DBP2:UNCFinal:2010

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Overview

Software

  • ARCTIC: Automatic Regional Cortical ThICkness
    • Description:
      • ARCTIC is an end-to-end application allowing individual lobar analysis of cortical thickness
      • Pipeline: performs tissue segmentation, regional atlas deformable registration, cortical thickness measurements, volume information stored in spreadsheets
      • Visualization: white matter and gray matter mesh creation
      • Quality control: optimal QC via 3D Slicer MRML scenes
    • Download:
      • Latest stable version is directly available as an extension in Slicer 3.6.1 release and soon in Slicer 3.6.2
      • Source code, executables and tutorial are available on NITRC
    • Documentation:
    • Tutorials:


  • GAMBIT: Group-wise Automatic Mesh Based analysis of cortIcal Thickness
    • Description:
      • GAMBIT is an end-to-end application allowing allowing group-wise automatic mesh-based analysis of cortical thickness as well as other surface area measurements
      • Pipeline: individual preprocessing pipeline, group-wise particle-based correspondence on inflated genus-zero white matter surfaces, group-wise statistical analysis
      • Visualization: inflated and folded white matter surfaces in correspondence, with cortical thickness and sulcal depth as overlays
      • Quality control: optimal QC via 3D Slicer MRML scenes
    • Download:
      • Latest stable version is available soon as an extension in Slicer 3.6.2
      • Source code, executables and tutorial are available on NITRC
    • Documentation:
    • Tutorials:

Listing and short description of the sample data

  • Pediatric Brain MRI data

Related pages

References

  • C. Vachet, H.C. Hazlett, M. Niethammer, I. Oguz, J.Cates, R. Whitaker, J. Piven, M. Styner, Mesh-based Local Cortical Thickness Framework, UNC Radiology Research Day 2010 abstract
  • I. Oguz, M. Niethammer, J. Cates, R. Whitaker, T. Fletcher, C. Vachet, and M. Styner, Cortical Correspondence with Probabilistic Fiber Connectivity, Information Processing in Medical Imaging, IPMI 2009, LNCS, 21:651-63
  • H.C. Hazlett, C. Vachet, C. Mathieu, M. Styner, J. Piven, Use of the Slicer3 Toolkit to Produce Regional Cortical Thickness Measurement of Pediatric MRI Data, presented at the 8th Annual International Meeting for Autism Research (IMFAR) Chicago, IL 2009
  • C. Vachet, H.C. Hazlett, M. Niethammer, I. Oguz, J.Cates, R. Whitaker, J. Piven, M. Styner, Mesh-based Local Cortical Thickness Framework, UNC Radiology Research Day 2009 abstract
  • C. Mathieu, C. Vachet, H.C. Hazlett, G. Geric, J. Piven, and M. Styner, ARCTIC – Automatic Regional Cortical ThICkness Tool, UNC Radiology Research Day 2009 abstract
  • Oguz, I., Cates, J., Fletcher, T., Whitaker, R., Cool, D., Aylward, S., Styner, M., Cortical correspondence using entropy-based particle systems and local features, IEEE Symposium on Biomedical Imaging ISBI 2008. 1637– 1640
  • J. Cates, P. Fletcher, M. Styner, H. Hazlett, R. Whitaker, Particle-based shape analysis of multi-object complexes, MICCAI 2008, 477-85
  • Cates, J., Fletcher, P., Whitaker, R.: Entropy-based particle systems for shape correspondence. MFCA Workshop, MICCAI 2006, 90–99