He worked with Ulf Grenander in the field of Computational Anatomy as it pertains to neuroscience, specializing in mapping the brain under various states of health and disease by applying data derived from medical imaging.

With Sachs and Young, Miller focused on rate-timing population codes of complex features of speech including voice-pitch[19] and consonant-vowel syllables [20] encoded in the discharge patterns across the primary auditory nerve.

During the mid 1990s, Miller joined the Pattern Theory group at Brown University and worked with Ulf Grenander on problems in image analysis within the Bayesian framework of Markov random fields.

[26] Grenander and Miller introduced Computational anatomy as a formal theory of human shape and form at a joint lecture in May 1997 at the 50th Anniversary of the Division of Applied Mathematics at Brown University,[27] and in a subsequent publication.

David Mumford appreciated the smoothness results on existence of flows, and encouraged collaboration between Miller and the École normale supérieure de Cachan group that had been working independently.

In 1998, Mumford organized a Trimestre on "Questions Mathématiques en Traitement du Signal et de l'Image" at the Institute Henri Poincaré; from this emerged the ongoing collaboration on shape between Miller, Alain Trouve and Laurent Younes.

[39] This was one of the papers that contributed to a deeper understanding of the disorder in its earlier stages and the recommendations of the working group to revise the diagnostic criteria for Alzheimer’s disease dementia for the first time in 27 years.