Femoroacetabular impingement (FAI) cam morphology is routinely assessed using two-dimensional alpha angles which do not provide specific data on cam size characteristics. The purpose of this study is to implement a novel, automated three-dimensional (3D) pipeline, CamMorph, for segmentation and measurement of cam volume, surface area and height from magnetic resonance (MR) images in patients with FAI. The CamMorph pipeline involves two processes: i) proximal femur segmentation using an approach integrating 3D U-net with focused shape modelling (FSM); ii) use of patient-specific anatomical information from 3D FSM to simulate healthy femoral bone models and pathological region constraints to identify cam bone mass. Agreement between manual and automated segmentation of the proximal femur was evaluated with the Dice similarity index (DSI) and surface distance measures. Independent t-tests or Mann-Whitney U rank tests were used to compare the femoral head volume, cam volume, surface area and height data between female and male patients with FAI. There was a mean DSI value of 0.964 between manual and automated segmentation of proximal femur volume. Compared to female FAI patients, male patients had a significantly larger mean femoral head volume (66.12cm3 v 46.02cm3, p<0.001). Compared to female FAI patients, male patients had a significantly larger mean cam volume (1136.87mm3 v 337.86mm3, p<0.001), surface area (657.36mm2 v 306.93mm2 , p<0.001), maximum-height (3.89mm v 2.23mm, p<0.001) and average-height (1.94mm v 1.00mm, p<0.001). Automated analyses of 3D MR images from patients with FAI using the CamMorph pipeline showed that, in comparison with female patients, male patients had significantly greater cam volume, surface area and height.