MR-guided radiotherapy requires strong imaging spatial integrity to deliver high quality plans and provide accurate dose calculation. The MRI system, however, can be compromised by the integrated linear accelerator (Linac), resulting in inaccurate imaging isocenter position and geometric distortion. Dependence on gantry position further complicates the correction of distortions. This work presents a new clinical application of a commercial phantom and software system that quantifies isocenter alignment and geometric distortion, as well as providing a deformation vector field (DVF). A large distortion phantom and a smaller grid phantom were imaged at multiple gantry angles from 0 to 330 • on a 0.35 T integrated MR-Linac. The software package was used to assess geometric distortion and generate DVFs to correct distortions within the phantom volume. The DVFs were applied to the grid phantom with resampling software then evaluated using structural similarity index measure (SSIM). Scans were also performed with a ferromagnetic clip near the phantom to investigate the correction of more severe artifacts. The mean magnitude isocenter shift was 0.67 mm, ranging from 0.25 to 1.04 mm across all angles. The DVF had a mean component value of 0.27 ± 0.02, 0.24 ± 0.01, and 0.19 ± 0.01 mm in the rightleft (RL), anterior-posterior (AP), and superior-inferior (SI) directions. The ferromagnetic clip increased isocenter position error from 1.98 mm to 2.20 mm and increased mean DVF component values in the RL and AP directions. The resampled grid phantom had an increased SSIM for all gantry angles compared to original images, increasing from 0.26 ± 0.001 to 0.70 ± 0.004. Through this clinical assessment, we were able to correct geometric distortion and isocenter shift related to gantry position on a 0.35 T MR-Linac using the distortion phantom and software package. This provides encouragement that it could be used for quality assurance and clinically to correct systematic distortion caused by imaging at different gantry angles.