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 # [[Algorithm:GATech:Rule_Based_Segmentation|Rule based segmentation: Striatum]] (Georgia Tech, Harvard, Isomics, Kitware)
 # [[Algorithm:GATech:Rule_Based_Segmentation|Rule based segmentation: DLPFC]] (Georgia Tech, UCI, Isomics, Kitware)
 # [[NA-MIC/Projects/Structural/Segmentation/Stochastic_Methods_for_Segmentation|Stochastic Methods for Segmentation]] (Georgia Tech)
 # [[Algorithm:GATech:Statistical_Segmentation_Slicer_2|Statistical/PDE methods for Segmentation]] (Georgia Tech)
@@ Line 54: / Line 55: @@
 # [[NA-MIC/Projects/Structural/Shape_Analysis/Caudate_and_Corpus_Callosum|Shape Analysis for the caudate and corpus callosum data]] (Harvard, UNC, Georgia Tech, Dartmouth)
 # [[NA-MIC/Projects/Structural/Shape_Analysis/Hippocampus|Shape Analysis of the hippocampus]] (Dartmouth, UNC, Harvard)
 # [[NA-MIC/Projects/Structural/Shape_Analysis/Using_LONI_Pipeline|UNC Shape Analysis with LONI pipeline for clinical investigators]] (UNC, UCLA)
 # [[NA-MIC/Projects/Structural/Population_Studies|Population Studies]] (UNC, GE)
@@ Line 59: / Line 61: @@
 # [[NA-MIC/Projects/Structural/Morphometric_Measures/Schizophrenia/Muti-site_Morphometry|Multi-site morphometry in Schizophrenia]] (UCI, FBIRN)
 # [[NA-MIC/Projects/Structural/Shape_Analysis/Automated_shape_model_construction|Automated shape model construction]] (Utah, Harvard)
 # [[NA-MIC/Projects/Structural/Morphometric_Measures/Schizophrenia/Neural_Substrates_of_Apathy|Neural substrates of apathy in schizophrenia]] (Dartmouth, Isomics)

