fMRI Data Visualization with BrainBlend and Blender Martin Pyka & Matthias Hertog & Raul Fernandez & Sascha Hauke & Dominik Heider & Udo Dannlowski & Carsten Konrad # Springer Science+Business Media, LLC 2009 Abstract The visualization and exploration of neuroimaging data is important for the analysis of anatomical and functional magnetic resonance (MR) images and thresholded statistical parametric maps. While two-dimensional orthogonal views of neuroimaging data are used to display statistical analyses, real three-dimensional (3d) depictions are helpful for showing the spatial distribution of a functional network, as well as its temporal evolution. However, viewers that are freely available on the internet offer only limited rendering capabilities and depictions of temporal changes of the blood oxygen level- dependent (BOLD) response. In this article, we present BrainBlend, a toolbox for the software package Statistical Parametric Mapping (SPM), that generates voxeldata files to be used with the open-source 3d-software ���Blender���. Our interface between SPM and Blender permits the use of any Analyze- and Nifti-file for the creation of images and animations of transparent volumetric objects. Different kinds of anatomical, functional and statistical data can be rendered as volumetric objects in order to convey an immediate understanding of the three-dimensional shape. Representa- tions of functional networks can be animated using a time course extracted from the general linear model or the independent component analysis. Relative BOLD activations of functional MR-images can be calculated for a time- resolved depiction of hemodynamic changes. The resulting animation can be displayed along with its corresponding paradigm matrix and the presented stimuli. BrainBlend is particularly suitable for the visual exploration of interactions between functional networks, for time-resolved animations of BOLD changes and meets high demands on visual quality in images and animations. Keywords fMRI . SPM . Blender . Toolbox . 3d . Visualization . Time-resolved Introduction With the evolution of functional magnetic resonance imaging (fMRI), the need to visualize statistical, neuroan- atomical and functional images has increased. Although M. Pyka (*) : M. Hertog : S. Hauke : U. Dannlowski : C. Konrad Department of Psychiatry, University of M��nster, Albert-Schweitzer-Stra��e 11, 48129 M��nster, Germany e-mail: martin.pyka@uni-muenster.de M. Pyka : M. Hertog : S. Hauke : U. Dannlowski : C. Konrad Interdisciplinary Center for Clinical Research (IZKF FG4), University of M��nster, M��nster, Germany M. Pyka : U. Dannlowski Otto Creutzfeld Centre for Cognitive and Behavioral Neuroscience, University of M��nster, M��nster, Germany M. Hertog : S. Hauke Institute of Computer Science, University of M��nster, M��nster, Germany R. Fernandez Facultad de Inform��tica y Telecomunicaciones, University of Pinar del Rio Hermanos Saiz, Pinar del Rio, Cuba D. Heider Department of Bioinformatics, Center for Medical Biotechnology, University of Duisburg-Essen, Duisburg, Germany C. Konrad Department of Psychiatry und Psychotherapy, Philipps-University Marburg, Marburg, Germany Neuroinform DOI 10.1007/s12021-009-9060-3

tables of clusters and coordinates provide a reliable way of ensuring that the results remain comparable, visualizations are an important way to convey the location and spatial extent of effects in functional neuroimaging studies. Traditionally, the human brain is visualized in three two- dimensional orthogonal planes (coronal, sagittal and axial projections) in order to show areas of increased activation or deactivation under certain conditions. However, such illustrations cannot convey the three-dimensional complexity of activated areas at a glance, particularly, in time-resolved depictions of functional activation changes of the whole brain. Therefore, novel applications are needed that facilitate a better understanding of the three-dimensional shape, distribution and time-dependent changes of brain areas. In order to address this issue, some software packages provide a three-dimensional view of anatomical and functional MR-data. MRIcro (www.mricro.com) is one of the most popular viewers of medical images that is freely available (Rorden et al. 2007). Voxeldata can be rendered as a surface or volume object and statistical maps can be used as overlays. Other packages, such as 3DView (http://www. rmrsystems.co.uk/volume_rendering.htm), Slicer (Gering et al. 2001), DataViewer3D (Gouws et al. 2009) or fMRIVis (R����ler et al. 2006) offer similar