Error extracting volumes with nibabel

I’m trying to extract two volumes with nibabel slicer:

>> image.slicer(:,:,:,[0,1])

but this throws an exception
IndexError: Cannot handle fancy indexing

Hi @mri!

In this simple case you could use the following:

>>> image.slicer[..., :2]

since the indices you want are consecutive.

If you have more complex cases though where the slices you want are non-consecutive and can’t be generated by e.g., a slice() instance you may need to coerce the underlying data object to a numpy array, fancy-index that, and then regenerate the image, e.g.:

>>> idx = [0, 5, 6, 10]
>>> data = np.asarray(image.dataobj)[..., idx]
>>> image = image.__class__(data, affine=image.affine, header=image.header, extra=image.extra)

Hope that helps!