses either NiftiLabelsMasker or NiftiMapsMasker
to extract the time series of each parcel
if bp_freq: data is band passfiltered at (hp, lp), if (None,None): no filter, if (None, .1) only lp...
tr in ms (e.g. from freesurfer ImageInfo())
returns np.array with parcellation time series and saves this array also to parcellation_time_series_file, and
path to pickled masker object
'''
from nilearn.input_data import NiftiLabelsMasker, NiftiMapsMasker, NiftiSpheresMasker
import os, pickle
import numpy as np
if parcellations_dict[parcellation_name][
'is_probabilistic'] == True: # use probab. nilearn
masker = NiftiMapsMasker(
maps_img=parcellations_dict[parcellation_name]['nii_path'],
standardize=True)
elif parcellations_dict[parcellation_name]['is_probabilistic'] == 'sphere':
atlas = pickle.load(
open(parcellations_dict[parcellation_name]['nii_path']))
coords = atlas.rois
masker = NiftiSpheresMasker(coords,
radius=5,
allow_overlap=True,
standardize=True)
else: # 0/1 labels
masker = NiftiLabelsMasker(
labels_img=parcellations_dict[parcellation_name]['nii_path'],
standardize=True)
# add bandpass filter (only executes if freq not None
hp, lp = bp_freqs
masker.low_pass = lp
masker.high_pass = hp
if tr is not None:
masker.t_r = tr
else:
masker.t_r = None
masker.standardize = True
masker_file = os.path.join(os.getcwd(), 'masker.pkl')
with open(masker_file, 'w') as f:
pickle.dump(masker, f)
parcellation_time_series = masker.fit_transform(in_data)
parcellation_time_series_file = os.path.join(
os.getcwd(), 'parcellation_time_series.npy')
np.save(parcellation_time_series_file, parcellation_time_series)
return parcellation_time_series, parcellation_time_series_file, masker_file
def extract_timeseries_probabilistic(filename, maps, confounds=None):
"""Because the power parcellation is given in coordinates and not labels,
we dedicate an exclusive function to deal with it.
"""
maps_masker = NiftiMapsMasker(maps,
resampling_target="data",
standardize=True)
time_series = maps_masker.fit_transform(filename, confounds=confounds)
return time_series
def test_nifti_maps_masker_report_image_in_fit(niftimapsmasker_inputs):
""""""
masker = NiftiMapsMasker(**niftimapsmasker_inputs)
image, _ = generate_random_img((13, 11, 12), affine=np.eye(4), length=3)
masker.fit(image)
html = masker.generate_report(2)
assert masker._report_content['report_id'] == 0
assert masker._report_content['number_of_maps'] == 9
assert masker._report_content['warning_message'] is None
assert html.body.count("<img") == 2
def spatial_correlations(mm, atlas=None):
if atlas is None:
from nilearn.datasets import fetch_atlas_msdl
atlas = fetch_atlas_msdl()
from nilearn.input_data import NiftiMapsMasker
masker = NiftiMapsMasker(maps_img=atlas['maps'])
rsns_masked = masker.fit_transform(atlas['maps'])
mm_masked = masker.fit_transform([mm])
cc = np.corrcoef(mm_masked, rsns_masked)
return cc
def run_mini_pipeline():
atlas = datasets.fetch_atlas_msdl()
atlas_img = atlas['maps']
labels = pd.read_csv(atlas['labels'])['name']
masker = NiftiMapsMasker(maps_img=atlas_img, standardize=True,
memory='/tmp/nilearn', verbose=0)
data = datasets.fetch_adhd(number_subjects)
figures_folder = '../figures/'
count=0
for func_file, confound_file in zip(data.func, data.confounds):
# fit the data to the atlas mask, regress out confounds
time_series = masker.fit_transform(func_file, confounds=confound_file)
correlation = np.corrcoef(time_series.T)
#plotting starts here
plt.figure(figsize=(10, 10))
plt.imshow(correlation, interpolation="nearest")
x_ticks = plt.xticks(range(len(labels)), labels, rotation=90)
y_ticks = plt.yticks(range(len(labels)), labels)
corr_file = figures_folder+'subject_number_' + str(count) + '_correlation.pdf'
plt.savefig(corr_file)
atlas_region_coords = [plotting.find_xyz_cut_coords(img) for img in image.iter_img(atlas_img)]
threshold = 0.6
