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.regions.Parcellations#
- class nilearn.regions.Parcellations(method, n_parcels=50, random_state=0, mask=None, smoothing_fwhm=4.0, standardize=False, detrend=False, low_pass=None, high_pass=None, t_r=None, target_affine=None, target_shape=None, mask_strategy='epi', mask_args=None, scaling=False, n_iter=10, memory=Memory(location=None), memory_level=0, n_jobs=1, verbose=1)[source]#
Learn parcellations on fMRI images.
Five different types of clustering methods can be used: kmeans, ward, complete, average and rena. kmeans will call MiniBatchKMeans whereas ward, complete, average are used within in Agglomerative Clustering and rena will call ReNA. kmeans, ward, complete, average are leveraged from scikit-learn. rena is built into nilearn.
New in version 0.4.1.
- Parameters
- method:obj:str, {‘kmeans’, ‘ward’, ‘complete’, ‘average’, ‘rena’,
‘hierarchical_kmeans’} A method to choose between for brain parcellations. For a small number of parcels, kmeans is usually advisable. For a large number of parcellations (several hundreds, or thousands), ward and rena are the best options. Ward will give higher quality parcels, but with increased computation time. ReNA is most useful as a fast data-reduction step, typically dividing the signal size by ten.
- n_parcels
int
, optional Number of parcels to divide the data into. Default=50.
- random_state
int
or RandomState, optional Pseudo-random number generator state used for random sampling. Default=0.
- maskNiimg-like object or
nilearn.maskers.NiftiMasker
,nilearn.maskers.MultiNiftiMasker
, optional Mask/Masker used for masking the data. If mask image if provided, it will be used in the MultiNiftiMasker. If an instance of MultiNiftiMasker is provided, then this instance parameters will be used in masking the data by overriding the default masker parameters. If None, mask will be automatically computed by a MultiNiftiMasker with default parameters.
- smoothing_fwhm
float
, optional. If
smoothing_fwhm
is notNone
, it gives the full-width at half maximum in millimeters of the spatial smoothing to apply to the signal. Default=4.0.- standardize
bool
, optional. If
standardize
is True, the data are centered and normed: their mean is put to 0 and their variance is put to 1 in the time dimension. Default=False.- detrend
bool
, optional Whether to detrend signals or not.
Note
This parameter is passed to
nilearn.signal.clean
. Please see the related documentation for details.Default=False.
- low_pass
float
or None, optional Low cutoff frequency in Hertz. If specified, signals above this frequency will be filtered out. If None, no low-pass filtering will be performed. Default=None.
Note
This parameter is passed to
nilearn.signal.clean
. Please see the related documentation for details.- high_pass
float
, optional High cutoff frequency in Hertz. If specified, signals below this frequency will be filtered out. Default=None.
Note
This parameter is passed to
nilearn.signal.clean
. Please see the related documentation for details.- t_r
float
or None, optional Repetition time, in seconds (sampling period). Set to
None
if not provided. Default=None.Note
This parameter is passed to
nilearn.signal.clean
. Please see the related documentation for details.- target_affine
numpy.ndarray
, optional. If specified, the image is resampled corresponding to this new affine.
target_affine
can be a 3x3 or a 4x4 matrix. Default=None.Note
This parameter is passed to
nilearn.image.resample_img
. Please see the related documentation for details.Note
The given affine will be considered as same for all given list of images.
- target_shape
tuple
orlist
, optional. If specified, the image will be resized to match this new shape.
len(target_shape)
must be equal to 3.Note
If
target_shape
is specified, atarget_affine
of shape(4, 4)
must also be given.Default=None.
Note
This parameter is passed to
nilearn.image.resample_img
. Please see the related documentation for details.- mask_strategy{‘background’, ‘epi’, ‘whole-brain-template’,’gm-template’, ‘wm-template’}, optional
The strategy used to compute the mask:
‘background’: Use this option if your images present a clear homogeneous background.
‘epi’: Use this option if your images are raw EPI images
‘whole-brain-template’: This will extract the whole-brain part of your data by resampling the MNI152 brain mask for your data’s field of view.
Note
This option is equivalent to the previous ‘template’ option which is now deprecated.
‘gm-template’: This will extract the gray matter part of your data by resampling the corresponding MNI152 template for your data’s field of view.
New in version 0.8.1.
‘wm-template’: This will extract the white matter part of your data by resampling the corresponding MNI152 template for your data’s field of view.
New in version 0.8.1.
Note
Depending on this value, the mask will be computed from
nilearn.masking.compute_background_mask
,nilearn.masking.compute_epi_mask
, ornilearn.masking.compute_brain_mask
.Default=’epi’.
- mask_args
dict
, optional If mask is None, these are additional parameters passed to masking.compute_background_mask or masking.compute_epi_mask to fine-tune mask computation. Please see the related documentation for details.
- scaling
bool
, optional Used only when the method selected is ‘rena’. If scaling is True, each cluster is scaled by the square root of its size, preserving the l2-norm of the image. Default=False.
