The Integrated Brain Analysis Toolbox for SPM (iBT)

2263 

Abstract Submission 

David Abbott^1,2, Aaron Capon¹, Chris Tailby^1,2, Bahman Tahayori¹, Marty Bryant¹, David Vaughan^1,2, Graeme Jackson^1,2, for the Australian Epilepsy Project Investigators¹

¹The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia, ²The University of Melbourne, Melbourne, Australia

David Abbott, PhD  
The Florey Institute of Neuroscience and Mental Health|The University of Melbourne
Melbourne, Australia|Melbourne, Australia

Aaron Capon, PhD  
The Florey Institute of Neuroscience and Mental Health
Melbourne, Australia

Chris Tailby, PhD  
The Florey Institute of Neuroscience and Mental Health|The University of Melbourne
Melbourne, Australia|Melbourne, Australia

Bahman Tahayori  
The Florey Institute of Neuroscience and Mental Health
Melbourne, Australia

Marty Bryant  
The Florey Institute of Neuroscience and Mental Health
Melbourne, Australia

David Vaughan, PhD  
The Florey Institute of Neuroscience and Mental Health|The University of Melbourne
Melbourne, Australia|Melbourne, Australia

Graeme Jackson  
The Florey Institute of Neuroscience and Mental Health|The University of Melbourne
Melbourne, Australia|Melbourne, Australia

for the Australian Epilepsy Project Investigators  
The Florey Institute of Neuroscience and Mental Health
Melbourne, Australia

The "Integrated Brain Analysis Toolbox for SPM" (iBT), also known as the "iBrain Analysis Toolbox for SPM" (iBrainTools)¹, is a functional neuroimaging analysis toolbox that adds additional pre-processing, analysis, display and automation features to the Statistical Parametric Mapping software SPM². iBT has been enhanced with many new features.

iBT is written in MATLAB and requires SPM². Some optional features also make use of tools from FSL³ and/or iBrain⁴, or output from fMRIPrep⁵.

iBT is designed to allow a complete a priori configuration of a computational pipeline that includes pre-processing, statistical analysis and display of functional Magnetic Resonance Imaging (fMRI) data. The toolbox is suitable for general linear model analysis of block and event-related designs, and functional connectivity. It allows easy access to features such as multi-session realignment to a single optimally auto-selected target volume, seed-timecourse regressor construction from regions of interest, configurable auto-generated motion-rejection regressors (to deal with excessive scan-to-scan motion), flexible regressor-orthogonalisation options, automated contrast generation taking into account nuisance regressors, adjustment of degrees of freedom for denoised input data, and automated generation of tiled output image montages in a print and display friendly format. The pipeline can be configured to automatically run for any number of subjects and sessions.

iBT can be configured to analyse and/or display results from other neuroimaging software. iBT includes inbuilt support for analysis and display of fMRI data that has been pre-processed with fMRIPrep⁵, including utilising any choice of confound regressors generated by fMRIPrep. One can also instruct iBT to call one's own custom MATLAB routine to undertake novel analyses.

iBT includes tools to objectively assess relative laterality of activity in specified pairs of regions of interest⁶. The toolbox plots curves of laterality as a function of activation volume, and it allows statistical comparison of an individual with a control group, in a manner largely independent of an activation map statistical threshold^6,7. New user-configurable display options are available to customise the output plots.

In addition to conventional SPM toolbox deployment, iBT now also supports containerisation. The containerised version includes compiled SPM together with iBT to allow it to utilise Runtime MATLAB (no MATLAB end-user licence required).

In a recent large-scale use case, the Australian Epilepsy Project (AEP)⁸ has been analysing functional MRI data at scale utilising fMRIPrep and iBT. The AEP has deployed containerised fMRIPrep and iBT on high-performance computing platforms at The University of Melbourne and Monash University, as well as on a Flywheel⁹ instance on AWS. Select iBT outputs, including functional MRI statistical maps (Figure 1) and Laterality Index (LI) results for a pseudoword language task (Figure 2), form part of an AEP Report for each participant that is returned to each participant's treating clinician.

iBT is a robust and flexible analysis toolbox for SPM that provides additional capabilities and facilitates advanced fully automated statistical parametric mapping. iBT is free and open-source software released under the GNU General Public License.
iBT is available at https://florey.edu.au/imaging-software

Activation (eg. BOLD task-fMRI)

Methods Development ²

Motion Correction and Preprocessing

Task-Independent and Resting-State Analysis

Workflows ¹

Data analysis

Design and Analysis

Epilepsy

FUNCTIONAL MRI

Informatics

Language

Open-Source Software

Statistical Methods

Workflows