Dr. Patrick Stroman

Queen's University Queen's University

Spinal Cord and Brainstem fMRI Analysis Software

written in MATLAB and python

screen shot image of the graphical user interface for fMRI analysis software in pythonThis software has been developed by P. Stroman over the past 20 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 spinal cord  functional MRI.

The python version is a more recent addition in order to make the analysis methods more widely accessible.

The most recent version includes tools for automated spatial normalization, including normalized reference templates, and improved methods for connectivity analyses.

It was developed for the sagittal slice imaging method used in the Stroman Lab, but is being adapted for any slice orientations/positions, with additional information required to guide spatial normalization. It was also developed initially for the cervical spinal cord and brainstem, but can be applied to any level of the spinal cord.

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.

The current MATLAB version ("spinalfmri9") is available upon request (the anatomical map files are large so I have not put a link here). This set of programs calls elements of the MIRT and CONN software packages, which I did not develop, and so they are not included in the spinalfmri9 package. For convenience, I have a link to download the MIRT software MIRT.zip (130 KB) (because I don't see it anymore on the NITRC web site) and to where you can get the CONN software

The current python version ("pyspinalfmri") continues to be under development and currently includes pre-processing (conversion to NIfTI format, coregistration, normalization, slice timing correction, smoothing), fMRI analysis using GLM fit to a predicted BOLD response, and connectivity analyses, for the brainstem and spinal cord. It is being expanded to include brain regions and more analysis options.  It is available upon request.

If you have any questions contact Dr Patrick Stroman by e-mail at stromanp@queensu.ca , or by phone at 613-533-3245.