Various topics on functional magnetic resonance imaging (fMRI) analyses have been in study through the last 30 years. This work delineates the pathways required for resting-state functional connectivity analyses, which illuminates the correlations between different rat brain regions and can be presented in a functional connectivity matrix. The matrix is built based on the category nomenclature system of Swanson Rat Atlas 1998. From which a structural connectivity matrix is also built. This work developed the complete functional connectivity counterpart to the physical connections and explored the relationships between the functional and structural connectivity matrices. The functional connectivity matrices developed in this work map the entire rat brain. The results demonstrate that where structural connectivities exist, functional connectivities exist as well. The methodologies used to create the functional and structural analyses were completely independent.

A common approach to segment an MRI dataset is to use a standard atlas to identify different regions of interest. Existing 2D atlases, prepared by freehand tracings of templates, are seldom complete for 3D volume segmentation. Although many of these atlases are prepared in graphics packages like Adobe Illustrator® (AI), which present the geometrical entities based on their mathematical description, the drawings are not numerically robust. This work presents an automatic conversion of graphical atlases suitable for further usage such as creation of a segmented 3D numerical atlas. The system begins with DXF (Drawing Exchange Format) files of individual atlas drawings. The drawing entities are mostly in cubic spline format. Each segment of the spline is reduced to polylines, which reduces the complexity of data. The system merges overlapping nodes and polylines to make the database of the drawing numerically integrated, i.e. each location within the drawing is referred by only one point, each line is uniquely defined by only two nodes, etc. Numerous integrity diagnostics are performed to eliminate duplicate or overlapping lines, extraneous markers, open-ended loops, etc. Numerically intact closed loops are formed using atlas labels as seed points. These loops specify the boundary and tissue type for each area. The final results preserve the original atlas with its 1272 different neuroanatomical regions which are complete, non-overlapping, contiguous sub-areas whose boundaries are composed of unique polylines