plotting.plot_connectome(correlation, atlas_region_coords, edge_threshold=threshold)
connectome_file = figures_folder+'subject_number_' + str(count) + '_connectome.pdf'
plt.savefig(connectome_file)
#graph setup
#binarize correlation matrix
correlation[correlation<threshold] = 0
correlation[correlation != 0] = 1
graph = nx.from_numpy_matrix(correlation)
partition=louvain.best_partition(graph)
values = [partition.get(node) for node in graph.nodes()]
plt.figure()
nx.draw_spring(graph, cmap = plt.get_cmap('jet'), node_color = values, node_size=30, with_labels=True)
graph_file = figures_folder+'subject_number_' + str(count) + '_community.pdf'
plt.savefig(graph_file)
count += 1
plt.close('all')
def get_data_in_rois_method2(ROIs, subjects, contrasts, condir, localizerf, threshold):
""" returns, for individual subjects, the average contrasts values in ROIs masked by individual localizers,
thresholded at a fixed theshold"""
values = np.zeros((len(subjects), len(contrasts), len(ROIs)))
for isub, sub in enumerate(subjects):
conlist = [op.join(sub, condir, x) for x in contrasts]
localizer_img = nibabel.load(op.join(sub, localizerf))
locmask = binarize_img(localizer_img, threshold)
masker = NiftiMapsMasker(ROIs, locmask)
values[isub, :] = masker.fit_transform(conlist)
return values
def get_data_in_rois_method2(ROIs, subjects, contrasts, condir, localizerf,
threshold):
""" returns, for individual subjects, the average contrasts values in ROIs masked by individual localizers,
thresholded at a fixed theshold"""
values = np.zeros((len(subjects), len(contrasts), len(ROIs)))
for isub, sub in enumerate(subjects):
conlist = [op.join(sub, condir, x) for x in contrasts]
localizer_img = nibabel.load(op.join(sub, localizerf))
locmask = binarize_img(localizer_img, threshold)
masker = NiftiMapsMasker(ROIs, locmask)
values[isub, :] = masker.fit_transform(conlist)
return values
def get_data_in_rois_method1(ROIs, subjects, contrasts, condir):
""" returns the average contratst in each ROI and for each subject """
masker = NiftiMapsMasker(ROIs)
print ROIs
values = np.zeros((len(subjects), len(contrasts), len(ROIs)))
for isub, sub in enumerate(subjects):
conlist = [op.join(sub, condir, x) for x in contrasts]
print conlist
res = masker.fit_transform(conlist)
values[isub, :] = masker.fit_transform(conlist)
#print values
return values
def get_data_in_rois_method1(ROIs, subjects, contrasts, condir):
""" returns the average contratst in each ROI and for each subject """
masker = NiftiMapsMasker(ROIs)
print ROIs
values = np.zeros((len(subjects), len(contrasts), len(ROIs)))
for isub, sub in enumerate(subjects):
conlist = [op.join(sub, condir, x) for x in contrasts]
print conlist
res = masker.fit_transform(conlist)
values[isub, :] = masker.fit_transform(conlist)
#print values
return values
def test_nifti_maps_masker_report_list_and_arrays_maps_number(
niftimapsmasker_inputs, displayed_maps):
"""Tests report generation for NiftiMapsMasker with displayed_maps
passed as a list of a Numpy arrays.
"""
masker = NiftiMapsMasker(**niftimapsmasker_inputs)
masker.fit()
html = masker.generate_report(displayed_maps)
assert masker._report_content['report_id'] == 0
assert masker._report_content['number_of_maps'] == 9
assert (masker._report_content['displayed_maps'] == list(displayed_maps))
msg = ("No image provided to fit in NiftiMapsMasker. "
"Plotting only spatial maps for reporting.")
assert masker._report_content['warning_message'] == msg
assert html.body.count("<img") == len(displayed_maps)
def series_times_ROI(Maps, func, typeF):
from nilearn.input_data import NiftiLabelsMasker, NiftiMapsMasker
from nilearn import plotting
import scipy.io as sio
import numpy as np
import os
##################################
Resul = os.getcwd() #+'-Results'
n_map = Maps[Maps.rfind('/') + 1:][:Maps[Maps.rfind('/') + 1:].find('.')]
