Can a negative d-dimer assay be used to effectively rule out cerebral venous thrombosis?

No. In a series of 73 patients with cerebral venous thrombosis of less than 30 days' duration, 26% of those who presented with isolated headache had normal D-dimer concentrations.


Source

Bouseer, M. and Ferro, J. "Cerebral venous thrombosis: an update" Lancet Neurology. 2007.