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Although model-based solution strategies for the ECGI were reported to deliver promising clinical results, they strongly rely on some a priori assumptions, which do not hold true for many pathological cases. The fastest route algorithm (FRA) is a well-established method for noninvasive imaging of ectopic activities. It generates test activation sequences on the heart and compares the corresponding test body surface potential maps (BSPMs) to the measured ones. The test excitation propagation patterns are constructed under the assumption of a global conduction velocity in the heart, which is violated in the cardiac resynchronization (CRT) patients suffering from conduction disturbances. In the present work, we propose to apply dynamic time warping (DTW) to the test and measured ECGs before measuring their similarity. The warping step is a non-linear pattern matching that compensates for local delays in the temporal sequences, thus accounting for the inhomogeneous excitation propagation, while aligning them in an optimal way with respect to a distance function. To evaluate benefits of the temporal warping for FRA-based BSPMs, we considered three scenarios. In the first setting, a simplified simulation example was constructed to illustrate the temporal warping and display the resulting distance map. Then, we applied the proposed method to eight BSPMs produced by realistic ectopic activation sequences and compared its performance to FRA. Finally, we assessed localization accuracy of both techniques in ten CRT patients. For each patient, we noninvasively imaged two paced ECGs: from left and right ventricular implanted leads. In all scenarios, FRA-DTW outperformed FRA in terms of LEs. For the clinical cases, the median (25–75% range) distance errors were reduced from 16 (8–23)mm to 5 (2–10)mm for all pacings, from 15 (11–25)mm to 8 (3–13)mm in the left, and from 19 (6–23)mm to 4 (2–8)mm in the right ventricle, respectively. The obtained results suggest the ability of temporal ECG warping to compensate for an inhomogeneous conduction profile, while retaining computational efficiency intrinsic to FRA.