The informatics of a C57BL/6J mouse brain atlas. - Allan MacKenzie-Graham; Eagle S. Jones; David W. Shattuck; Ivo D. Dinov; Mihail Bota; Arthur W. Toga (Neuroinformatics, 2003)

DUFF: Software Tools for Visualization and Processing of Neuroimaging Data. - David W. Shattuck; Allan MacKenzie-Graham; Arthur W. Toga (ISBI, 2004)

LONI Visualization Environment. - Ivo D. Dinov; Daniel J. Valentino; Bae Cheol Shin; Fotios Konstantinidis; Guogang Hu; Allan MacKenzie-Graham; Erh-Fang Lee; David W. Shattuck; Jeff Ma; Craig Schwartz; Arthur W. Toga (J. Digit. Imaging, 2006)

Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis. - Allan MacKenzie-Graham; Matthew R. Tinsley; Kaanan P. Shah; Cynthia Aguilar; Lauren V. Strickland; Jyl Boline; Melanie Martin; Laurie Morales; David W. Shattuck; Russell E. Jacobs; Rhonda R. Voskuhl; Arthur W. Toga (NeuroImage, 2006)

Genetic Algorithms for Finite Mixture Model Based Voxel Classification in Neuroimaging. - Jussi Tohka; Evgeny Krestyannikov; Ivo D. Dinov; Allan MacKenzie-Graham; David W. Shattuck; Ulla Ruotsalainen; Arthur W. Toga (IEEE Trans. Medical Imaging, 2007)

Neuroimaging Data Provenance Using the LONI Pipeline Workflow Environment. - Allan MacKenzie-Graham; Arash Payan; Ivo D. Dinov; John D. Van Horn; Arthur W. Toga (IPAW, 2008)

Provenance in neuroimaging. - Allan MacKenzie-Graham; John D. Van Horn; Roger P. Woods; Karen L. Crawford; Arthur W. Toga (NeuroImage, 2008)

Efficient, distributed and interactive neuroimaging data analysis using the LONI pipeline. - Ivo D. Dinov; John D. Van Horn; Kamen Lozev; Rico Magsipoc; Petros Petrosyan; Zhizhong Liu; Allan MacKenzie-Graham; Paul R. Eggert; Douglas Stott Parker; Arthur W. Toga (Frontiers Neuroinformatics, 2009)

Purkinje cell loss in experimental autoimmune encephalomyelitis. - Allan MacKenzie-Graham; Seema K. Tiwari-Woodruff; Gaurav Sharma; Cynthia Aguilar; Kieumai T. Vo; Lauren V. Strickland; Laurie Morales; Boma Fubara; Melanie Martin; Russell E. Jacobs; G. Allan Johnson; Arthur W. Toga; et al. (NeuroImage, 2009)

In vivo vs. ex vivo Magnetic Resonance Imaging In Mice. - Allan MacKenzie-Graham (Frontiers Neuroinformatics, 2012)

Cortical atrophy in experimental autoimmune encephalomyelitis: In vivo imaging. - Allan MacKenzie-Graham; Gilda A. Rinek; Andrea Avedisian; Stefan M. Gold; Andrew J. Frew; Cynthia Aguilar; David R. Lin; Elizabeth Umeda; Rhonda R. Voskuhl; Jeffry R. Alger (NeuroImage, 2012)

Bringing CLARITY to gray matter atrophy. - Rory D. Spence; Florian Kurth; Noriko Itoh; Chandler R. L. Mongerson; Shannon H. Wailes; Mavis S. Peng; Allan MacKenzie-Graham (NeuroImage, 2014)

In vivo magnetic resonance images reveal neuroanatomical sex differences through the application of voxel-based morphometry in C57BL/6 mice. - Cassandra E. Meyer; Florian Kurth; Stefano Lepore; Josephine L. Gao; Hadley Johnsonbaugh; Mandavi R. Oberoi; Stephen J. Sawiak; Allan MacKenzie-Graham (NeuroImage, 2017)

Mouse brain extraction using 2-Stage CNNs. - Yeun Kim; Evelyn Malamut; Cassandra E. Meyer; Allan MacKenzie-Graham; David W. Shattuck (Image Processing, 2022)