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Abstract Fully CMR-guided electrophysiological interventions (EP-CMR) have recently been introduced but data on the optimal CMR imaging protocol are scarce. This study determined the clinical utility of 3D non-selective whole heart steady-state free precession imaging using compressed SENSE (nsWHcs) for automatic segmentation of cardiac cavities as the basis for targeted catheter navigation during EP-CMR cavo-tricuspid isthmus ablation. Fourty-two consecutive patients with isthmus-dependent right atrial flutter underwent EP-CMR radiofrequency ablations. nsWHcs succeeded in all patients (nominal scan duration, 98 ± 10 s); automatic segmentation/generation of surface meshes of right-sided cavities exhibited short computation times (16 ± 3 s) with correct delineation of right atrium, right ventricle, tricuspid annulus and coronary sinus ostium in 100%, 100%, 100% and 95%, respectively. Point-by-point ablation adhered to the predefined isthmus line in 62% of patients (26/42); activation mapping confirmed complete bidirectional isthmus block (conduction time difference, 136 ± 28 ms). nsWHcs ensured automatic and reliable 3D segmentation of targeted endoluminal cavities, multiplanar reformatting and image fusion (e.g. activation time measurements) and represented the basis for precise real-time active catheter navigation during EP-CMR ablations of isthmus-dependent right atrial flutter. Hence, nsWHcs can be considered a key component in order to advance EP-CMR towards the ultimate goal of targeted substrate-based ablation procedures.