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.

nilearn.masking.compute_brain_mask¶

nilearn.masking.compute_brain_mask(target_img, threshold=0.5, connected=True, opening=2, memory=None, verbose=0, mask_type='whole-brain')[source]¶

Compute the whole-brain, grey-matter or white-matter mask.

This mask is calculated using MNI152 1mm-resolution template mask onto the target image.

Parameters:

target_imgNiimg-like object

See Input and output: neuroimaging data representation. Images used to compute the mask. 3D and 4D images are accepted. Only the shape and affine of target_img will be used here.

thresholdfloat, default=0.5

The value under which the MNI template is cut off.

connectedbool, optional

If connected is True, only the largest connect component is kept. Default=True.

openingbool or int, optional

This parameter determines whether a morphological opening is performed, to keep only large structures. This step is useful to remove parts of the skull that might have been included. opening can be:

A bool : If False, no opening is performed. If True, it is equivalent to opening=1.
An int n: The opening is performed via n erosions (see scipy.ndimage.binary_erosion). The largest connected component is then estimated if connected is set to True, and 2`n` dilation operations are performed (see scipy.ndimage.binary_dilation) followed by n erosions. This corresponds to 1 opening operation of order n followed by a closing operator of order n.

Note

Turning off opening (opening=False) will also prevent any smoothing applied to the image during the mask computation.

Default=2.

memoryNone, instance 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.

verboseint, default=0

Verbosity level (0 means no message).

mask_type{“whole-brain”, “gm”, “wm”}, default=”whole-brain”

Type of mask to be computed:

"whole-brain": Computes the whole-brain mask.
"gm": Computes the grey-matter mask.
"wm": Computes the white-matter mask.

Added in version 0.8.1.

Returns:

masknibabel.nifti1.Nifti1Image: The whole-brain mask (3D image).