FMRI Analysis Software - "Pantheon"

FMRI Analysis Software for all levels of the CNS


This software package is freely available on GitHub at

PANTHEON is a python software package for the analysis of functional MRI data. It was developed to be able to analyze data from the entire central nervous system (CNS), including all levels of the spinal cord, brainstem, and brain.

This software has been developed by P. Stroman over the past 25 years over many versions, and incorporates all of the methods that have been developed to overcome problems of physiological motion, image artifacts, and challenges of functional MRI, including specialized methods for the spinal cord and brainstem.

Previous versions were developed in MATLAB but the currently supported python version is intended to make the analysis methods more widely accessible. The current version has been tested on both Windows and MacOs.

The software includes tools for managing databases, automated spatial normalization including normalized reference templates, data pre-processing (co-registration, applying spatial normalization, slice-timing correction, definition of basis sets including physiological noise, and removal of noise), analysis by fitting to a predicted BOLD response, improved methods for connectivity analyses including our lab's recent development of structural and physiological modeling (SAPM), characterizations of BOLD responses with regression analyses, and group-level analyses.

The software is shared freely to encourage further development and applications of spinal cord fMRI, but we request that if you use any part of it you reference relevant methods papers by P. W. Stroman, Queen's University.

Fore more information contact Dr. Patrick Stroman by e-mail at 

User interfaces used for data analysis software developed by Dr. P. Stroman