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A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels

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Abstract

With the increased frequency of multisite, large-scale collaborative neuro-imaging studies, the need for a general, self-documenting framework for the storage and retrieval of activation maps and anatomical labels becomes evident. To address this need, we have developed and extensible markup language (XML) schema and associated tools for the storage of neuro-imaging activation maps and anatomical labels. This schema, as part of the XML-based Clinical Experiment Data Exchange (XCEDE) schema, provides storage capabilities for analysis annotations, activation threshold parameters, and cluster and voxel-level statistics. Activation parameters contain information describing the threshold, degrees of freedom, FWHM smoothness, search volumes voxel sizes, expected voxels per cluster, and expected number of clusters in the statistical map. Cluster and voxel statistics can be stored along with the coordinates, threshold, and anatomical label information. Multiple threshold types can be documented for a given cluster or voxel along with the uncorrected and corrected probability values. Multiple atlases can be used to generate anatomical labels and stored for each significant voxel or cluter. Additionally, a toolbox for Statistical Parametric Mapping software (http://www. fil.ion.ucl.ac.uk/spm/) was created to capture the results from activation maps using the XML schema that supports both SPM99 and SPM2 versions (http:/nnbirn.net/Resources/Users/ Applications/xcede/SPM_XMLTools.htm). Support for anatomical labeling is available via the Talairach Daemon (http://ric.uthcsa. edu/projects/talairachdaemon.htm1) and Automated Anatomical Labeling (http://www. cyceron.fr/freeware/).

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Authors and Affiliations

  1. University of California, Irvine, CA

    David Bryant Keator, Derek V. Taylor & Steven G. Potkin

  2. Duke University, Durham, NC

    Syam Gadde

  3. University of California, San Diego, La Jolla, CA

    Jeffrey S. Grethe

  4. Functional Imaging Research Schizophrenia, Testbed-Biomedical Informatics Research Network, NIH-NCRR, Bethesda, MD

    First Birn

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  1. David Bryant Keator
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  2. Syam Gadde
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  3. Jeffrey S. Grethe
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  4. Derek V. Taylor
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  5. Steven G. Potkin
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  6. First Birn
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Correspondence to David Bryant Keator.

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Keator, D.B., Gadde, S., Grethe, J.S. et al. A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels. Neuroinform 4, 199–211 (2006). https://doi.org/10.1385/NI:4:2:199

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