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_imgwill be used here.- threshold
float, default=0.5 The value under which the MNI template is cut off.
- connected
bool, optional If connected is True, only the largest connect component is kept. Default=True.
- opening
boolorint, 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 boolean : If False, no opening is performed. If True, it is equivalent to opening=1.
An integer 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 (seescipy.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, orpathlib.Path Used to cache the masking process. By default, no caching is done. If a
stris given, it is the path to the caching directory.- verbose
int, 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:
- mask
nibabel.nifti1.Nifti1Image The whole-brain mask (3D image).
- mask