fMRI at subcortical resolution in rat whisker barrel cortex

In the present study, gradient coil, RF coils and pulse sequences that are tailored for high resolution rat imaging are developed. Specifically, a momentum-weighted conjugate gradient descent algorithm for gradient coil optimization has been developed. This method allows more compact wire patterns, resulting in designs with improved coil efficiency and field uniformity. A water-cooled three-axis torque-balanced local gradient coil was designed based on this method and applied in this study. An interleaved partial/full k-space EPI sequence has been developed. Phase corrections employing phase-encoded calibration scans can align even and odd k-space lines with less off-resonance effects, improving half k-space image formation.; Functional specificity of fMRI using BOLD and CBV contrast was investigated in a rat whisker barrel stimulation model at 3T. The high-resolution GE-BOLD data (voxel volume: 156 x 156 x 2000 mum3) demonstrate that BOLD response at a subcortical spatial resolution can be achieved at 3T. The BOLD activation maps are primarily located in the gray matter of the whisker barrel cortex. Most of the activated voxels with high BOLD responses have relatively high blood volume weightings. No laminar-specific BOLD response was observed in this animal model using gradient echo sequences at 3T. These data support the hypothesis that the localization of the BOLD response using gradient echo sequences is dictated by the local vasculature of microcirculation. The high-resolution SE-BOLD activation maps (voxel volume: 208 x 208 x 2000 mum 3) are highly localized. Laminar distribution of activated pixels in SE-BOLD fMRI is more homogenous than that of the neuronal activity localized by Fos expression, suggesting BOLD effect from relatively large vessels. The high-resolution CBV-weighted fMRI data (voxel volume: 208 x 208 x 2000 mum3) suggest that laminar-specific functional specificity can be achieved at 3T by cross-correlating the CBV response with the stimulus paradigm using a high dose of contrast agent to suppress intra- and extra-vascular BOLD effects.