n_plot = 'empty_plot'
#os.system('mkdir '+Resul)
##################################
if typeF == 'Labels':
masker = NiftiLabelsMasker(labels_img=Maps, standardize=True)
plot_atlas = plotting.plot_roi(Maps)
n_plot = Resul + '/Atlas_' + n_map + '_' + typeF + '.svg'
plot_atlas.savefig(n_plot)
if typeF == 'Maps':
masker = NiftiMapsMasker(maps_img=Maps,
standardize=True,
memory='nilearn_cache',
verbose=5)
time_series = masker.fit_transform(func)
print('Shape of serial times ', np.shape(time_series))
out_mat = Resul + '/Time_series_' + n_map + '_' + typeF + '.mat'
sio.savemat(out_mat, {'time_series': time_series})
return out_mat, n_plot
def compute_connectivity_subjects(func_list, atlas, mask, conn, n_jobs=-1):
""" Returns connectivities for all subjects
tril matrix n_subjects * n_rois_tril
"""
if len(nib.load(atlas).shape) == 4:
masker = NiftiMapsMasker(maps_img=atlas,
mask_img=mask,
detrend=True,
low_pass=.1,
high_pass=.01,
t_r=3.,
resampling_target='data',
smoothing_fwhm=6,
memory=CACHE_DIR,
memory_level=2)
else:
masker = NiftiLabelsMasker(labels_img=atlas,
mask_img=mask,
t_r=3.,
detrend=True,
low_pass=.1,
high_pass=.01,
resampling_target='data',
smoothing_fwhm=6,
memory=CACHE_DIR,
memory_level=2)
p = Parallel(n_jobs=n_jobs, verbose=5)(delayed(
compute_connectivity_subject)(conn, func, masker)\
for func in func_list)
return np.asarray(p)
def getConnectome(imgPath=None,
atlasPath=None,
viewInBrowser=False,
displayCovMatrix=False):
"""
Gets the connectome of a functional MRI scan
imgPath -> absolute or relative path to the .nii file
atlasPath -> download path for the reference MSDL atlas
viewInBrowser (optional, default=False) -> if True, opens up an interactive viewer in the browser
displayCovMatrix (optional, default=False) -> display the inverse covariance matrix
Returns a tuple of shape (estimator, atlas)
"""
# Download the reference atlas
atlas = datasets.fetch_atlas_msdl(data_dir=atlasPath)
# Loading atlas image stored in 'maps'
atlasFilename = atlas['maps']
# Get the time series for the fMRI scan
masker = NiftiMapsMasker(maps_img=atlasFilename,
standardize=True,
memory='nilearn_cache',
verbose=5)
timeSeries = masker.fit_transform(imgPath)
# Compute the connectome using sparse inverse covariance
estimator = GraphicalLassoCV()
estimator.fit(timeSeries)
if (displayCovMatrix):
labels = atlas['labels']
plotting.plot_matrix(estimator.covariance_,
labels=labels,
figure=(9, 7),
vmax=1,
vmin=-1,
title='Covariance')
plotting.plot_matrix(estimator.precision_,
labels=labels,
figure=(9, 7),
vmax=1,
vmin=-1,
title='Inverse covariance (Precision)')
#covPlot.get_figure().savefig('Covariance.png')
# precPlot.get_figure().savefig('Inverse Covariance.png')
if (viewInBrowser):
coords = atlas.region_coords
view = plotting.view_connectome(-estimator.precision_, coords, '60.0%')
#view.save_as_html(file_name='Connectome Test.html')
view.open_in_browser()
return (estimator, atlas)
def get_data(subj, mask, sessions=None, dtype='jacobian'):
"""
Parameters
----------
subj : (N,) list of img_like
mask : Niimg_like
sessions : list of str
Returns
-------
data : (N x M) np.ndarray
Data extracted from ``imgs``, where ``M`` is the number of parcels in
``mask``
"""
# check mask is correct
if not isinstance(mask, BaseMasker):
if not isinstance(mask, str):
raise ValueError('Mask must be a mask object or filepath.')
if 'probabilistic' in mask:
mask = NiftiMapsMasker(mask, resampling_target='maps')
else:
mask = NiftiLabelsMasker(mask, resampling_target='labels')
# only fit mask if it hasn't been fitted to save time
if not hasattr(mask, 'maps_img_'):
mask = mask.fit()
# get images for supplied sessions (or all images)
subj_dir = pjoin(DERIV_DIR, subj)
if sessions is not None:
imgs = list(
itertools.chain.from_iterable(
[glob.glob(pjoin(subj_dir, f'*_ses-{ses}_*_{dtype}.nii.gz'))
for ses in sorted(sessions)]
)
)
else:
imgs = sorted(glob.glob(pjoin(subj_dir, '*{dtype}.nii.gz')))
# extract subject / session information from data (BIDS format)
demo = np.row_stack([REGEX.findall(i) for i in imgs])
# fit mask to data and stack across sessions
data = np.row_stack([mask.transform(check_niimg(img, atleast_4d=True))
for img in imgs])
return data, demo
def _fmri_roi_extract_image(data, atlas_path, atlas_type, radius, overlap_ok,mask = None):
if 'label' in atlas_type:
logging.debug('Labels Extract')
label_masker = NiftiLabelsMasker(atlas_path, mask_img=mask)
timeseries = label_masker.fit_transform(data)
if 'sphere' in atlas_type:
atlas_path = np.loadtxt(atlas_path)
logging.debug('Sphere Extract')
spheres_masker = NiftiSpheresMasker(atlas_path, float(radius),mask_img=mask, allow_overlap = overlap_ok)
timeseries = spheres_masker.fit_transform(data)
if 'maps' in atlas_type:
logging.debug('Maps Extract')
maps_masker = NiftiMapsMasker(atlas_path,mask_img=mask, allow_overlap = overlap_ok)
timeseries = maps_masker.fit_transform(data)
timeseries[timeseries == 0.0] = np.nan
return timeseries
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 extract_parcellation_time_series(in_data, parcellation_name, parcellations_dict, bp_freqs, tr):
'''
Depending on parcellation['is_probabilistic'] this function chooses either NiftiLabelsMasker or NiftiMapsMasker
to extract the time series of each parcel
if bp_freq: data is band passfiltered at (hp, lp), if (None,None): no filter, if (None, .1) only lp...
