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.

8.7.5. nilearn.masking.compute_background_mask

nilearn.masking.compute_background_mask(data_imgs, border_size=2, connected=False, opening=False, target_affine=None, target_shape=None, memory=None, verbose=0)[source]

Compute a brain mask for the images by guessing the value of the background from the border of the image.

Parameters
data_imgsNiimg-like object

See http://nilearn.github.io/manipulating_images/input_output.html Images used to compute the mask. 3D and 4D images are accepted.

Note

If a 3D image is given, we suggest to use the mean image.

border_sizeint, optional

The size, in voxel of the border used on the side of the image to determine the value of the background. Default=2.

connectedbool, optional

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

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:

Note

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

Default=False.

target_affinenumpy.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.

target_shapetuple or list, 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, a target_affine of shape (4, 4) must also be given.

Default=None.

Note

This parameter is passed to nilearn.image.resample_img.

memoryinstance of joblib.Memory or str

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, optional

Verbosity level (0 means no message). Default=0.

Returns
masknibabel.nifti1.Nifti1Image

The brain mask (3D image).