Create a 10mm sphere ROI mask around a given coordinate

[Remi-Gau]

OK so I am adapting things from @emdupre in this post.

Turn masker object from NiftiSpheresMasker into boolean mask

Hi there I’m using the NiftiSpheresMasker to create a spherical mask around a coordinate with a radius of 10mm. Next, I would like to turn this mask into a boolean mask, so that I get a numpy array of booleans for my sphere. I thought the best way of doing this is to first turn the mask into an image and then into a boolean or something of that sort, but haven’t been able to figure it out. Then I ran into this from nifti_spheres_masker that ought to help me, especially the first …

from nilearn import datasets, plotting
from nilearn.masking import _unmask_3d
from nilearn.maskers import nifti_spheres_masker
import nibabel as nib
from nibabel import Nifti1Image

# let's assume we are in MNI space
brain_mask = datasets.load_mni152_brain_mask()

_, A = nifti_spheres_masker._apply_mask_and_get_affinity(
    seeds=[(-42, -36, 16)],
    niimg=None,
    radius=10,
    allow_overlap=False, 
    mask_img=brain_mask)

sphere_mask = _unmask_3d(
    X=A.toarray().flatten(), 
    mask=brain_mask.get_fdata().astype(bool))

sphere_mask = Nifti1Image(sphere_mask, brain_mask.affine)

nib.save(sphere_mask, "sphere.nii.gz")

# plot the result to make sure it makes sense
plotting.plot_roi("sphere.nii.gz")
plotting.show()