tr in ms (e.g. from freesurfer ImageInfo())
returns np.array with parcellation time series and saves this array also to parcellation_time_series_file, and
path to pickled masker object
'''
from nilearn.input_data import NiftiLabelsMasker, NiftiMapsMasker, NiftiSpheresMasker
import os, pickle
import numpy as np
if parcellations_dict[parcellation_name]['is_probabilistic'] == True: # use probab. nilearn
masker = NiftiMapsMasker(maps_img=parcellations_dict[parcellation_name]['nii_path'], standardize=True)
elif parcellations_dict[parcellation_name]['is_probabilistic'] == 'sphere':
atlas = pickle.load(open(parcellations_dict[parcellation_name]['nii_path']))
coords = atlas.rois
masker = NiftiSpheresMasker(coords, radius=5, allow_overlap=True, standardize=True)
else: # 0/1 labels
masker = NiftiLabelsMasker(labels_img=parcellations_dict[parcellation_name]['nii_path'],
standardize=True)
# add bandpass filter (only executes if freq not None
hp, lp = bp_freqs
masker.low_pass = lp
masker.high_pass = hp
if tr is not None:
masker.t_r = tr
else:
masker.t_r = None
masker.standardize = True
masker_file = os.path.join(os.getcwd(), 'masker.pkl')
with open(masker_file, 'w') as f:
pickle.dump(masker, f)
parcellation_time_series = masker.fit_transform(in_data)
parcellation_time_series_file = os.path.join(os.getcwd(), 'parcellation_time_series.npy')
np.save(parcellation_time_series_file, parcellation_time_series)
return parcellation_time_series, parcellation_time_series_file, masker_file
def _set_volume_masker(roi_file, as_voxels=False, **kwargs):
"""Check and see if multiple ROIs exist in atlas file"""
if not isinstance(roi_file, str):
raise ValueError('roi_file must be a file name string')
if roi_file.endswith('.csv') or roi_file.endswith('.tsv'):
roi = _read_coords(roi_file)
n_rois = len(roi)
print(' {} region(s) detected from coordinates'.format(n_rois))
if kwargs.get('radius') is None:
warnings.warn('No radius specified for coordinates; setting '
'to nilearn.input_data.NiftiSphereMasker default '
'of extracting from a single voxel')
masker = NiftiSpheresMasker(roi, **kwargs)
elif roi_file.endswith('.nii.gz'):
# remove args for NiftiSpheresMasker
if 'radius' in kwargs:
kwargs.pop('radius')
if 'allow_overlap' in kwargs:
kwargs.pop('allow_overlap')
roi_img = image.load_img(roi_file)
if len(roi_img.shape) == 4:
n_rois = roi_img.shape[-1]
print(' {} region(s) detected from {}'.format(n_rois,
roi_img.get_filename()))
masker = NiftiMapsMasker(roi_img, allow_overlap=True,**kwargs)
else:
n_rois = len(np.unique(roi_img.get_fdata())) - 1
print(' {} region(s) detected from {}'.format(n_rois,
roi_img.get_filename()))
if n_rois > 1:
masker = NiftiLabelsMasker(roi_img, **kwargs)
elif n_rois == 1:
# binary mask for single ROI
if as_voxels:
if 'mask_img' in kwargs:
kwargs.pop('mask_img')
masker = NiftiMasker(roi_img, **kwargs)
else:
# more computationally efficient if only wanting the mean
masker = NiftiLabelsMasker(roi_img, **kwargs)
else:
raise ValueError('No ROI detected; check ROI file')
else:
raise ValueError('Invalid file type for roi_file. Must be one of: '
'.nii.gz, .csv, .tsv')
return masker, n_rois
def __init__(self,
atlas_name,
metric,
mask,
detrend=True,
low_pass=.1,
high_pass=.01,
t_r=3.,
resampling_target='data',
smoothing_fwhm=6.,
memory='',
memory_level=2,
n_jobs=1):
""" - Setting attributes
- Preparing maskers
"""
self.atlas = fetch_atlas(atlas_name)
self.metric = metric
self.mask = mask
self.n_jobs = n_jobs
self.masker_vox = NiftiMasker(mask_img=self.mask,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
smoothing_fwhm=smoothing_fwhm,
memory=memory,
memory_level=memory_level)
if len(nib.load(self.atlas).shape) == 4:
self.masker_ROI = NiftiMapsMasker(
maps_img=self.atlas,
mask_img=self.mask,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
resampling_target=resampling_target,
smoothing_fwhm=smoothing_fwhm,
memory=memory,
memory_level=memory_level)
else:
self.masker_ROI = NiftiLabelsMasker(
labels_img=self.atlas,
mask_img=self.mask,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
resampling_target=resampling_target,
smoothing_fwhm=smoothing_fwhm,
memory=memory,
memory_level=memory_level)
def signal_extract(data,atlas,t_r=2.2,masker_type='Spheres',saveas='file'):
"""
Extracts BOLD time-series from regions of interest
Parameters
----------
data: Filenames of subjects.