capabilities. These packages provide helpful functionality for display- ing three-dimensional voxel volumes of anatomical and functional data. For instance, MRIcron depicts slices of anatomical MRI data along with functional overlays. These overlays can also be rendered as 3d-projections on a non- transparent voxel volume of the human brain. DataViewer3D is a recently published viewer for multi-modal neuroimaging data that depicts structural and functional MRI data as well as DTI and MEG/EEG data (Gouws et al. 2009). It supports 2d- and 3d-projections and the combination of data from different acquisition techniques. However, no software tool provides the ability to render animated functional and statistical, time-resolved MRI data and can combine them along with supplementary materials. Spectus3D (http:// netedge.co.uk/s3d/) provides the functionality to display hemodynamic changes, but this application is apparently unavailable at present. We present a toolbox for the widely-used Matlab application SPM (Friston 2008) which allows the com- putation and visualization of time-resolved functional neuroimaging data in the free 3d-software Blender (www.blender.org) (Hess 2007). We refer to this applica- tion as BrainBlend. BrainBlend offers algorithms for the computation of relative BOLD activation changes. The increase and decrease of BOLD activity can be computed as relative difference to baseline images or as relative difference to the preceding image. Thereby, the temporal effect of perceptually and cognitively demanding tasks can be investigated on individual and on group level. The resulting images can be saved in the Nifti-format (http:// nifti.nimh.nih.gov/nifti-1/) for further analysis in SPM and other fMRI tools. Furthermore, BrainBlend allows the export of the results to the new voxeldata format for the voxeldata renderer of Blender, which has been developed to visualize volumetric objects through transparent voxeldata. With the new voxeldata renderer the computed hemodynamic changes can be visualized for the entire brain through voxel volumes, allowing a direct and intuitive view on the changes occurring in the brain. The usage of Blender for visualization enables the creation of high-quality pictures and animations of the human brain and hemodynamic responses. Supplementary materials can be integrated in the animation to view hemodynamic changes along with the experimental design and the presented stimuli, for instance. Additionally, any anatomical, functional and thresholded statistical parametric map in the Nifti-format can be exported with BrainBlend to Blender for the creation of comprehensive and illustrative 3d-images and animations of hemodynamic and statistical effects. In contrast to other software packages, BrainBlend represents a toolbox that combines and supplements the statistical analysis capabilities of SPM with the visualiza- tion capabilities of the universal open-source 3d-software Blender. This application has been widely used in neuro- imaging and molecular biology for the creation of visual stimuli (Creem-Regehr et al. 2007 Eger et al. 2008 Engel et al. 2008 Tavares et al. 2008), as a 3d-engine for a virtual-reality platform for clinical psychology and behavioral neurosciences (Gatti et al. 2008 Riva et al. 2007), for three-dimensional modeling of MRI data (Ventura et al. 2008), and for the visualization of scientific data (Heider et al. 2009 Morris et al. 2007 N��gerl et al. 2007 Palombi et al. 2006 Rivera-Calzada et al. 2005). In bioinformatics, the high demand for visualization techni- ques has already led to the formation of a new scientific field, the so-called ���bioimaging informatics���, in which, among other software packages, Blender is used for visualizing molecular models (see Review by Peng 2008). Blender was originally designed to provide a powerful and sophisticated environment for the production of 3d-pictures and animations. Beside 3d-modeling techniques, this tool enables advanced compositing and post-production. The combination of BrainBlend for the computation and export of Nifti data to Blender and Blenders 3d-capabilities allow scientists to visualize time-resolved BOLD activation changes for block- and event-related experimental settings, enabling a better and simultaneous understanding of hemodynamic activations in the spatial and temporal domain. In order to demonstrate the functionality of the toolbox, we used a freely available functional dataset acquired by B��chel and Friston (1997) to show how the temporal evolution of functional networks can be depicted. Neuroinform