Here you can download the source code of PEIS that was implemented in C++ within the image registration toolkit (IRTK), which is provided as precompiled libraries.
Please note that PEIS works on segmentations in NIfTI format (.nii, .nii.gz). Segmentations stored in other file formats can be converted to NIfTI format using for example Convert3D. 

[Download PEIS]

Contains:

• Ubuntu 13.04, 64 bit: precompiled libraries/binary
• Windows 7, 64 bit: precompiled libraries/binary
• MacOSX Mavericks 10.9.3, 64 bit: precompiled libraries/binary
• MacOSX Snow Leopard 10.6.8, 64 bit: binary only

This software package implements the following paper:

C. Ledig, W. Shi, W. Bai, and D. Rueckert, “Patch-based evaluation of image segmentation,” CVPR, pp. 3065-3072, 2014. [bib] [pdf]