atlas: regions or coordinates to extract signals from.
masker_type : Type of masker used to extract BOLD signals . types are : 'Spheres','Maps','Labels'
saveas : Destination to save and load output (.npz)
Returns
---------
subject_ts : array-like , 2-D (n_subjects,n_regions)
Array of BOLD time-series
"""
subjects_ts=[]
if os.path.exists(saveas):
subjects_ts=np.load(saveas)['arr_0']
else:
if masker_type== 'Spheres':
masker = NiftiSpheresMasker(
seeds=atlas, smoothing_fwhm=6, radius=4 ,mask_img=brainmask,
detrend=False, standardize=True, low_pass=0.1, high_pass=0.01, t_r=t_r)
elif masker_type == 'Maps':
masker = NiftiMapsMasker(maps_img=atlas,mask_img=brainmask,standardize=True,
high_pass=0.01,low_pass=0.1,detrend=False,t_r=t_r,
memory_level=2,smoothing_fwhm=5,resampling_target='data',
memory=mem,verbose=5)
elif masker_type == 'Labels':
masker = NiftiLabelsMasker(labels_img=atlas,mask_img=brainmask,standardize=True,
high_pass=0.01,low_pass=0.1,detrend=False,t_r=t_r,
memory_level=2,smoothing_fwhm=5,resampling_target='data',
memory=mem,verbose=5)
else:
raise ValueError("Please provide masker type")
for func_file in data:
time_series = masker.fit_transform(func_file)
subjects_ts.append(time_series)
np.savez(saveas,subjects_ts)
return subjects_ts
def test_nifti_maps_masker_report_displayed_maps_errors(
niftimapsmasker_inputs, displayed_maps):
"""Tests that a TypeError is raised when the argument `displayed_maps`
of `generate_report()` is not valid.
"""
masker = NiftiMapsMasker(**niftimapsmasker_inputs)
masker.fit()
with pytest.raises(TypeError, match=("Parameter ``displayed_maps``")):
masker.generate_report(displayed_maps)
def test_nifti_maps_masker_report_maps_number_errors(niftimapsmasker_inputs,
displayed_maps):
"""Tests that a ValueError is raised when the argument `displayed_maps`
contains invalid map numbers.
"""
masker = NiftiMapsMasker(**niftimapsmasker_inputs)
masker.fit()
with pytest.raises(ValueError,
match="Report cannot display the following maps"):
masker.generate_report(displayed_maps)
def main(argv):
## atlas 3
atlas = "Schaefer200Yeo17Pauli" # msdl or haox or mmp
schaefer_atlas = datasets.fetch_atlas_schaefer_2018(n_rois=200, yeo_networks=17, resolution_mm=1, data_dir=None, base_url=None, resume=True, verbose=1) #atlas_filename = "MMP1_rois.nii" #Glasser et al., 2016
schaefer_filename = schaefer_atlas.maps
schaefer_labels = schaefer_atlas.labels
schaefer_masker = NiftiLabelsMasker(labels_img=schaefer_filename, standardize=True,
memory='nilearn_cache', verbose=5)
pauli_atlas = datasets.fetch_atlas_pauli_2017()
pauli_filename = pauli_atlas.maps
pauli_labels = pauli_atlas.labels
pauli_masker = NiftiMapsMasker(maps_img=pauli_filename, standardize=True, verbose=5)
all_labels = np.hstack([schaefer_labels, pauli_labels])
#print(all_labels)
correlation_measure = ConnectivityMeasure(kind='correlation')
def __init__(self,
atlas_name,
metric,
mask,
rois=False,
detrend=True,
low_pass=.1,
high_pass=.01,
t_r=3.,
resampling_target='data',
smoothing_fwhm=6.,
memory='',
memory_level=2,
n_jobs=1):
self.fc_ = None
self.atlas, self.rois = fetch_atlas(atlas_name, rois)
self.metric = metric
self.mask = mask
self.n_jobs = n_jobs
if len(nii_shape(self.atlas)) == 4:
self.masker = NiftiMapsMasker(maps_img=self.atlas,
mask_img=self.mask,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
resampling_target=resampling_target,
smoothing_fwhm=smoothing_fwhm,
memory=memory,
memory_level=memory_level,
verbose=5)
else:
self.masker = NiftiLabelsMasker(
labels_img=self.atlas,
mask_img=self.mask,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
resampling_target=resampling_target,
smoothing_fwhm=smoothing_fwhm,
memory=memory,
memory_level=memory_level,
verbose=5)
def __init__(self,
atlas_name,
rois,
metric,
mask,
detrend=True,
low_pass=.1,
high_pass=.01,
t_r=3.,
resampling_target='data',
smoothing_fwhm=6.,
memory='',
memory_level=2,
n_jobs=1):
self.atlas = fetch_atlas(atlas_name)
self.rois = np.asarray(rois)
self.metric = metric
self.mask = mask
self.n_jobs = n_jobs
if len(nib.load(self.atlas).shape) == 4:
self.masker = NiftiMapsMasker(maps_img=self.atlas,
mask_img=self.mask,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
resampling_target=resampling_target,
smoothing_fwhm=smoothing_fwhm,
memory=memory,
memory_level=memory_level)
else:
self.masker = NiftiLabelsMasker(
labels_img=self.atlas,
mask_img=self.mask,
detrend=detrend,
low_pass=low_pass,
high_pass=high_pass,
t_r=t_r,
resampling_target=resampling_target,
smoothing_fwhm=smoothing_fwhm,
memory=memory,
memory_level=memory_level)
def get_loader_pipe(parc,
pipe='elastic_pipe',
obj_params=None,
**loader_params):
'''TODO write doc - then add to docs.'''