- n_iter
int
, optional Used only when the method selected is ‘rena’. Number of iterations of the recursive neighbor agglomeration. Default=10.
- memoryinstance of
joblib.Memory
orstr
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_level
int
, optional. Rough estimator of the amount of memory used by caching. Higher value means more memory for caching. Default=0.
- n_jobs
int
, optional. The number of CPUs to use to do the computation. -1 means ‘all CPUs’. Default=1.
- verbose
int
, optional Verbosity level (0 means no message). Default=0.
Notes
Transforming list of Nifti images to data matrix takes few steps. Reducing the data dimensionality using randomized SVD, build brain parcellations using KMeans or various Agglomerative methods.
This object uses spatially-constrained AgglomerativeClustering for method=’ward’ or ‘complete’ or ‘average’ and spatially-constrained ReNA clustering for method=’rena’. Spatial connectivity matrix (voxel-to-voxel) is built-in object which means no need of explicitly giving the matrix.
- Attributes
- `labels_img_`
nibabel.nifti1.Nifti1Image
Labels image to each parcellation learned on fmri images.
- `masker_`
nilearn.maskers.NiftiMasker
ornilearn.maskers.MultiNiftiMasker
The masker used to mask the data.
- `connectivity_`
numpy.ndarray
Voxel-to-voxel connectivity matrix computed from a mask. Note that this attribute is only seen if selected methods are Agglomerative Clustering type, ‘ward’, ‘complete’, ‘average’.
- `labels_img_`
- __init__(method, n_parcels=50, random_state=0, mask=None, smoothing_fwhm=4.0, standardize=False, detrend=False, low_pass=None, high_pass=None, t_r=None, target_affine=None, target_shape=None, mask_strategy='epi', mask_args=None, scaling=False, n_iter=10, memory=Memory(location=None), memory_level=0, n_jobs=1, verbose=1)[source]#
- VALID_METHODS = ['kmeans', 'ward', 'complete', 'average', 'rena', 'hierarchical_kmeans']#
- transform(imgs, confounds=None)[source]#
Extract signals from parcellations learned on fMRI images.
- Parameters
- imgs
list
of Niimg-like objects See input-output. Images to process.
- confounds
list
of CSV files, arrays-like, orpandas.DataFrame
, optional Each file or numpy array in a list should have shape (number of scans, number of confounds) Must be of same length as imgs.
Note
This parameter is passed to
nilearn.signal.clean
. Please see the related documentation for details.
- imgs
- Returns
- region_signals
list
of or 2Dnumpy.ndarray
Signals extracted for each label for each image. Example, for single image shape will be (number of scans, number of labels)
- region_signals
- fit_transform(imgs, confounds=None)[source]#
Fit the images to parcellations and then transform them.
- Parameters
- imgs
list
of Niimg-like objects See input-output. Images for process for fit as well for transform to signals.
- confounds
list
of CSV files, arrays-like orpandas.DataFrame
, optional Each file or numpy array in a list should have shape (number of scans, number of confounds). Given confounds should have same length as images if given as a list.
Note
This parameter is passed to
nilearn.signal.clean
. Please see the related documentation for details.Note
Confounds will be used for cleaning signals before learning parcellations.
- imgs
- Returns
- region_signals
list
of or 2Dnumpy.ndarray
Signals extracted for each label for each image. Example, for single image shape will be (number of scans, number of labels)
- region_signals
- inverse_transform(signals)[source]#
Transform signals extracted from parcellations back to brain images.
Uses labels_img_ (parcellations) built at fit() level.
- Parameters
- signals
list
of 2Dnumpy.ndarray
Each 2D array with shape (number of scans, number of regions).
- signals
- Returns
- imgs
list
of Niimg-like objects See input-output. Brain image(s).
- imgs
- fit(imgs, y=None, confounds=None)[source]#
Compute the mask and the components across subjects
- Parameters
- imgslist of Niimg-like objects
See http://nilearn.github.io/manipulating_images/input_output.html Data on which the mask is calculated. If this is a list, the affine is considered the same for all.
- confoundslist of CSV file paths or numpy.ndarrays or pandas DataFrames, optional
This parameter is passed to nilearn.signal.clean. Please see the related documentation for details. Should match with the list of imgs given.
- Returns
- selfobject
Returns the instance itself. Contains attributes listed at the object level.
- 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.
- score(imgs, confounds=None, per_component=False)[source]#
Score function based on explained variance on imgs.
Should only be used by DecompositionEstimator derived classes
- Parameters
- imgsiterable of Niimg-like objects
See http://nilearn.github.io/manipulating_images/input_output.html Data to be scored
- confoundsCSV file path or numpy.ndarray or pandas DataFrame, optional
This parameter is passed to nilearn.signal.clean. Please see the related documentation for details
- per_componentbool, optional
Specify whether the explained variance ratio is desired for each map or for the global set of components. Default=False.
- Returns
- scorefloat
Holds the score for each subjects. Score is two dimensional if per_component is True. First dimension is squeezed if the number of subjects is one
- 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.
Examples using nilearn.regions.Parcellations
#
Clustering methods to learn a brain parcellation from fMRI