Quantitative susceptibility mapping (QSM) is a post-processing technique for gradient-recalled-echo (GRE) phase data, which provides information about tissue composition complementary to common Susceptibility Weighted Imaging (SWI). To date, QSM’s multiple complex processing steps has limited its clinical application. In this work, we present an automated and robust inline QSM post-processing pipeline compatible with flow-compensated GRE and VIBE sequences. The QSM pipeline includes morphological and atlas-based segmentation, two different QSM algorithms and is compatible with SWI processing. Two clinical cases of QSM in Traumatic Brain Injury and Multiple Sclerosis are presented.