We present a new method allowing direct comparison between images obtained by present digital scanning modalities and histological sections from the same object. More specifically the paper illustrates how to orientate, embed, and section large irregular tissue blocks after magnetic resonance imaging (MRI) in such a way that accurate correlation of the digital data sets to histological sections is possible. The functionality and capability of the described procedure and slicing machine is illustrated by results from the pig brain. Accordingly, three pigs were MR-scanned, followed by perfusion fixation. The brains were removed, oriented according to the MR scans, embedded in alginate, and cut on a newly developed slicing machine. The tissue blocks were then stained to reveal grey and white matter and photographed before final sectioning on a cryostat into 80 microm thick sections which were Nissl-stained with toluidine. The results demonstrate how our method enables direct comparison between the pig brain MR images and the later obtained histological sections. The alginate embedding method and slicing machine offer the same possibilities for other parenchymateous organs and soft tissues and may, in addition, be of use in stereological analysis.