from ..main.funcs import pipeline_check
from ..main.input import Loader
if obj_params is None:
obj_params = {}
try:
from neurotools.transform import SurfLabels, SurfMaps
from neurotools.loading import load
from nilearn.input_data import NiftiLabelsMasker, NiftiMapsMasker
except ImportError:
raise ImportError('neurotools must be installed!')
# Apply pipeline check
pipe = pipeline_check(pipe)
# Get dimensionality of parcellation
parc_dims = len(load(parc).shape)
# Get correct object based off
if parc_dims == 1:
obj = SurfLabels(labels=parc, **obj_params)
elif parc_dims == 2:
obj = SurfMaps(maps=parc, **obj_params)
elif parc_dims == 3:
obj = NiftiLabelsMasker(labels_img=parc, **obj_params)
elif parc_dims == 4:
obj = NiftiMapsMasker(maps_img=parc, **obj_params)
# Init loader from object
loader = Loader(obj, **loader_params)
# Add loader before rest of steps
pipe.steps = [loader] + pipe.steps
return pipe
def make_masker_from_atlas(atlas, memory=None, memory_level=1):
"""Construct a maker from a given atlas.
Parameters
----------
atlas : str or 3D/4D Niimg-like object,
The atlas to use to create the masker. If string, it should corresponds
to the path of a Nifti image.
memory : instance of joblib.Memory or string, (default=None)
Used to cache the masking process. By default, no caching is done. If a
string is given, it is the path to the caching directory.
memory_level : integer, optional (default=1)
Rough estimator of the amount of memory used by caching. Higher value
means more memory for caching.
Returns
-------
masker : Nilearn Masker
Nilearn Masker.
"""
atlas_ = check_niimg(atlas)
atlas_dim = len(atlas_.shape)
if atlas_dim == 3:
masker = NiftiLabelsMasker(atlas_,
memory=memory,
memory_level=memory_level,
smoothing_fwhm=6,
detrend=True,
verbose=1)
elif atlas_dim == 4:
masker = NiftiMapsMasker(atlas_,
memory=memory,
memory_level=memory_level,
smoothing_fwhm=6,
detrend=True,
verbose=1)
return masker
def extract_parcellation_time_series(in_data, parcellation_name, parcellations_dict, bp_freqs, tr):
"""
Depending on parcellation['is_probabilistic'] this function chooses either NiftiLabelsMasker or NiftiMapsMasker
to extract the time series of each parcel
if bp_freq: data is band passfiltered at (hp, lp), if (None,None): no filter, if (None, .1) only lp...
tr in ms (e.g. from freesurfer ImageInfo())
returns np.array with parcellation time series and saves this array also to parcellation_time_series_file, and
path to pickled masker object
"""
from nilearn.input_data import NiftiLabelsMasker, NiftiMapsMasker
import os, pickle
import numpy as np
if parcellations_dict[parcellation_name]["is_probabilistic"]: # use probab. nilearn
masker = NiftiMapsMasker(maps_img=parcellations_dict[parcellation_name]["nii_path"])
else: # 0/1 labels
masker = NiftiLabelsMasker(labels_img=parcellations_dict[parcellation_name]["nii_path"])
# add bandpass filter (only executes if freq not None
hp, lp = bp_freqs
masker.low_pass = lp
masker.high_pass = hp
if tr is not None:
masker.t_r = float(tr) / 1000.0
else:
masker.t_r = None
masker.standardize = True
masker_file = os.path.join(os.getcwd(), "masker.pkl")
with open(masker_file, "w") as f:
pickle.dump(masker, f)
parcellation_time_series = masker.fit_transform(in_data)
parcellation_time_series_file = os.path.join(os.getcwd(), "parcellation_time_series.npy")
np.save(parcellation_time_series_file, parcellation_time_series)
return parcellation_time_series, parcellation_time_series_file, masker_file
def test_nifti_maps_masker_report_integer_and_all_displayed_maps(
niftimapsmasker_inputs, displayed_maps):
"""Tests NiftiMapsMasker reporting with no image provided to fit
and displayed_maps provided as an integer or as 'all'.
