With Ekam’s data analysis package, we offer quick and precise analysis of each subject. Our proprietary algorithms use registration and atlas-based segmentation to accurately identify brain regions. Results are presented in a simple spreadsheet format and can be easily visualized through a secure web portal.
Analysis Pipelines
Blood oxygen level dependent (BOLD) responses to stimulus provocations represent the canonical method for non-invasive measurements of neural activation in real-time. While most stimulus presentation is achieved through the nose to take advantage of the primacy of the olfactory sensory modality in rodents, we also regularly use tactile stimulation and pharmacological agents (known as phMRI). Stimulation of other sensory modalities (e.g. sound) is under development. BOLD functional imaging is performed in awake animals using single-epoch stimulus provocation paradigms that allow us to image the unfolding pattern of activation across the entire brain in real time.
Scans typically last 10-45 min.
Good for assessing stimulus-induced changes in neural activation across the entire brain, in real-time.
Quantitative anisotropy reflects the degree to which the diffusion of water (protons) varies in different directions. At a microscopic level there are many determinants of diffusion as the microarchitecture of brain parenchyma is composed of many components, including neurons and their axonal and dendritic fibers, glia, connective tissue, capillaries, and intracellular and extracellular water. Axonal properties and general microarchitecture within a voxel are the key determinants of diffusion anisotropy at a microscopic level, and the coherence of the axons in a voxel (i.e., are they parallel or crossing) is the key determinant of diffusion anisotropy at a macroscopic level.
Scans typically last 1 to 1.5 hrs and are performed on anesthetized animals.
Good for assessing changes in structure, regional microarchitecture.
High-resolution anatomical scans can provide quantitative volumetric measurements of all regions included in each species’ 3D atlas. In this work we used predefined MRI Brain Atlas (Ekam Solutions LLC, Boston, MA) and registered the standard structural template image onto high resolution T2 weighted images for each individual subject using non-linear registration method implemented by Unix based software package Deformable Registration via Attribute Matching and Mutal-Saliency Weighting (DRAMMS). The atlas (image size 256x256x63) was then warped from the standard space into the subject image space (image size 256x256x40) using the deformation obtained from the above step using nearest-neighbor interpolation method. In the volumetric analysis, each brain region was therefore segmented and the volume values were extracted for all 171 ROIs, calculated by multiplying unit volume of voxel in mm3 by the number of voxels using in-house MATLAB script. To account for different brain sizes all the ROI volumes were normalized by dividing each ROI volume by total brain volume of that subject.