Quick Project Snapshot

Quantitative voxel-based analysis of qualitative images

Abnormalities in the brain can manifest on MRI as changes in shape (morphometry) or changes in the nature of the tissue (signal intensity). Quantitative assessment across the whole brain is possible. For example Voxel Based Morphometry (VBM) is a whole brain quantitative way of assessing morphometric changes, and Voxel Based Relaxometry (VBR) directly assesses signal intensity changes in quantitative maps of T2 relaxation time. Unfortunately signal intensity analysis is not straightforward with conventional clinical imaging. This is because typical clinical images, such as T2-weighted MRI, are qualitative in nature: the values can vary from scan-to-scan and assessment of a scan is typically undertaken by a radiologist viewing an image by eye and relying on relative contrast within the image. Whilst quantitative imaging is possible, it usually requires specialised multiple-echo acquisition sequences that can take longer to acquire and are not often available at clinical sites.

To allow quantitative analysis of clinical images, we have developed an objective voxel-based statistical method for evaluation of signal intensity in groups of routinely acquired qualitative images. We call the method Voxel-Based Iterative Sensitivity (VBIS) analysis. It adaptively optimises the relative global scaling of images in an effort to standardise the overall intensity of different images to maximise sensitivity to regional effects. It also includes a final iteration to avoid potentially significant voxels contaminating the scaling factor.

We applied and validated this method of analysis for T2-weighted images of the human brain, by directly comparing with Voxel Based Relaxometry. We studied a group of patients with left hemisphere hippocampal sclerosis and a group of healthy controls. Expected signal abnormalities in the patients were detectable with VBIS-T2, confirming the feasibility of the technique. This opens the door to use of a voxel-based analysis approach for group studies of clinical T2-weighted MRI. More generally, when a quantitative modality is not available, VBIS can be an effective way to quantify differences between groups: for example, the method may assist quantitative analysis of other qualitative modalities such as T1-weighted MRI, SPECT and CT.

Selected publications

Abbott DF, Pell GS, Pardoe HR, Jackson GD. Selecting appropriate voxel-based methods for neuroimaging studies. NeuroImage 59(2)885–886 (2012).

Abbott DF, Pell GS, Pardoe H, Jackson GD. Voxel-Based Iterative Sensitivity (VBIS) analysis: methods and a validation of intensity scaling for T2-weighted imaging of hippocampal sclerosis. NeuroImage 44(3):812-819 (2009).

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