← Older revision		Revision as of 14:04, 18 December 2006
Line 1:		Line 1:
−	'''~~Abstract~~'''~~<nowiki>~~: ~~</nowiki>~~[[~~FE_Mesh_Project_Abstract~~\|~~FE Mesh Project Abstract~~]]	+	{\| border="1"
		+	\|- bgcolor="#ddffff"
		+	\| '''Contents'''
		+	\| '''Presentation'''
		+	\| '''Data'''
		+	\|- bgcolor="#ddffff"
		+	\| '''Slicer'''
		+	\|
		+	\|
		+	\|- bgcolor="#ddffff"
		+	\| Loading and Viewing Data
		+	\|
		+	[[Media:SlicerTraining1LoadingAndViewingData.ppt\|Slicer Training 1 ]]
		+	\|
		+	[[Media:Tutorial-with-dicom.zip\|Dataset Training 1]]
		+	\|- bgcolor="#ddffff"
		+	\| Manual Segmentation and Model Making
		+	\|
		+	[[Media:Slicer_Segmentation_Tutorial.ppt\|Slicer Training 2 ]]
		+	\|
		+	[[Media:Tutorial-with-dicom.zip\|Dataset Training 2]]
		+	\|- bgcolor="#ddffff"
		+	\| Level-Set Segmentation
		+	\|
		+	[[Media:03-LevelSet.ppt\|Slicer Training 3]]
		+	\|
		+	[[Media:Tutorial-with-dicom.zip\|Dataset Training 3]]
		+	\|- bgcolor="#ddffff"
		+	\| Diffusion Tensor Imaging
		+	\|
		+	[[Media:Slicer_DTMRI_Training4.ppt\| Slicer Training 4]]
		+	\|
		+	[[Media:SlicerSampleDTI.zip\| Dataset Training 4.1]] [[Media:Dwi-dicom.zip\|Dataset Training 4.2]]
		+	\|- bgcolor="#ddffff"
		+	\| Functional Magnetic Resonance Imaging
		+	\|
		+	[[Media:SlicerTraining5_fMRI.ppt\| Slicer Training 5]]
		+	\|
		+	[[Media:FMRIData1_short.zip\|Dataset Training 5.1]] [[Media:FMRIData2_long.zip\|Dataset Training 5.2]]
		+	\|- bgcolor="#ddffff"
		+	\| vtkFreeSurferReaders
		+	\|
		+	[[Media:SlicerTraining6_vtkFreeSurferReaders.ppt\| Slicer Training 6 ]]
		+	\|
		+	[[Media:FreeSurferSubjects.zip\|Dataset Training 6 ]]
		+	\|- bgcolor="#ddffff"
		+	\| Saving Data
		+	\|
		+	[[Media:SlicerTraining7SavingData.ppt\| Slicer Training 7]]
		+	\|
		+	[[Media:Tutorial-with-dicom.zip\|Dataset Training 7]]
		+	\|- bgcolor="#ddffff"
		+	\| Nrrd File Format
		+	\|
		+	[[Media:SlicerTraining8-NrrdFileFormat.ppt\| Slicer Training 8]]
		+	\|
		+	[[Media:Tensor_data.zip\|Dataset Training 8]]
		+	\|- bgcolor="#ddffff"
		+	\| Dicom to Nrrd Conversion
		+	\|
		+	[[Media:SlicerTraining9_DTI-FromDicomToNrrd.ppt\| Slicer Training 9]]
		+	\|
		+	[[Media:Dwi-dicom.zip\|Dataset Training 9]]
		+	\|- bgcolor="#ddffff"
		+	\| EMBrainAtlasClassifier
		+	\|
		+	[[Media:SlicerAdvancedTraining_EMBrainAtlasClassifier_V1.0.ppt\| Slicer Advanced: EMBrainAtlasClassifier ]]
		+	\|
		+	[[Media:BrainAtlasClassifier.zip\|Dataset Training 10 ]]
		+	\|- bgcolor="#ddffff"
		+	\| '''fMRI Statistical Analysis'''
		+	\|
		+	[http://ocw.mit.edu/OcwWeb/Health-Sciences-and-Technology/HST-583Fall-2004/CourseHome/ HST.583 Functional Magnetic Resonance Imaging]
		+	\|
		+	[http://mgh-edu.nbirn.net/tutorial.html Tutorial documentation]
		+	\|
		+	<br />
		+	\|}

−	~~'''Grant #'''<nowiki>: 1R01EB005973 </nowiki>~~	+	<br />
−
−	~~'''Key Personnel'''<nowiki>: Nicole Grosland, Vincent Magnotta, Steve Pieper, and Simon Warfield. </nowiki>~~
−
−	~~'''Projects'''<nowiki>: Active projects in this collaboration are listed here:~~ </~~nowiki~~>~~[[NA-MIC_Collaborations#PAR-06-223_Automated_FE_Mesh_Development\|NA-MIC_Collaborations#PAR-06-223_Automated_FE_Mesh_Development]]~~
−
−	~~'''Publications'''<nowiki>: </nowiki>~~
−
−	~~'''Meetings and Events Specific to this Collaboration'''<nowiki>: </nowiki>~~
−
−	* Vince Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006\|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt\|Validation of Bone Models using 3D Surface Scanning]]).
−	* [[2006_November_Meshing_Project_Visit\|November 7-8, 2006: Meshing Collaborator Project Visit to BWH]]
−
−	~~'''Resource Links'''~~
−
−	* [http://www.hpfem.jku.at/netgen/ netget]
−	* [http://libmesh.sourceforge.net/ libmesh]
−
−	* Mesh warping project at the SPL (Steve Haker):
−	** http://splweb.bwh.harvard.edu:8000/pages/papers/haker/haker-miccai2004.pdf

