Difference between revisions of "DBP2:UNCFinal:2010"
From NAMIC Wiki
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=Software= | =Software= | ||
*ARCTIC: Automatic Regional Cortical ThICkness | *ARCTIC: Automatic Regional Cortical ThICkness | ||
| − | ** Description: | + | **Description: |
***ARCTIC is an end-to-end application allowing individual lobar analysis of cortical thickness | ***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 | ***Pipeline: performs tissue segmentation, regional atlas deformable registration, cortical thickness measurements, volume information stored in spreadsheets | ||
| Line 14: | Line 14: | ||
**Download: | **Download: | ||
***Latest stable version is directly available as an extension in [http://www.slicer.org/pages/Special:SlicerDownloads Slicer 3.6.1 release] and soon in Slicer 3.6.2 | ***Latest stable version is directly available as an extension in [http://www.slicer.org/pages/Special:SlicerDownloads Slicer 3.6.1 release] and soon in Slicer 3.6.2 | ||
| − | ***Source code, executables and tutorial are available on [http://www.nitrc.org/projects/ | + | ***Source code, executables and tutorial are available on [http://www.nitrc.org/projects/gambit NITRC] |
**Documentation: | **Documentation: | ||
***[http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage NITRC wiki page] | ***[http://www.nitrc.org/plugins/mwiki/index.php/arctic:MainPage NITRC wiki page] | ||
| Line 20: | Line 20: | ||
**Tutorials: | **Tutorials: | ||
***ARCTIC tutorials: [[Media:ARCTIC-Slicer3-Tutorial.ppt| [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf| [pdf]]] | ***ARCTIC tutorials: [[Media:ARCTIC-Slicer3-Tutorial.ppt| [ppt]]][[Media:ARCTIC-Slicer3-Tutorial.pdf| [pdf]]] | ||
| − | **** 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 |
***[http://www.slicer.org/slicerWiki/index.php/Modules:ARCTIC-Documentation-3.6 Online documentation within Slicer 3.6] | ***[http://www.slicer.org/slicerWiki/index.php/Modules:ARCTIC-Documentation-3.6 Online documentation within Slicer 3.6] | ||
***[http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip Download ARCTIC Example dataset] | ***[http://www.nitrc.org/frs/download.php/545/ARCTIC_Tutorial_example_1.0.zip 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 [http://www.nitrc.org/projects/gambit NITRC] | ||
| + | **Documentation: | ||
| + | ***[http://www.nitrc.org/plugins/mwiki/index.php/gambit:MainPage NITRC wiki page] | ||
| + | **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]] | ||
| + | ***[http://www.nitrc.org/frs/download.php/2185/GAMBIT_Tutorial_example_1.0.zip Download GAMBIT Example dataset] | ||
=Listing and short description of the sample data= | =Listing and short description of the sample data= | ||
Revision as of 19:34, 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:
- 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
- ARCTIC tutorials: [ppt] [pdf]
- 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:
- GAMBIT tutorial presentations: [ppt] [pdf]
- Download GAMBIT Example dataset
- 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.
- ARCTIC Tutorial dataset:
- Brain Atlases
Related pages
References
- 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
