Functional reorganization in rat somatosensory cortex assessed by fMRI: Elastic image registration based on structural landmarks in fMRI images and application to spinal cord injured rats. - Esther Sydekum; Christof Baltes; Arko Ghosh; Thomas Mueggler; Martin E. Schwab; Markus Rudin (NeuroImage, 2009)

Hybrid Small Animal Imaging System Combining Magnetic Resonance Imaging With Fluorescence Tomography Using Single Photon Avalanche Diode Detectors. - Florian Stuker; Christof Baltes; Katerina Dikaiou; Divya Vats; Lucio Carrara; Edoardo Charbon; Jorge Ripoll; Markus Rudin (IEEE Trans. Medical Imaging, 2011)

MRI signature in a novel mouse model of genetically induced adult oligodendrocyte cell death. - Thomas Mueggler; Hartmut Pohl; Christof Baltes; Dieter Riethmacher; Ueli Suter; Markus Rudin (NeuroImage, 2012)

Functional MRI to assess alterations of functional networks in response to pharmacological or genetic manipulations of the serotonergic system in mice. - Florence Razoux; Christof Baltes; Thomas Mueggler; Aline Seuwen; Holger Russig; Isabelle Mansuy; Markus Rudin (NeuroImage, 2013)

Optimization of anesthesia protocol for resting-state fMRI in mice based on differential effects of anesthetics on functional connectivity patterns. - Joanes Grandjean; Aileen Schroeter; Imene Batata; Markus Rudin (NeuroImage, 2014)

Specificity of stimulus-evoked fMRI responses in the mouse: The influence of systemic physiological changes associated with innocuous stimulation under four different anesthetics. - Aileen Schroeter; Felix Schlegel; Aline Seuwen; Joanes Grandjean; Markus Rudin (NeuroImage, 2014)

Rapid functional reorganization of the forelimb cortical representation after thoracic spinal cord injury in adult rats. - Esther Sydekum; Arko Ghosh; Miriam Gullo; Christof Baltes; Martin E. Schwab; Markus Rudin (NeuroImage, 2014)

The hemodynamic response to somatosensory stimulation in mice depends on the anesthetic used: Implications on analysis of mouse fMRI data. - Felix Schlegel; Aileen Schroeter; Markus Rudin (NeuroImage, 2015)

Metabolic changes assessed by MRS accurately reflect brain function during drug-induced epilepsy in mice in contrast to fMRI-based hemodynamic readouts. - Aline Seuwen; Aileen Schroeter; Joanes Grandjean; Markus Rudin (NeuroImage, 2015)

Mapping the mouse brain with rs-fMRI: An optimized pipeline for functional network identification. - Valerio Zerbi; Joanes Grandjean; Markus Rudin; Nicole Wenderoth (NeuroImage, 2015)

FEM-based simulation of a fluorescence tomography experiment using anatomical MR images. - Wuwei Ren; Andreas Elmer; Mark-Aurel Augath; Markus Rudin (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2016)

Random Forest Segregation of Drug Responses May Define Regions of Biological Significance. - Qasim Bukhari; David Borsook; Markus Rudin; Lino Becerra (Frontiers Comput. Neurosci., 2016)

Chronic psychosocial stress in mice leads to changes in brain functional connectivity and metabolite levels comparable to human depression. - Joanes Grandjean; Damiano Azzinnari; Aline Seuwen; Hannes Sigrist; Erich Seifritz; Christopher R. Pryce; Markus Rudin (NeuroImage, 2016)

Complex interplay between brain function and structure during cerebral amyloidosis in APP transgenic mouse strains revealed by multi-parametric MRI comparison. - Joanes Grandjean; Rebecca Derungs; Luka Kulic; Tobias Welt; R. Mark Henkelman; Roger M. Nitsch; Markus Rudin (NeuroImage, 2016)

LabbookDB: A Wet-Work-Tracking Database Application Framework. - Horea-Ioan Ioanas; Bechara John Saab; Markus Rudin (SciPy, 2017)

Dynamic reorganization of intrinsic functional networks in the mouse brain. - Joanes Grandjean; Maria Giulia Preti; Thomas William Arthur Bolton; Michaela Buerge; Erich Seifritz; Christopher R. Pryce; Dimitri Van De Ville; Markus Rudin (NeuroImage, 2017)

Altered regional connectivity reflecting effects of different anaesthesia protocols in the mouse brain. - Tong Wu; Joanes Grandjean; Simone C. Bosshard; Markus Rudin; David C. Reutens; Tianzi Jiang (NeuroImage, 2017)

Dual Ring Prototype Electronic System for the Small Animal Fast Insert for MRI. - Robert Becker; Alfred Buck; Volker Commichau; Diogo Di Calafiori; Günther Dissertori; Lubomir Djambazov; Afroditi Eleftheriou; Peter Fischer; Mikiko Ito; Parisa Khateri; Werner Lüstermann; Josep F. Oliver; et al. (ICECS, 2018)

Exploring experimental autoimmune optic neuritis using multimodal imaging. - Praveena Manogaran; Christine Walker-Egger; Marijana Samardzija; Conny Waschkies; Christian Grimm; Markus Rudin; Sven Schippling (NeuroImage, 2018)

COSplay: Contrast Optimized Stimulation Player. - Florian Aymanns; Markus Rudin; Horea-Ioan Ioanas (J. Open Source Softw., 2019)

Inhibiting mGluR5 activity by AFQ056/Mavoglurant rescues circuit-specific functional connectivity in Fmr1 knockout mice. - Valerio Zerbi; Marija Markicevic; Fabrizio Gasparini; Aileen Schroeter; Markus Rudin; Nicole Wenderoth (NeuroImage, 2019)

An Automated Open-Source Workflow for Standards-Compliant Integration of Small Animal Magnetic Resonance Imaging Data. - Horea-Ioan Ioanas; Markus Marks; Clément M. Garin; Marc Dhenain; Mehmet Fatih Yanik; Markus Rudin (Frontiers Neuroinformatics, 2020)

Retrieving neuronal orientations using 3D scanning SAXS and comparison with diffusion MRI. - Marios Georgiadis; Aileen Schroeter; Zirui Gao; Manuel Guizar-Sicairos; Dmitry S. Novikov; Els Fieremans; Markus Rudin (NeuroImage, 2020)

Smart Toolkit for Fluorescence Tomography: Simulation, Reconstruction, and Validation. - Wuwei Ren; Helene Isler; Martin Wolf; Jorge Ripoll; Markus Rudin (IEEE Trans. Biomed. Eng., 2020)

Psilocybin exerts distinct effects on resting state networks associated with serotonin and dopamine in mice. - Joanes Grandjean; David Buehlmann; Michaela Buerge; Hannes Sigrist; Erich Seifritz; Franz X. Vollenweider; Christopher R. Pryce; Markus Rudin (NeuroImage, 2021)

An optimized registration workflow and standard geometric space for small animal brain imaging. - Horea-Ioan Ioanas; Markus Marks; Valerio Zerbi; Mehmet Fatih Yanik; Markus Rudin (NeuroImage, 2021)