fMRat: an extension of SPM for a fully automatic analysis of rodent brain functional magnetic resonance series Articles uri icon

publication date

  • May 2016

start page

  • 743

end page

  • 752


  • 5


  • 54

International Standard Serial Number (ISSN)

  • 0140-0118

Electronic International Standard Serial Number (EISSN)

  • 1741-0444


  • The purpose of this study was to develop a multi-platform automatic software tool for full processing of fMRI rodent studies. Existing tools require the usage of several different plug-ins, a significant user interaction and/or programming skills. Based on a user-friendly interface, the tool provides statistical parametric brain maps (t and Z) and percentage of signal change for user-provided regions of interest. The tool is coded in MATLAB (MathWorks(A (R))) and implemented as a plug-in for SPM (Statistical Parametric Mapping, the Wellcome Trust Centre for Neuroimaging). The automatic pipeline loads default parameters that are appropriate for preclinical studies and processes multiple subjects in batch mode (from images in either Nifti or raw Bruker format). In advanced mode, all processing steps can be selected or deselected and executed independently.


  • fmri; automatic analysis; rat; spm; rat-brain; somatosensory stimulation; hemodynamic-response; time-series; mri; dynamics; atlas