Finding the location of a voxel coordinate

>>> import numpy as np
>>> import numpy.linalg as npl
>>> import nibabel as nib

We can load some data matched to a standard brain template:

>>> img = nib.load('filtered_func_data_mni.nii.gz')

>>> img.shape
(91, 109, 91, 240)

The affine attribute of the image contains the mapping from voxel coordinates to millimeters in the space of the image. In this case the image is matched a particular standard template called the MNI template:

>>> img.affine
array([[  -2.,    0.,    0.,   90.],
       [   0.,    2.,    0., -126.],
       [   0.,    0.,    2.,  -72.],
       [   0.,    0.,    0.,    1.]])

We can get the mm coordinate for a particular voxel coordinate by applying this affine to a particular voxel coordinate. See Coordinate transformations for a full explanation.

>>> vox_to_mm = img.affine
>>> nib.affines.apply_affine(vox_to_mm, [2, 3, 4])
array([  86., -120.,  -64.])

The mapping from millmeter coordinate to voxel coordinates is just the inverse of img.affine:

>>> mm_to_vox = npl.inv(img.affine)
>>> nib.affines.apply_affine(mm_to_vox, [0, 0, 10])
array([ 45.,  63.,  41.])