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

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/).

Access this article

Log in via an institution

Subscribe and save

• Starting from 10 chapters or articles per month
• Access and download chapters and articles from more than 300k books and 2,500 journals
• Cancel anytime View plans

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

• Cox, R. W. (1996) AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. Comput. Biomed. Res. 29(3), 162–173.
  Article CAS Google Scholar
• Fox, P. T. and Lancaster, J. L. (2002) Opinion: mapping context and content: the BrainMap model. Nat. Rev. Neurosci. 3(4), 319–321.
  Article CAS Google Scholar
• Friston, K. J. H. A., Worsley, K. J., Poline, J. P., Frith, C. D., Frackowiak, R. S. J. (1995) Statistical parametric maps in functional imaging: a general linear approach. Human Brain Mapping 2, 189–210.
  Article Google Scholar
• Kennedy, D. N., Haselgrove, C., McInerney, S., et al. (2003) MRI-based morphometric of typical and atypical brain development. Ment. Retard. Dev. Disabil. Res. Rev. 9(3), 155–160.
  Article Google Scholar
• Ozyurt, B. W., Keator, D., Potkin, S., Brown, G., Grethe J., and Morphometry BIRN, FIRST BIRN (2004) A general and extensible database system for the storage, retrieval and maintenance of human brain imaging and clinical data. 10th Annual Meeting of the Organization for Human Brain Mapping, Budapest, Hungary. http://www.meeting assistant.com/ohbm/meeting_plan/ohmb_mtg_index_search.php. WE 376, 2004.
• Smith, S. M., Jenkinson, M., Woolrich, M. W., et al. (2004) Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage 23(S1), 208–219.
  Article Google Scholar
• Trelease, R. B. (2002) Anatomical informatics: millennial perspectives on a newer frontier. Anat. Rec. 269(5), 224–235.
  Article Google Scholar
• Van Essen, D. C., Drury, H. A., Dickson, J., et al. (2001) An integrated software suite for surface-based analyses of cerebral cortex. J. Am. Med. Inform. Assoc. 8(5), 443–459.
  Google Scholar
• Van Horn, J. D., Grafton, S. T., Rockmore, D., et al. (2004) Sharing neuroimaging studies of human cognition. Nat. Neurosci. 7(5), 473–481.
  Article Google Scholar
• Van Horn, J. D., Grethe, J. S., Kostelec, P., et al. (2001) The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies. Philos. Trans. R Soc. Lond. B Biol. Sci. 356(1412), 1323–1339.
  Article Google Scholar

Download references

Author information

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

Authors

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

Corresponding author

Correspondence toDavid Bryant Keator.

Rights and permissions

About this article

Cite this article

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

Download citation

• Issue date: June 2006
• DOI: https://doi.org/10.1385/NI:4:2:199

Index Entries