Iterative algorithm for spatial and intensity normalization of MEMRI images. Application to tract-tracing of rat...

Manganese (Mn)-enhanced magnetic resonance imaging (MEMRI) is an emerging technique for visualizing neuronal pathways and mapping brain activity modulation in animal models. Spatial and intensity normalizations of MEMRI images acquired from different subjects are crucial steps as they can influence the results of groupwise analysis. However, no commonly accepted procedure has yet emerged. Here, a normalization method is proposed that performs both spatial and intensity normalizations in a single iterative process without the arbitrary choice of a reference image. Spatial and intensity normalizations benefit from this iterative process. On one hand, spatial normalization increases the accuracy of region of interest (ROI) positioning for intensity normalization. On the other hand, improving the intensity normalization of the different MEMRI images leads to a better-averaged target on which the images are spatially registered. After automatic fast brain segmentation and optimization of the normalization process, this algorithm revealed the presence of Mn up to the posterior entorhinal cortex in a tract-tracing experiment on rat olfactory pathways. Quantitative comparison of registration algorithms showed that a rigid model with anisotropic scaling is the best deformation model for intersubject registration of three-dimensional MEMRI images. Furthermore, intensity normalization errors may occur if the ROI chosen for intensity normalization intersects regions where Mn concentration differs between experimental groups. Our study suggests that cross-comparing Mn-injected animals against a Mn-free group may provide a control to avoid bias introduced by intensity normalization quality. It is essential to optimize spatial and intensity normalization as the detectability of local between-group variations in Mn concentration is directly tied to normalization quality.