Purpose:Evaluate commonly used segmentation algorithms on a commercially available real‐time MR image guided radiotherapy (MR‐IGRT) system (ViewRay), compare the strengths and weaknesses of each method, with the purpose of improving motion tracking for more accurate radiotherapy.Methods:MR motion images of bladder, kidney, duodenum, and liver tumor were acquired for three patients using a commercial on‐board MR imaging system and an imaging protocol used during MR‐IGRT. A series of 40 frames were selected for each case to cover at least 3 respiratory cycles. Thresholding, Canny edge detection, fuzzy k‐means (FKM), k‐harmonic means (KHM), and reaction‐diffusion level set evolution (RD‐LSE), along with the ViewRay treatment planning and delivery system (TPDS) were included in the comparisons. To evaluate the segmentation results, an expert manual contouring of the organs or tumor from a physician was used as a ground‐truth. Metrics value of sensitivity, specificity, Jaccard similarity, and Dice coefficient were computed for comparison.Results:In the segmentation of single image frame, all methods successfully segmented the bladder and kidney, but only FKM, KHM and TPDS were able to segment the liver tumor and the duodenum. For segmenting motion image series, the TPDS method had the highest sensitivity, Jarccard, and Dice coefficients in segmenting bladder and kidney, while FKM and KHM had a slightly higher specificity. A similar pattern was observed when segmenting the liver tumor and the duodenum. The Canny method is not suitable for consistently segmenting motion frames in an automated process, while thresholding and RD‐LSE cannot consistently segment a liver tumor and the duodenum.Conclusion:The study compared six different segmentation methods and showed the effectiveness of the ViewRay TPDS algorithm in segmenting motion images during MR‐IGRT. Future studies include a selection of conformal segmentation methods based on image/organ‐specific information, different filtering methods and their influences on the segmentation results.Parag Parikh receives research grant from ViewRay.Sasa Mutic has consulting and research agreements with ViewRay.Yanle Hu receives travel reimbursement from ViewRay.Iwan Kawrakow and James Dempsey are ViewRay employees.