Difference between revisions of "DBP2:UNCFinal:2010"
From NAMIC Wiki
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=Overview= | =Overview= | ||
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=Software= | =Software= | ||
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****1st Prize: NAMIC tutorial contest AHM 2009 | ****1st Prize: NAMIC tutorial contest AHM 2009 | ||
****2nd Prize: NAMIC tutorial contest summer project week 2009 | ****2nd Prize: NAMIC tutorial contest summer project week 2009 | ||
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**Tutorials: | **Tutorials: | ||
***GAMBIT tutorial presentations: [http://wiki.na-mic.org/Wiki/index.php/File:GAMBIT_TutorialContestSummer2010.ppt [ppt]] [http://wiki.na-mic.org/Wiki/index.php/File:GAMBIT_TutorialContestSummer2010.pdf [pdf]] | ***GAMBIT tutorial presentations: [http://wiki.na-mic.org/Wiki/index.php/File:GAMBIT_TutorialContestSummer2010.ppt [ppt]] [http://wiki.na-mic.org/Wiki/index.php/File:GAMBIT_TutorialContestSummer2010.pdf [pdf]] | ||
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=Listing and short description of the sample data= | =Listing and short description of the sample data= | ||
*Pediatric Brain MRI data | *Pediatric Brain MRI data | ||
**[http://insight-journal.org/midas/community/view/24 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. | **[http://insight-journal.org/midas/community/view/24 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. | ||
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*Brain Atlases | *Brain Atlases | ||
| − | ** Average T1-weighted images (with/without skull) are provided with tissue segmentation probability maps, subcortical structures probability maps and lobar parcellation maps | + | ** Average T1-weighted images (with/without skull) are provided with tissue segmentation probability maps (white matter, gray matter, csf, rest), subcortical structures probability maps (amygdala, caudate, hippocampus, pallidus, putamen) and lobar parcellation maps |
**[http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas] | **[http://www.insight-journal.org/midas/item/view/2277 Pediatric atlas] | ||
**[http://www.insight-journal.org/midas/item/view/2328 Adult atlas] | **[http://www.insight-journal.org/midas/item/view/2328 Adult atlas] | ||
**[http://www.insight-journal.org/midas/item/view/2330 Elderly atlas] | **[http://www.insight-journal.org/midas/item/view/2330 Elderly atlas] | ||
**[http://www.insight-journal.org/midas/item/view/2283 Primate atlas] | **[http://www.insight-journal.org/midas/item/view/2283 Primate atlas] | ||
| + | *Tutorial datasets: | ||
| + | **[http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download ARCTIC tutorial dataset] | ||
| + | **[http://www.nitrc.org/frs/download.php/2185/GAMBIT_Tutorial_example_1.0.zip Download GAMBIT tutorial dataset] | ||
=Related pages= | =Related pages= | ||
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=References= | =References= | ||
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*C. Vachet, H.C. Hazlett, M. Niethammer, I. Oguz, J.Cates, R. Whitaker, J. Piven, M. Styner, Group-wise Automatic Mesh-Based Analysis of Cortical Thickness, accepted to SPIE 2011 | *C. Vachet, H.C. Hazlett, M. Niethammer, I. Oguz, J.Cates, R. Whitaker, J. Piven, M. Styner, Group-wise Automatic Mesh-Based Analysis of Cortical Thickness, accepted to SPIE 2011 | ||
*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 | *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 | ||
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*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 | *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 | *J. Cates, P. Fletcher, M. Styner, H. Hazlett, R. Whitaker, Particle-based shape analysis of multi-object complexes, MICCAI 2008, 477-85 | ||
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Revision as of 20:01, 27 October 2010
Home < DBP2:UNCFinal:2010back to DBP2 Main
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:
- Description:
- 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:
- Description:
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.
- Brain Atlases
- Average T1-weighted images (with/without skull) are provided with tissue segmentation probability maps (white matter, gray matter, csf, rest), subcortical structures probability maps (amygdala, caudate, hippocampus, pallidus, putamen) and lobar parcellation maps
- Pediatric atlas
- Adult atlas
- Elderly atlas
- Primate atlas
- Tutorial datasets:
Related pages
- Slicer 3.6 download
- Slicer 3.6 documentation
- Neuro Image Research and Analysis Laboratory, UNC Chapel Hill
- UNC Carolina Institute for Developmental Disabilities
References
- C. Vachet, H.C. Hazlett, M. Niethammer, I. Oguz, J.Cates, R. Whitaker, J. Piven, M. Styner, Group-wise Automatic Mesh-Based Analysis of Cortical Thickness, accepted to SPIE 2011
- 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. 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
