Statistical image reconstruction in X-Ray computed tomography yields large-scale regularized linear least-squares problems with nonnegativity bounds, where the memory footprint of the operator is a concern. Discretizing images in cylindrical coordinates results in significant memory savings, and allows parallel operator-vector products without on-the-fly computation of the operator, without necessarily decreasing image quality. However, it deteriorates the conditioning of the operator. We improve the Hessian conditioning by way of a block-circulant scaling operator and we propose a strategy to handle nondiagonal scaling in the context of projected-directions methods for bound-constrained problems. We describe our implementation of the scaling strategy using two algorithms: TRON, a trust-region method with exact second derivatives, and L-BFGS-B, a linesearch method with a limited-memory quasi-Newton Hessian approximation. We compare our approach with one where a change of variable is made in the problem. On two reconstruction problems, our approach converges faster than the change of variable approach, and achieves much tighter accuracy in terms of optimality residual than a first-order method.