Note

This page is a reference documentation. It only explains the class signature, and not how to use it. Please refer to the user guide for the big picture.

nilearn.maskers.NiftiLabelsMasker#

class nilearn.maskers.NiftiLabelsMasker(labels_img, labels=None, background_label=0, mask_img=None, smoothing_fwhm=None, standardize=False, standardize_confounds=True, high_variance_confounds=False, detrend=False, low_pass=None, high_pass=None, t_r=None, dtype=None, resampling_target='data', memory=Memory(location=None), memory_level=1, verbose=0, strategy='mean', keep_masked_labels=True, reports=True, **kwargs)[source]#

Class for extracting data from Niimg-like objects using labels of non-overlapping brain regions.

NiftiLabelsMasker is useful when data from non-overlapping volumes should be extracted (contrarily to nilearn.maskers.NiftiMapsMasker).

Use case: summarize brain signals from clusters that were obtained by prior K-means or Ward clustering.

For more details on the definitions of labels in Nilearn, see the Extraction of signals from regions: NiftiLabelsMasker, NiftiMapsMasker section.

Parameters:
labels_imgNiimg-like object

See Input and output: neuroimaging data representation. Region definitions, as one image of labels.

labelslist of str, optional

Full labels corresponding to the labels image. This is used to improve reporting quality if provided.

Warning

The labels must be consistent with the label values provided through labels_img.

background_labelint or float, default=0

Label used in labels_img to represent background. Warning: This value must be consistent with label values and image provided.

mask_imgNiimg-like object, optional

See Input and output: neuroimaging data representation. Mask to apply to regions before extracting signals.

smoothing_fwhmfloat, optional.

If smoothing_fwhm is not None, it gives the full-width at half maximum in millimeters of the spatial smoothing to apply to the signal.

standardize{‘zscore_sample’, ‘zscore’, ‘psc’, True, False}, default=False

Strategy to standardize the signal:

  • ‘zscore_sample’: The signal is z-scored. Timeseries are shifted to zero mean and scaled to unit variance. Uses sample std.

  • ‘zscore’: The signal is z-scored. Timeseries are shifted to zero mean and scaled to unit variance. Uses population std by calling default numpy.std with N - ddof=0.

  • ‘psc’: Timeseries are shifted to zero mean value and scaled to percent signal change (as compared to original mean signal).

  • True: The signal is z-scored (same as option zscore). Timeseries are shifted to zero mean and scaled to unit variance.

  • False: Do not standardize the data.

standardize_confoundsbool, default=True

If set to True, the confounds are z-scored: their mean is put to 0 and their variance to 1 in the time dimension.

high_variance_confoundsbool, default=False

If True, high variance confounds are computed on provided image with nilearn.image.high_variance_confounds and default parameters and regressed out.

detrendbool, optional

Whether to detrend signals or not.

low_passfloat or None, default=None

Low cutoff frequency in Hertz. If specified, signals above this frequency will be filtered out. If None, no low-pass filtering will be performed.

high_passfloat, default=None

High cutoff frequency in Hertz. If specified, signals below this frequency will be filtered out.

t_rfloat or None, default=None

Repetition time, in seconds (sampling period). Set to None if not provided.

dtype{dtype, “auto”}, optional

Data type toward which the data should be converted. If “auto”, the data will be converted to int32 if dtype is discrete and float32 if it is continuous.

resampling_target{“data”, “labels”, None}, default=”data”

Gives which image gives the final shape/size. For example, if resampling_target is "data", the atlas is resampled to the shape of the data if needed. If it is "labels" then mask_img and images provided to fit() are resampled to the shape and affine of maps_img. "None" means no resampling: if shapes and affines do not match, a ValueError is raised.

memoryinstance of joblib.Memory, str, or pathlib.Path

Used to cache the masking process. By default, no caching is done. If a str is given, it is the path to the caching directory.

memory_levelint, default=1

Rough estimator of the amount of memory used by caching. Higher value means more memory for caching. Zero means no caching.

verboseint, default=0

Verbosity level (0 means no message).

strategystr, default=’mean’

The name of a valid function to reduce the region with. Must be one of: sum, mean, median, minimum, maximum, variance, standard_deviation.

keep_masked_labelsbool, default=True

When a mask is supplied through the “mask_img” parameter, some atlas regions may lie entirely outside of the brain mask, resulting in empty time series for those regions. If True, the masked atlas with these empty labels will be retained in the output, resulting in corresponding time series containing zeros only. If False, the empty labels will be removed from the output, ensuring no empty time series are present.

