DBP2:UNCFinal:2010

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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:
    • NITRC wiki page
    • Slicer 3.6 documentation
  • Tutorials:
    • ARCTIC tutorials: ‏ [ppt]‏ [pdf]
      • 1st Prize: NAMIC tutorial contest AHM 2009
      • 2nd Prize: NAMIC tutorial contest summer project week 2009
    • Online documentation within Slicer 3.6
    • Download ARCTIC Example dataset

• 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:
    • NITRC wiki page
  • Tutorials:
    • GAMBIT tutorial presentations: [ppt] [pdf]
    • Download GAMBIT Example dataset

Listing and short description of the sample data

• Pediatric Brain MRI data
  • Data of 2 autistic children and 2 normal controls (male, female) scanned at 2 years with follow up at 4 years from a 1.5T Siemens scanner. Files include structural data, tissue segmentation label map and subcortical structures segmentation.

• ARCTIC Tutorial dataset:
  • Download Example dataset

• Brain Atlases
  • Average T1-weighted images (with/without skull) are provided with tissue segmentation probability maps, subcortical structures probability maps and lobar parcellation maps
  • Pediatric atlas
  • Adult atlas
  • Elderly atlas
  • Primate atlas

Related pages

• Slicer 3.6 download
• Slicer 3.6 documentation

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