Diagnostic ultrasound (US) and magnetic resonance imaging (MRI) are important medical imaging methods in modern radiology. Our research is focused on imaging brain structures in neurology. In this paper we present differences of digital image analysis of the substantia nigra (SN) between US and MRI using the same algorithm. In the past, we developed an application for analyzing substantia nigra echogenicity in BMODE US images. Our developed application is based on a principle of binary thresholding in Region of Interest (ROI) to evaluate echogenicity grade. Increased echogenicity of SN is one of important markers for Parkinson’s Disease (PD) progress. The goal of this paper is to analyze if the same principle used for US B-MODE imaging is also applicable for different MR sequences to find out SN changes. From the achieved results detectable SN changes using MRI are possible at least as a complementary examination to US imaging. We need to prove if echogenicity index (called Echo-Index) is well reproducible value between two different MR sequences; SWI and T2-TSE; how to distinguish between pathological SN and normal anatomy. In the first pilot analysis, it seems that the principle of Echo-Index measurement could be a starting point to create a new large clinical study in this field. Totally 23 MR images from two different sequences (T1 and T2) were analyzed in this pilot study. However, it seems that Echo-Index cannot distinguish normal and diseased SN.