Difference between revisions of "NA-MIC Brains Collaboration"
From NAMIC Wiki
| (26 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | Back to [[NA-MIC_External_Collaborations]] | + | __NOTOC__ |
| + | Back to [[NA-MIC_External_Collaborations|NA-MIC External Collaborations]] | ||
==Abstract== | ==Abstract== | ||
This project is not an NCBC collaboration grant, but instead a Continued Development and Maintenance of Software grant. The intent of this application is to update the '''BRAINS''' image analysis software developed at the University of Iowa. | This project is not an NCBC collaboration grant, but instead a Continued Development and Maintenance of Software grant. The intent of this application is to update the '''BRAINS''' image analysis software developed at the University of Iowa. | ||
| − | ==Grant #== | + | ==Grant#== |
| − | + | R01NS050568 | |
==Key Personnel== | ==Key Personnel== | ||
| − | + | *University of Iowa: Vincent Magnotta, PI, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen | |
| + | *NA-MIC: Steve Pieper (Isomics) | ||
| + | |||
| + | ==Funding Duration== | ||
| + | 05/15/2007-03/31/2010 | ||
==Projects== | ==Projects== | ||
| Line 17: | Line 22: | ||
*[[Support for Batch Processing]] | *[[Support for Batch Processing]] | ||
*[[Visual Review and Verification of Results]] | *[[Visual Review and Verification of Results]] | ||
| + | *[[Build GUI using Slicer3 Interface]] | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | === Validation of Pipeline | + | === Validation of Pipeline === |
*[[Evaluate MIND MCIC Human Phantom Sample Using Automated Pipeline]] | *[[Evaluate MIND MCIC Human Phantom Sample Using Automated Pipeline]] | ||
| − | *[[Evaluate | + | *[[Evaluate of DTI Reliability Across Sites and Platforms]] |
| + | |||
| + | ===Tools Developed=== | ||
| + | Here is a list of tools that are being developed as part of this project. A number of these tools have been contributed to the NITRC website. All of the tools are built upon the Slicer3 execution model and therefore will readily plug-in to Slicer3. | ||
| + | *[[BRAINSFit]] - Linear fitting of two 3D image sets using a mutual information similarity metric. [http://www.nitrc.org/projects/multimodereg/ NITRC Link] | ||
| + | *[[BRAINSDemonsWarp]] - Non-linear registration of two image sets. This includes the diffeomorphic demons algorithm along with a number of useful enhancements. [http://www.nitrc.org/projects/brainsdemonwarp/ NITRC Link] | ||
| + | *[[BRAINSMush]] - Tool to combine T1 and T2 datasets into a composite image. The resulting image is then used to perform brain extraction. [http://www.nitrc.org/projects/brainsmush/ NITRC Link] | ||
| + | *[[BRAINSCut]] - Automated segmentation of subcortical and cerebellar regions of interest using an artificial neural network. [http://www.nitrc.org/projects/brainscut/ NITRC Link] | ||
| + | *[[BRAINSTracer]] - Tracing tool that uses thge vtkContourWidget for defining a region of interest manually. [http://www.nitrc.org/projects/brainstracer/ NITRC Link] | ||
| + | *[[GTRACT]] - Diffusion tensor analysis and Fiber tracking tool. [http://www.nitrc.org/projects/vmagnotta/ NITRC Link] | ||
| + | *[[BRAINS Automated Pipeline]] - Fully automated image analysis pipeline for generation of volumetric measurements. [http://www.nitrc.org/projects/brains/ NITRC Link] | ||
=== BRAINS Features === | === BRAINS Features === | ||
| − | <gallery caption="BRAINS Gallery" widths="200px" heights="200px" perrow=" | + | <gallery caption="BRAINS Gallery" widths="200px" heights="200px" perrow="3"> |
Image:Surface-Depth.gif|BRAINS Surface showing cortical depth | Image:Surface-Depth.gif|BRAINS Surface showing cortical depth | ||
Image:Surface-Curvature.gif|BRAINS Surface showing curvature (ie sulcal and gyral labels) | Image:Surface-Curvature.gif|BRAINS Surface showing curvature (ie sulcal and gyral labels) | ||
