Kikinis is the founding director of the Surgical Planning Laboratory in the Department of Radiology at Brigham and Women's Hospital, in Boston, Massachusetts.

Kikinis established the SPL as a center for clinical collaboration with other medical specialties in the areas of radiology, surgery, and internal medicine.

The SPL has advanced specific technologies such as image segmentation,[3] data set registration,[4] medical visualization,[5] intraoperative imaging,[6] surgical navigation,[7] and user interfaces;[8] tailored them to address specific medical problems; and disseminated them through open source software development in addition to traditional academic publication.

[11] In May 2020, he was appointed as the B. Leonard Holman Professor at Harvard Medical School, and vice-chair for Biomedical Informatics Research, Department of Radiology, Brigham Health.

NA-MIC's unique organization under the Roadmap Initiative consisted of multiple computer science and medical teams throughout the United States.