Automatic cropping of MRI rat brain volumes using pulse coupled neural networks

The Pulse Coupled Neural Network (PCNN) was developed by Eckhorn to model the observed synchronization of neural assemblies in the visual cortex of small mammals such as a cat. In this paper we show the use of the PCNN as an image segmentation strategy to crop MR images of rat brain volumes. We then show the use of the associated PCNN image 'signature' to automate the brain cropping process with a trained artificial neural network. We tested this novel algorithm on three T2 weighted acquisition configurations comprising a total of 42 rat brain volumes. The datasets included 40 ms, 48 ms and 53 ms effective TEs, acquisition field strengths of 4.7 T and 9.4 T, image resolutions from 64x64 to 256x256, slice locations ranging from +6 mm to -11 mm AP, two different surface coil manufacturers and imaging protocols. The results were compared against manually segmented gold standards and Brain Extraction Tool (BET) V2.1 results. The Jaccard similarity index was used for numerical evaluation of the proposed algorithm. Our novel PCNN cropping system averaged 0.93 compared to BET scores circa 0.84.