Image:BRAINS-Tissue-Clasification.gif|BRAINS Continuous Tissue Classification | Image:BRAINS-Tissue-Clasification.gif|BRAINS Continuous Tissue Classification | ||
Image:ANN-Axial.gif|Automated segmentation of Subcortical nuclei using Neural Networks | Image:ANN-Axial.gif|Automated segmentation of Subcortical nuclei using Neural Networks | ||
| − | Image:BRAINS-Image-Registration|BRAINS Image Registration using ITK Mutual Information | + | Image:BRAINS-Image-Registration.gif|BRAINS Image Registration using ITK Mutual Information |
| + | Image:FLAIR-Lesion-Labels.gif|Lesion identification with FLAIR, T1 and T2 weighted images | ||
| + | Image:BRAINS-Talairach-Labels.gif|Talairach lobar labels | ||
| + | Image:GTRACT-Fiber-Tracking.gif|GTRACT DTI fiber tracking | ||
</gallery> | </gallery> | ||
==Publications== | ==Publications== | ||
| − | + | *Powell S., Magnotta V.A., Johnson H., Jammalamadaka V.K., Pierson R., Andreasen N.C. [http://www.na-mic.org/publications/item/view/1755 Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures.] Neuroimage. 2008 Jan 1;39(1):238-47. PMID: 17904870. PMCID: PMC2253948. | |
| − | |||
==Meetings== | ==Meetings== | ||
==Resource Links== | ==Resource Links== | ||
Latest revision as of 16:57, 14 December 2016
Home < NA-MIC Brains CollaborationBack to NA-MIC External Collaborations
Abstract
This project is not an NCBC collaboration grant, but instead a Continued Development and Maintenance of Software grant. The intent of this application is to update the BRAINS image analysis software developed at the University of Iowa.
Grant#
R01NS050568
Key Personnel
- University of Iowa: Vincent Magnotta, PI, Hans Johnson, Jeremy Bockholt, and Nancy Andreasen
- NA-MIC: Steve Pieper (Isomics)
Funding Duration
05/15/2007-03/31/2010
Projects
There are three main thrusts of this application as outlined below.
Implement an Automated Brain Analysis Pipeline
- BRAINS Automated Pipeline
- Support for Batch Processing
- Visual Review and Verification of Results
- Build GUI using Slicer3 Interface
Validation of Pipeline
- Evaluate MIND MCIC Human Phantom Sample Using Automated Pipeline
- Evaluate of DTI Reliability Across Sites and Platforms
Tools Developed
Here is a list of tools that are being developed as part of this project. A number of these tools have been contributed to the NITRC website. All of the tools are built upon the Slicer3 execution model and therefore will readily plug-in to Slicer3.
- BRAINSFit - Linear fitting of two 3D image sets using a mutual information similarity metric. NITRC Link
- BRAINSDemonsWarp - Non-linear registration of two image sets. This includes the diffeomorphic demons algorithm along with a number of useful enhancements. NITRC Link
- BRAINSMush - Tool to combine T1 and T2 datasets into a composite image. The resulting image is then used to perform brain extraction. NITRC Link
- BRAINSCut - Automated segmentation of subcortical and cerebellar regions of interest using an artificial neural network. NITRC Link
- BRAINSTracer - Tracing tool that uses thge vtkContourWidget for defining a region of interest manually. NITRC Link
- GTRACT - Diffusion tensor analysis and Fiber tracking tool. NITRC Link
- BRAINS Automated Pipeline - Fully automated image analysis pipeline for generation of volumetric measurements. NITRC Link
BRAINS Features
- BRAINS Gallery
BRAINS Surface showing cortical depth
BRAINS Surface showing curvature (ie sulcal and gyral labels)
BRAINS Continuous Tissue Classification
Automated segmentation of Subcortical nuclei using Neural Networks
BRAINS Image Registration using ITK Mutual Information
Lesion identification with FLAIR, T1 and T2 weighted images
Talairach lobar labels
GTRACT DTI fiber tracking
Publications
- Powell S., Magnotta V.A., Johnson H., Jammalamadaka V.K., Pierson R., Andreasen N.C. Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. Neuroimage. 2008 Jan 1;39(1):238-47. PMID: 17904870. PMCID: PMC2253948.
