iBrain™ software packages
iBrain™ and the iBrain™ Analysis Toolbox for SPM are software packages that can work independently or together to perform neuroimage processing, analysis and visualisation. iBrain™ software is free for non-commercial use, and the iBrain™ Analysis Toolbox for SPM is free software released under the GNU General Public License. More information can be found below.
iBrain™ Analysis Toolbox for SPM
Principal developer: David Abbott, PhD
The iBrain™ Analysis Toolbox for SPM is an automated functional MRI analysis pipeline. The toolbox is compatible with SPM2, SPM5, SPM8 and SPM12. Version 3.0 of the toolbox was presented at the 17th Annual Meeting of the Organisation for Human Brain Mapping, Quebec City, June 2011.
The iBrain™ Analysis Toolbox for SPM is free software released under the GNU General Public License, and is available for download below.Download iBrain™ Analysis Toolbox for SPM
iBrain™ Laterality Toolbox
Developers: David Abbott, PhD and Tony Waites, PhD
The iBrain™ Laterality Toolbox is written in Matlab and was used to generate the figures in the following manuscript:
Abbott DF, Waites AB, Lillywhite LM, Jackson GD. fMRI assessment of language lateralization: An objective approach. Neuroimage 50(4):1446-1455 (2010).
All of the functions in this toolbox have now been incorporated into the more general iBrain™ Analysis Toolbox for SPM (above).
Principal developer: David Abbott, PhD
iBrain™ is an easy-to-use neuroimage processing and visualisation package. The software is free for non-commercial use. From its roots in 1995 as an in-house software platform for functional MRI research, iBrain has grown over the years to accommodate various requirements of neuroimaging analysis that could be difficult to achieve in other packages. iBrain is designed primarily to be utilised interactively from a graphical user interface, however some functions are also available via the command line. iBrain can also be utilised to advantage by the iBrain Analysis Toolbox for SPM. iBrain is typically deployed to complement other neuroimaging software packages such as SPM or FSL.
iBrain has been demonstrated at the following conferences:
June 2006: 12th International Conference on Functional Mapping of the Human Brain, Florence, Italy Abstract: Masterton, R. et. al. A software utility for measuring tissue-type partial volumes for MRS data. On CD-ROM in NeuroImage 2006;31(S1);208 T-PM
June 2001: 7th International Conference on Functional Mapping of the Human Brain, Brighton, UK. Abstract: Abbott D., Jackson G., iBrain – Software for analysis and visualisation of functional MR images. NeuroImage 2001;13(6):S59
May 2001: 5th Australian Functional Brain Mapping Symposium, Melbourne, Australia, May 2001. Abstract: Abbott D., Jackson G., fMRI image processing and analysis using iBrain software. Proc. 5th Australian Functional Brain Mapping Symposium, p22.
The following is a selection of some of the features of iBrain:
- interactive image calculator with many filters including resample, resize, threshold, mask and arithmetic operations
- automatic selection of optimum target image for time-series image realignment (selects the image volume that is “closest” to most of the other images)
- calculation of sensitivity maps of SPM results (i.e. maps of the minimum signal difference that would have been required for a voxel to reach a given threshold)
- sample size calculator (using results of a pilot study)
- quantitative 2D and 3D (multi-slice) region of interest (ROI) tools including summary statistics and scriptable ROI analysis of multiple data sets
- time-course extraction (e.g. for use in functional connectivity analyses)
- flexible result displays including colour overlays with quantitative colour scale
- interactive visualisation of raw and processed time-course data via single and multi-voxel plots
- quality control including image stack display and quantitative assessment tools
- animated “cine” display
- automated image conversion, including from DICOM and proprietary GE image file formats to Analyze file format.
- Reading of NIfTI-1 files (including compressed .nii.gz files) is supported, as is header pass-through NIfTI-1 write support.
- ability to load voxel data of many “unknown” file formats
- ability to call certain functions from command line, allowing integration with other processing streams (e.g. the iBrain Analysis Toolbox for SPM)
- real-time analysis is possible when used with real-time image acquisition on the GE Visual Processing workstation
- Supports Windows, Mac and GNU/Linux workstations
- Requires IDL v6.3 or later (the free IDL Virtual Machine is sufficient for most functions)
- Licence: The iBrain licence is a free-of-charge non-exclusive licence that permits use for non-commercial research or academic purposes.
- Availability: Please email iBrain at the domain florey.edu.au for more information.