Deprecated since version 0.10.2: The ‘True’ option for keep_masked_labels is deprecated. The default value will change to ‘False’ in 0.13, and the keep_masked_labels parameter will be removed in 0.15.

reportsbool, default=True

If set to True, data is saved in order to produce a report.

kwargsdict

Keyword arguments to be passed to functions called within the masker. Kwargs prefixed with ‘clean__’ will be passed to clean. Within clean, kwargs prefixed with ‘butterworth__’ will be passed to the Butterworth filter (i.e., clean__butterworth__).

Attributes:
mask_img_nibabel.nifti1.Nifti1Image

The mask of the data, or the computed one.

labels_img_nibabel.nifti1.Nifti1Image

The labels image.

n_elements_int

The number of discrete values in the mask. This is equivalent to the number of unique values in the mask image, ignoring the background value.

New in version 0.9.2.

region_ids_dict[str | int, int]

A dictionary containing the region ids corresponding to each column in the region_signal returned by fit_transform. The region id corresponding to region_signal[:,i] is region_ids_[i]. region_ids_['background'] is the background label.

New in version 0.10.3.

region_names_dict[int, str]

A dictionary containing the region names corresponding to each column in the region_signal returned by fit_transform. The region names correspond to the labels provided in labels in input. The region name corresponding to region_signal[:,i] is region_names_[i].

New in version 0.10.3.

region_atlas_Niimg-like object

Regions definition as labels. The labels correspond to the indices in region_ids_. The region in region_atlas_ that takes the value region_ids_[i] is used to compute the signal in region_signal[:,i].

New in version 0.10.3.

__init__(labels_img, labels=None, background_label=0, mask_img=None, smoothing_fwhm=None, standardize=False, standardize_confounds=True, high_variance_confounds=False, detrend=False, low_pass=None, high_pass=None, t_r=None, dtype=None, resampling_target='data', memory=Memory(location=None), memory_level=1, verbose=0, strategy='mean', keep_masked_labels=True, reports=True, **kwargs)[source]#
generate_report()[source]#

Generate a report.

fit(imgs=None, y=None)[source]#

Prepare signal extraction from regions.

Parameters:
imgslist of Niimg-like objects

See Input and output: neuroimaging data representation. Image data passed to the reporter.

yNone

This parameter is unused. It is solely included for scikit-learn compatibility.

fit_transform(imgs, confounds=None, sample_mask=None)[source]#

Prepare and perform signal extraction from regions.

Parameters:
imgs3D/4D Niimg-like object

See Input and output: neuroimaging data representation. Images to process. If a 3D niimg is provided, a singleton dimension will be added to the output to represent the single scan in the niimg.

confoundsCSV file or array-like or pandas.DataFrame, optional

This parameter is passed to signal.clean. Please see the related documentation for details. shape: (number of scans, number of confounds)

sample_maskAny type compatible with numpy-array indexing, optional

shape: (number of scans - number of volumes removed, ) Masks the niimgs along time/fourth dimension to perform scrubbing (remove volumes with high motion) and/or non-steady-state volumes. This parameter is passed to signal.clean.

New in version 0.8.0.

Returns:
region_signals2D numpy.ndarray

Signal for each label. shape: (number of scans, number of labels)

transform_single_imgs(imgs, confounds=None, sample_mask=None)[source]#

Extract signals from a single 4D niimg.

Parameters:
imgs3D/4D Niimg-like object

See Input and output: neuroimaging data representation. Images to process. If a 3D niimg is provided, a singleton dimension will be added to the output to represent the single scan in the niimg.

confoundsCSV file or array-like or pandas.DataFrame, optional

This parameter is passed to signal.clean. Please see the related documentation for details. shape: (number of scans, number of confounds)

sample_maskAny type compatible with numpy-array indexing, optional

shape: (number of scans - number of volumes removed, ) Masks the niimgs along time/fourth dimension to perform scrubbing (remove volumes with high motion) and/or non-steady-state volumes. This parameter is passed to signal.clean.

New in version 0.8.0.

Returns:
region_signals2D numpy.ndarray

Signal for each label. shape: (number of scans, number of labels)

Warns:
DeprecationWarning

If a 3D niimg input is provided, the current behavior (adding a singleton dimension to produce a 2D array) is deprecated. Starting in version 0.12, a 1D array will be returned for 3D inputs.

inverse_transform(signals)[source]#

Compute voxel signals from region signals.

Any mask given at initialization is taken into account.

Changed in version 0.9.2: This method now supports 1D arrays, which will produce 3D images.

Parameters:
signals1D/2D numpy.ndarray

Signal for each region. If a 1D array is provided, then the shape should be (number of elements,), and a 3D img will be returned. If a 2D array is provided, then the shape should be (number of scans, number of elements), and a 4D img will be returned.