@@ Line 1: / Line 1: @@
- Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]
+'''Abstract'''<nowiki>: </nowiki>[[FE_Mesh_Project_Abstract|FE Mesh Project Abstract]]
-'''Objective:''' We are developing new denoising methods for diffusion tensor MRI. These methods are based on physical noise models in DT-MRI.
+'''Grant #'''<nowiki>: 1R01EB005973 </nowiki>
-'''Progress:''' We have implemented several filtering methods for DT-MRI, including our new method and also several methods from the literature. One goal is to determine whether it is best to filter the estimated tensor fields or the original diffusion weighted images. The method that we developed filters the original diffusion weighted images and takes into account the physical properties of the imaging noise. We are comparing this method with others in the literature, including methods that filter the estimated tensor fields. Our preliminary findings are that it is advantageous to filter the DWIs and to include a physical model of the noise.
+'''Key Personnel'''<nowiki>: Nicole Grosland, Vincent Magnotta, Steve Pieper, and Simon Warfield. </nowiki>
-'''Key Investigators:'''
+'''Projects'''<nowiki>: Active projects in this collaboration are listed here: </nowiki>[[NA-MIC_Collaborations#PAR-06-223_Automated_FE_Mesh_Development|NA-MIC_Collaborations#PAR-06-223_Automated_FE_Mesh_Development]]
-* Utah: Saurav Basu, Tom Fletcher, Ross Whitaker
+'''Publications'''<nowiki>: </nowiki>
-'''Links'''
+'''Meetings and Events Specific to this Collaboration'''<nowiki>: </nowiki>
-* [[AHM_2006:ProjectsRiemmanianDTIFilters|Programming Event Project Page (January 2006)]]
+* Vince Magnotta presented background information about the data acquisitioin and validation at the [[AHM_2006:AHM_2006|2006 NA-MIC AHM]] (Slides: [[Media:NA-MIC_Surface-Scan.ppt|Validation of Bone Models using 3D Surface Scanning]]).
-'''Representative Image and Descriptive Caption:'''
+'''Resource Links'''
-<div class="thumb tleft"><div style="width: 602px">[[Image:DTIFiltering.jpg|[[Image:DTIFiltering.jpg|Coronal slice from a noisy diffusion tensor image (left). The same slice after applying our DTI filtering method (right).]]]]<div class="thumbcaption"><div class="magnify" style="float: right">[[Image:DTIFiltering.jpg|[[Image:magnify-clip.png|Enlarge]]]]</div>Coronal slice from a noisy diffusion tensor image (left). The same slice after applying our DTI filtering method (right).</div></div></div>
+* [http://www.hpfem.jku.at/netgen/ netget]

@@ Line 1: / Line 1: @@
   Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]
-'''Objective:''' We are developing a software infrastructure within ITK for DTI analysis. This includes algorithms for statistical analysis of diffusion tensors, fiber tractography, image filtering and registration.
+'''Objective:''' We are developing new denoising methods for diffusion tensor MRI. These methods are based on physical noise models in DT-MRI.
-'''Progress:'''
+'''Progress:''' We have implemented several filtering methods for DT-MRI, including our new method and also several methods from the literature. One goal is to determine whether it is best to filter the estimated tensor fields or the original diffusion weighted images. The method that we developed filters the original diffusion weighted images and takes into account the physical properties of the imaging noise. We are comparing this method with others in the literature, including methods that filter the estimated tensor fields. Our preliminary findings are that it is advantageous to filter the DWIs and to include a physical model of the noise.
 '''Key Investigators:'''
-* Utah: Tom Fletcher, Ross Whitaker
+* Utah: Saurav Basu, Tom Fletcher, Ross Whitaker
-* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+* Harvard PNL: Sylvain Bouix, Doug Marchant, Adam Cohen, Marc Niethammer, Marek Kubicki, Mark Dreusicke, Martha Shenton
-'''Links:'''
+'''Links'''
-* [[Progress_Report:Diffusion_Tensor_Statistics|Diffusion Tensor Statistics Progress Report]]
+* [[AHM_2006:ProjectsRiemmanianDTIFilters|Programming Event Project Page (January 2006)]]
 '''Representative Image and Descriptive Caption:'''
-<div class="thumb tleft"><div style="width: 822px">[[Image:Tensor_interp.jpg|[[Image:Tensor_interp.jpg|Interpolation from a coronal slice of a DTI using the nonlinear averaging. Original data is on the left; the right image is created by up-sampling the image by two.]]]]<div class="thumbcaption"><div class="magnify" style="float: right">[[Image:Tensor_interp.jpg|[[Image:magnify-clip.png|Enlarge]]]]</div>Interpolation from a coronal slice of a DTI using the nonlinear averaging. Original data is on the left; the right image is created by up-sampling the image by two.</div></div></div>
+<div class="thumb tleft"><div style="width: 602px">[[Image:DTIFiltering.jpg|[[Image:DTIFiltering.jpg|Coronal slice from a noisy diffusion tensor image (left). The same slice after applying our DTI filtering method (right).]]]]<div class="thumbcaption"><div class="magnify" style="float: right">[[Image:DTIFiltering.jpg|[[Image:magnify-clip.png|Enlarge]]]]</div>Coronal slice from a noisy diffusion tensor image (left). The same slice after applying our DTI filtering method (right).</div></div></div>

