We address the computational challenges related to the extraction of the arterial-lumen geometry, mesh generation and starting-point determination in the computation of arterial fluid–structure interactions (FSI) with patient-specific data. The methods we propose here to address those challenges include techniques for constructing suitable cutting planes at the artery inlets and outlets and specifying on those planes proper boundary conditions for the fluid mechanics, structural mechanics and fluid mesh motion and a technique for the improved calculation of an estimated zero-pressure arterial geometry. We use the stabilized space–time FSI technique, together with a number of special techniques recently developed for arterial FSI. We focus on three patient-specific cerebral artery segments with aneurysm, where the lumen geometries are extracted from 3D rotational angiography. Copyright © 2010 John Wiley & Sons, Ltd.