Quick Project Snapshot

Functional MRI Processing Pipelines

There are many processing and analysis steps undertaken on functional MRI (fMRI) images after they are acquired by the MRI scanner. For example: image format conversion, slice timing temporal interpolation, within-run image realignment, within-brain masking, spatial normalisation across subjects, spatial smoothing, response modelling, statistical inference and display of results. There are many optional processing steps, and indeed even in those steps listed above there are many choices of methods. Optimal choices depend upon the type of study, scanner and hypotheses to be tested. Often the optimal choices will require use of multiple software packages. The neuroinformatics laboratory developed the iBrain Analysis Toolbox for SPM to address many of the challenges of automating neuroimaging analyses, ensuring analyses can be repeated and providing provenance of the resultant data (a detailed history of the steps undertaken). The toolbox is designed to work together with the SPM neuroimaging software package, however it also utilises other software packages for some steps when that is advantageous.

See also the iBrain Analysis Toolbox for SPM.

A/Prof David Abbott

Epilepsy Neuroinformatics Laboratory

The Neuroinformatics Laboratory undertakes advanced neuroimaging analysis methods development and applied research to further our understanding of the human brain in health and disease. Whilst the work in the laboratory is relevant to a wide range of brain mapping applications, a particular emphasis of the research is towards methods that can help better understand the causes and consequences of epileptic seizures. This includes implementation, development and application of advanced image analysis procedures for structural and functional magnetic resonance imaging (MRI, fMRI) and electroencephalography (EEG) - including simultaneous EEG & fMRI. These non-invasive imaging modalities together with advanced computational methods are capable of mapping human brain activity at millimetre spatial resolution and millisecond temporal resolution. Our scientists work collaboratively with local and international clinical research teams, sharing analysis methods and data in a multidisciplinary pursuit of discovery.

The Neuroinformatics Laboratory has a range of software publicly available.  Please click below for further information and downloads.

Software Available


All Projects by this Lab

Functional neuroimaging analysis to identify brain abnormality in epilepsyArtefact reduction in functional MRIFunctional connectivity and the human brain functional connectomeFunctional MRI Processing PipelinesLaterality of brain functionMorphometryQuantitative voxel-based analysis of qualitative imagesSimultaneous EEG-fMRIT2 relaxometry


The Florey's Epilepsy division is a world-leading centre for epilepsy research. The division has major groups at both the Florey’s Austin and Parkville campus. The group studies mechanisms that cause epilepsy from the level of cells to the function of the whole brain. We use technologies including advanced MRI and cutting edge cellular physiology techniques to allow us to understand genetic and acquired mechanisms that give rise to epilepsy. Together with our colleagues from The University of Melbourne and across Australia we are working towards finding a cure for epilepsy.

All Labs that operate in this Division

Epilepsy Cognition LaboratoryEpilepsy Neuroinformatics LaboratoryImaging and EpilepsyInnate Phagocytosis LaboratoryIon Channels and Human Diseases LaboratoryNeural Networks LaboratoryNeurophysiology of Excitable Networks LaboratoryPsychology and Experimental NeurophysiologySleep and CognitionTraumatic Brain Injury Laboratory