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DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool.

Gouws A, Woods W, Millman R, Morland A, Green G - Front Neuroinform (2009)

Bottom Line: Formats for other data types are supported.DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP.DV3D is offered for free download with an extensive set of tutorial resources and example data.

View Article: PubMed Central - PubMed

Affiliation: Department of Psychology, York NeuroImaging Centre University of York UK.

ABSTRACT
Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.

No MeSH data available.


Related in: MedlinePlus

Viewing 3D Surfaces in DV3D. (A) Example of a rough estimate of a scalp using the surface extraction technique. (B) Example of arough estimate of a cortex using the same technique. Here the data set has been skull stripped first using FSL's Brain Extraction Tool. (C) A rough cortical extraction of the 1 × 1 × 1 mm3 MNI brain distributed with FSL 4.0.
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Figure 6: Viewing 3D Surfaces in DV3D. (A) Example of a rough estimate of a scalp using the surface extraction technique. (B) Example of arough estimate of a cortex using the same technique. Here the data set has been skull stripped first using FSL's Brain Extraction Tool. (C) A rough cortical extraction of the 1 × 1 × 1 mm3 MNI brain distributed with FSL 4.0.

Mentions: It may be interesting to generate surfaces from underlying data for a number of reasons. In Figure 6 we show an example of a rough estimate of a scalp (Figure 6A) and rough cortical surface (Figure 6B) representative of the white-matter/gray-matter boundary, extracted from the same individual's data. Isosurfaces extraction is highly sensitive to homogeneity inconsistencies in the MRI image volume and produces better results with intensity normalized volumes. In Figure 6C we show the same routine applied to the skull-stripped 1 × 1 × 1 mm3 MNI brain distributed with FSL 4.0. It should be evident that this result is less noisy than that shown in Figure 6B, a result of the intensity normalization of the MNI brain. Surface generation for cortical surfaces using DV3D is meant to aid quick data exploration and is not nearly as informative or accurate as the algorithms utilized by programs like FreeSurfer, FSL's FAST28 or SurfRelax. The speed with which an individual can extract a rough representation of this surface is however very useful. DV3D can give a user a quick insight into the cortical shape in just 30 s, where other packages take between 15 min and several hours to run.


DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool.

Gouws A, Woods W, Millman R, Morland A, Green G - Front Neuroinform (2009)

Viewing 3D Surfaces in DV3D. (A) Example of a rough estimate of a scalp using the surface extraction technique. (B) Example of arough estimate of a cortex using the same technique. Here the data set has been skull stripped first using FSL's Brain Extraction Tool. (C) A rough cortical extraction of the 1 × 1 × 1 mm3 MNI brain distributed with FSL 4.0.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666199&req=5

Figure 6: Viewing 3D Surfaces in DV3D. (A) Example of a rough estimate of a scalp using the surface extraction technique. (B) Example of arough estimate of a cortex using the same technique. Here the data set has been skull stripped first using FSL's Brain Extraction Tool. (C) A rough cortical extraction of the 1 × 1 × 1 mm3 MNI brain distributed with FSL 4.0.
Mentions: It may be interesting to generate surfaces from underlying data for a number of reasons. In Figure 6 we show an example of a rough estimate of a scalp (Figure 6A) and rough cortical surface (Figure 6B) representative of the white-matter/gray-matter boundary, extracted from the same individual's data. Isosurfaces extraction is highly sensitive to homogeneity inconsistencies in the MRI image volume and produces better results with intensity normalized volumes. In Figure 6C we show the same routine applied to the skull-stripped 1 × 1 × 1 mm3 MNI brain distributed with FSL 4.0. It should be evident that this result is less noisy than that shown in Figure 6B, a result of the intensity normalization of the MNI brain. Surface generation for cortical surfaces using DV3D is meant to aid quick data exploration and is not nearly as informative or accurate as the algorithms utilized by programs like FreeSurfer, FSL's FAST28 or SurfRelax. The speed with which an individual can extract a rough representation of this surface is however very useful. DV3D can give a user a quick insight into the cortical shape in just 30 s, where other packages take between 15 min and several hours to run.

Bottom Line: Formats for other data types are supported.DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP.DV3D is offered for free download with an extensive set of tutorial resources and example data.

View Article: PubMed Central - PubMed

Affiliation: Department of Psychology, York NeuroImaging Centre University of York UK.

ABSTRACT
Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data.

No MeSH data available.


Related in: MedlinePlus