Mouse lung models facilitate the study of the pathogenesis of various pulmonary diseases such as infections and inflammatory diseases. The co-registration of ex vivo histological data and pre-excised magnetic resonance imaging (MRI) in preclinical mouse models would allow for determination and validation of imaging signatures for different pathobiologies within the lung. While slice-based co-registration could be used, this approach assumes that (a) slice correspondences between the two different modalities exist, and (b) finding slice correspondences often requires the intervention of an expert and is time consuming. A more practical approach is to first reconstruct the 3D histological volume from individual slices, then perform 3D registration with the MR volume. Before the histological reconstruction, image registration is required to compensate for geometric differences between slices. Pairwise algorithms work by registering pairs of successive slices. However, even if successive slices are registered reasonably well, the propagation of registration errors over slices can yield a distorted volumetric reconstruction significantly different in shape from the shape of the true specimen. Groupwise registration can reduce the error propagation by considering more than two successive images during the registration, but existing algorithms are computationally expensive. In this paper, we present an efficient groupwise registration approach, which yields consistent volumetric reconstruction and yet runs equally fast as pairwise registration. The improvements are based on 1) natural gradient which speeds up the transform warping procedure and 2) efficient optimization of the cost function of our groupwise registration. The strength of the natural gradient technique is that it could help mitigate the impact of the uncertainties of the gradient direction across multiple template slices. Experiments on two mouse lung datasets show that compared to pairwise registration, our groupwise approach runs faster in terms of registration convergence, and yields globally more consistent reconstruction.