"""
masker = NiftiMapsMasker(**niftimapsmasker_inputs)
masker.fit()
expected_n_maps = 9 if displayed_maps == 'all' else min(9, displayed_maps)
if displayed_maps != 'all' and displayed_maps > 9:
with pytest.warns(UserWarning, match="masker only has 9 maps."):
html = masker.generate_report(displayed_maps)
else:
html = masker.generate_report(displayed_maps)
assert masker._report_content['report_id'] == 0
assert masker._report_content['number_of_maps'] == 9
assert (masker._report_content['displayed_maps'] == list(
range(expected_n_maps)))
msg = ("No image provided to fit in NiftiMapsMasker. "
"Plotting only spatial maps for reporting.")
assert masker._report_content['warning_message'] == msg
assert html.body.count("<img") == expected_n_maps
atlas4d = nib.load(atlas['maps'])
atlas4d_data = atlas4d.get_data()
atlas3d_data = np.sum(atlas4d_data, axis=3)
atlas3d = nib.Nifti1Image(atlas3d_data, atlas4d.get_affine())
n_subjects = len(func_files)
subjects = []
cov_feat = []
for subject_n in range(n_subjects):
filename = func_files[subject_n]
print("Processing file %s" % filename)
print("-- Computing region signals ...")
masker = NiftiMapsMasker(atlas["maps"],
resampling_target="maps", standardize=False,
memory=CACHE_DIR, memory_level=1, verbose=0)
region_ts = masker.fit_transform(filename)
subjects.append(region_ts)
print("-- Computing covariances")
cov_matrix = np.cov(region_ts.T)
cov_feat.append(cov_matrix[np.tril_indices(len(cov_matrix))])
from sklearn.svm import SVC
from sklearn.cross_validation import StratifiedShuffleSplit
cov_feat = np.array(cov_feat)
nb_iter = 100
pg_counter = 0
groups = [['AD', 'Normal'], ['AD', 'EMCI'], ['AD', 'LMCI'],
atlas = datasets.fetch_atlas_msdl()
# Loading atlas image stored in 'maps'
atlas_filename = atlas['maps']
# Loading atlas data stored in 'labels'
labels = atlas['labels']
# Load the functional datasets
data = datasets.fetch_adhd(n_subjects=1)
print('First subject resting-state nifti image (4D) is located at: %s' %
data.func[0])
############################################################################
# Extract the time series
from nilearn.input_data import NiftiMapsMasker
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]
dyn_fc = []
for subject in dyn_dataset.subjects:
dyn_fc.append(loader.load_dynacomp_fc(subject_id=subject, session='func1',
metric='pc', msdl=False,
preprocessing_folder='pipeline_1')[ind])
dyn_fc = np.asarray(dyn_fc)
##############################################################################
# NYU rs-fMRI
##############################################################################
nyu_func = fetch_nyu_rest()['func']
masker = NiftiMapsMasker(maps_img=roi_imgs,
low_pass=.1,
high_pass=.01,
t_r=2.,
smoothing_fwhm=6., detrend=True, standardize=False,
resampling_target='maps', memory_level=0,
verbose=5)
masker.fit()
def mask_and_covariance(f):
x = masker.transform(f)
return np.corrcoef(x.T)[ind]
# gl = GraphLassoCV(verbose=2)
# gl.fit(x)
# return gl.covariance_[ind]
from joblib import delayed, Parallel
nyu_fc = Parallel(n_jobs=20, verbose=5)(delayed(mask_and_covariance)(f)
import numpy as np
from loader import load_dynacomp
from nilearn.datasets import fetch_msdl_atlas
from nilearn.input_data import NiftiMapsMasker
dataset = load_dynacomp(preprocessing_folder='pipeline_2',
prefix='resampled_wr')
atlas = fetch_msdl_atlas()
# add mask, smoothing, filtering and detrending
masker = NiftiMapsMasker(maps_img=atlas['maps'],
mask_img=dataset.mask,
low_pass=.1,
high_pass=.01,
t_r=1.05,
smoothing_fwhm=6.,
detrend=True,
standardize=False,
resampling_target='data',
memory_level=0,
verbose=5)
for i in range(len(dataset.subjects)):
tic = time.clock()
output_path, _ = os.path.split(dataset.func1[i])
if not os.path.isfile(os.path.join(output_path, 'func1_msdl_filter.npy')):
print i, dataset.subjects[i]
output_path, _ = os.path.split(dataset.func1[i])
x = masker.fit_transform(dataset.func1[i])
np.save(os.path.join(output_path, 'func1_msdl_filter') , x)
x = masker.fit_transform(dataset.func2[i])
from nilearn.input_data import NiftiMapsMasker
from nilearn import datasets
import pandas as pd
import os
prepdir = "/oak/stanford/groups/russpold/data/ds000030/1.0.3/derivatives/fmriprep_0.4.4"
subs = [x for x in os.listdir(prepdir) if x.startswith('sub-') and not x.endswith(".html")]
atlas = datasets.fetch_atlas_msdl()
atlas_filename = atlas['maps']
