Note

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

6.6.2. nilearn.masking.compute_multi_epi_mask

nilearn.masking.compute_multi_epi_mask(epi_imgs, lower_cutoff=0.2, upper_cutoff=0.85, connected=True, opening=2, threshold=0.5, target_affine=None, target_shape=None, exclude_zeros=False, n_jobs=1, memory=None, verbose=0)

Compute a common mask for several sessions or subjects of fMRI data.

Uses the mask-finding algorithms to extract masks for each session or subject, and then keep only the main connected component of the a given fraction of the intersection of all the masks.

Parameters:

epi_imgs: list of Niimg-like objects :

See http://nilearn.github.io/building_blocks/manipulating_mr_images.html#niimg. A list of arrays, each item being a subject or a session. 3D and 4D images are accepted. If 3D images is given, we suggest to use the mean image of each session

threshold: float, optional :

the inter-session threshold: the fraction of the total number of session in for which a voxel must be in the mask to be kept in the common mask. threshold=1 corresponds to keeping the intersection of all masks, whereas threshold=0 is the union of all masks.

lower_cutoff: float, optional :

lower fraction of the histogram to be discarded.

upper_cutoff: float, optional :

upper fraction of the histogram to be discarded.

connected: boolean, optional :

if connected is True, only the largest connect component is kept.

exclude_zeros: boolean, optional :

Consider zeros as missing values for the computation of the threshold. This option is useful if the images have been resliced with a large padding of zeros.

target_affine: 3x3 or 4x4 matrix, optional :

This parameter is passed to image.resample_img. Please see the related documentation for details.

target_shape: 3-tuple of integers, optional :

This parameter is passed to image.resample_img. Please see the related documentation for details.

memory: instance of joblib.Memory or string :

Used to cache the function call.

n_jobs: integer, optional :

The number of CPUs to use to do the computation. -1 means ‘all CPUs’.

Returns:

mask : 3D nibabel.Nifti1Image

The brain mask.