Returns:
imgnibabel.nifti1.Nifti1Image

Signal for each voxel shape: (X, Y, Z, number of scans)

get_metadata_routing()#

Get metadata routing of this object.

Please check User Guide on how the routing mechanism works.

Returns:
routingMetadataRequest

A MetadataRequest encapsulating routing information.

get_params(deep=True)#

Get parameters for this estimator.

Parameters:
deepbool, default=True

If True, will return the parameters for this estimator and contained subobjects that are estimators.

Returns:
paramsdict

Parameter names mapped to their values.

set_fit_request(*, imgs='$UNCHANGED$')#

Request metadata passed to the fit method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to fit if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to fit.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a Pipeline. Otherwise it has no effect.

Parameters:
imgsstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED

Metadata routing for imgs parameter in fit.

Returns:
selfobject

The updated object.

set_inverse_transform_request(*, signals='$UNCHANGED$')#

Request metadata passed to the inverse_transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to inverse_transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to inverse_transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a Pipeline. Otherwise it has no effect.

Parameters:
signalsstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED

Metadata routing for signals parameter in inverse_transform.

Returns:
selfobject

The updated object.

set_output(*, transform=None)#

Set output container.

See Introducing the set_output API for an example on how to use the API.

Parameters:
transform{“default”, “pandas”}, default=None

Configure output of transform and fit_transform.

  • “default”: Default output format of a transformer

  • “pandas”: DataFrame output

  • “polars”: Polars output

  • None: Transform configuration is unchanged

New in version 1.4: “polars” option was added.

Returns:
selfestimator instance

Estimator instance.

set_params(**params)#

Set the parameters of this estimator.

The method works on simple estimators as well as on nested objects (such as Pipeline). The latter have parameters of the form <component>__<parameter> so that it’s possible to update each component of a nested object.

Parameters:
**paramsdict

Estimator parameters.

Returns:
selfestimator instance

Estimator instance.

set_transform_request(*, confounds='$UNCHANGED$', imgs='$UNCHANGED$', sample_mask='$UNCHANGED$')#

Request metadata passed to the transform method.

Note that this method is only relevant if enable_metadata_routing=True (see sklearn.set_config). Please see User Guide on how the routing mechanism works.

The options for each parameter are:

  • True: metadata is requested, and passed to transform if provided. The request is ignored if metadata is not provided.

  • False: metadata is not requested and the meta-estimator will not pass it to transform.

  • None: metadata is not requested, and the meta-estimator will raise an error if the user provides it.

  • str: metadata should be passed to the meta-estimator with this given alias instead of the original name.

The default (sklearn.utils.metadata_routing.UNCHANGED) retains the existing request. This allows you to change the request for some parameters and not others.

New in version 1.3.

Note

This method is only relevant if this estimator is used as a sub-estimator of a meta-estimator, e.g. used inside a Pipeline. Otherwise it has no effect.

Parameters:
confoundsstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED

Metadata routing for confounds parameter in transform.

imgsstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED

Metadata routing for imgs parameter in transform.

sample_maskstr, True, False, or None, default=sklearn.utils.metadata_routing.UNCHANGED

Metadata routing for sample_mask parameter in transform.

Returns:
selfobject

The updated object.

transform(imgs, confounds=None, sample_mask=None)[source]#

Apply mask, spatial and temporal preprocessing.

Parameters:
imgs3D/4D Niimg-like object

See Input and output: neuroimaging data representation. Images to process. If a 3D niimg is provided, a singleton dimension will be added to the output to represent the single scan in the niimg.

confoundsCSV file or array-like, optional

This parameter is passed to signal.clean. Please see the related documentation for details. shape: (number of scans, number of confounds)

sample_maskAny type compatible with numpy-array indexing, optional

shape: (number of scans - number of volumes removed, ) Masks the niimgs along time/fourth dimension to perform scrubbing (remove volumes with high motion) and/or non-steady-state volumes. This parameter is passed to signal.clean.

New in version 0.8.0.

Returns:
region_signals2D numpy.ndarray

Signal for each element. shape: (number of scans, number of elements)

Warns:
DeprecationWarning

If a 3D niimg input is provided, the current behavior (adding a singleton dimension to produce a 2D array) is deprecated. Starting in version 0.12, a 1D array will be returned for 3D inputs.

Examples using nilearn.maskers.NiftiLabelsMasker#

Comparing connectomes on different reference atlases

Comparing connectomes on different reference atlases

Extracting signals from a brain parcellation

Extracting signals from a brain parcellation

Extracting signals from brain regions using the NiftiLabelsMasker

Extracting signals from brain regions using the NiftiLabelsMasker

Computing a Region of Interest (ROI) mask manually

Computing a Region of Interest (ROI) mask manually