outdir = os.path.join(os.environ.get("SCRATCH"),"CNP_ts")
if not os.path.exists(outdir):
os.mkdir(outdir)
for sub in subs:
subnum = float(sub.split("-")[1])
outfile = os.path.join(outdir,"%s_MSDL.csv"%sub)
if os.path.exists(outfile):
continue
preprocd = os.path.join(prepdir,sub,'func','%s_task-rest_bold_space-MNI152NLin2009cAsym_preproc.nii.gz'%sub)
if not os.path.exists(preprocd):
continue
masker = NiftiMapsMasker(maps_img=atlas_filename, standardize=True,memory='nilearn_cache', verbose=5)
time_series = masker.fit_transform(preprocd)
ts = pd.DataFrame(time_series)
ts.to_csv(outfile,index=False,header=False)
size_in_GB = all_sub_rs_maps.get_data().nbytes / 1e9
print('% rs images: %.2f GB' % (cur_shape[-1], size_in_GB))
###############################################################################
# dump network projections
###############################################################################
# retrieve network projections
from nilearn import datasets as ds
smith_pkg = ds.fetch_atlas_smith_2009()
icas_path = smith_pkg['rsn20']
from nilearn.input_data import NiftiMapsMasker
nmm = NiftiMapsMasker(
mask_img=mask_file, maps_img=icas_path, resampling_target='mask',
standardize=True, detrend=True)
nmm.fit()
nmm.maps_img_.to_filename('dbg_ica_maps.nii.gz')
FS_netproj = nmm.transform(all_sub_rs_maps)
np.save('%i_nets_timeseries' % sub_id, FS_netproj)
# compute network sparse inverse covariance
from sklearn.covariance import GraphLassoCV
from nilearn.image import index_img
from nilearn import plotting
try:
gsc_nets = GraphLassoCV(verbose=2, alphas=20)
gsc_nets.fit(FS_netproj)
dataset = load_dynacomp(preprocessing_folder='pipeline_2',
prefix='resampled_wr')
# func1, func2
for idx, func in enumerate([dataset.func1, dataset.func2]):
# all the subjects
for i in range(len(dataset.subjects)):
tic = time.clock()
output_path, _ = os.path.split(func[i])
print dataset.subjects[i]
maps_img = dict_to_list(dataset.rois[i])
# add mask, smoothing, filtering and detrending
masker = NiftiMapsMasker(maps_img=maps_img,
mask_img=dataset.mask,
low_pass=.1,
high_pass=.01,
smoothing_fwhm=6.,
t_r=1.05,
detrend=True,
standardize=False,
resampling_target='data',
memory_level=0,
verbose=5)
output_path, _ = os.path.split(func[i])
# extract the signal to x
x = masker.fit_transform(func[i])
np.save(os.path.join(output_path,
'func' + str(idx+1) + '_rois_filter'), x)
toc = time.clock()
print toc - tic
Script to test functions Created on Thu Mar 26 15:02:11 2015 @author: [email protected] """ from loader import load_dynacomp, list_of_dicts_to_key_list, dict_to_list from nilearn.input_data import NiftiMapsMasker import time # Load Dynacomp dataset dataset = load_dynacomp() # Dataset keys print 'keys\n', dataset.keys() # Dataset functional 1 print 'func1\n', dataset.func1 # Dataset behaviordata : prePerf print 'prePerf\n', list_of_dicts_to_key_list(dataset.behavior, 'prePerf') # Generate seed-masker for subject 0 maps_img = dict_to_list(dataset.rois[1]) tic = time.clock() masker = NiftiMapsMasker(maps_img, verbose=5) x = masker.fit_transform(dataset.func1[1]) toc = time.clock() print toc - tic
# print('Warning: several func reference files: '+func_ref_file[0]+' will be used')
#func_ref = nb.load(func_ref_file[0])
#func_template = nibabel.load
display_atlas= nilearn.plotting.plot_prob_atlas(visu, anat_img=anat_ref_file[0],
title=atlas_name+'_anat',
cut_coords = (5,0,0),threshold=0.)
at_check =[plt.gcf()] #figure handle for atlas check
#masker for raw time series
masker_r = NiftiMapsMasker(atlas_filename, mask_img=mask, smoothing_fwhm=None,
standardize=stdz,detrend=detr, low_pass=None,
high_pass=None,t_r=TR, resampling_target='data',
memory=mem_dir,memory_level=5, verbose=0)
# prepare pairs for pairwise comparisons between groups
comps = []
for func_index in range(len(func_type_list)-1) :
if func_index != len(func_type_list)-func_index:
for i in range(func_index,len(func_type_list)-func_index):
if i+1<len(func_type_list):
comps.append([func_type_list[func_index],func_type_list[i+1]])
else:
comps.append([func_type_list[func_index],func_type_list[func_index+1]])
Bonf = len(comps)
all_time_series_r = {} #regressed time series
def get_data_in_roi(path_roi, data_file):
"""Using of the NiftiMapsMasker """
masker = NiftiMapsMasker([path_roi])
nifti_obj = nibabel.load(data_file)
data = masker.fit_transform(nifti_obj)
return data