@@ Line 1: / Line 1: @@
   Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]
-'''Objectives''' The primary dissemination goal in the second year of NA-MIC was to focus on outreach to the broader research community
+'''Objective:''' We are developing a software infrastructure within ITK for DTI analysis. This includes algorithms for statistical analysis of diffusion tensors, fiber tractography, image filtering and registration.
-'''Progress''' This outreach goal was accomplished using several mechanisms. In addition to the training events reported by the Training core, three workshops and two birds-of-a-feather meetings were held in collaboration with the Service core. Three invited talks were presented about NA-MIC, and the wiki-based collaborative web presence was also approximately doubled in this time.
+'''Progress:'''
-'''Key Investigators'''
+* ''Geometric tools for diffusion tensor analysis.'' We have built a framework for geometric computations on tensors. This includes vector space operations on tensors as well as nonlinear operations that preserve the positive eigenvalues of the tensors. These geometric methods are the foundation for many of the tools below.
-* Tina Kapur, Epiphany Medical
+''Reference:'' Corouge, I., Fletcher, P.T., Joshi, S., Gilmore, J.H., Gerig, G. Fiber Tract-Oriented Statistics for Quantitative Diffusion Tensor MRI Analysis, presented at MICCAI 2005.
-'''Links'''
+'''Key Investigators:'''
-* [[Dissemination:Progress_Report:2006|Dissemination:Progress Report:2006]]
+* Utah: Tom Fletcher, Ross Whitaker

@@ Line 1: / Line 1: @@
   Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]
-'''Objective:'''
+'''Objective:''' To provide the infrastructure necessary to represent, manage, and transform between the variety of coordinate frames used in medical imaging.
-To simplify cross-platform development of software, and to integrate NAMIC software into the quality process.
+<br />'''Progress:''' A new image class, itk::OrientedImage, has been developed and added to ITK. This image class caches the image direction cosines. ITK's IO mechanisms have been updated to read and write orientation information. Filters which implictly manipulate orientation (flip, resample, etc.) have been modified to explictly modify the cached image orientation.
 '''Key Investigators:'''
-* Kitware: Andy Cedilnik, Bill Hoffman, Brad King, Ken Martin
+* GE Research: Bill Lorensen, Jim Miller
 '''Links:'''
-* http://www.cmake.org
+* [http://www.itk.org/Wiki/Proposals:Orientation Image Orientation in ITK]

@@ Line 1: / Line 1: @@
   Back to [[NA-MIC_Collaborations|NA-MIC_Collaborations]]
-'''Objective:''' To develop a generic framework for access, processing and analysis in population studies
+'''Objective:''' In this project, an event-related auditory semantic memory task is administered. Participants are presented with a semantic category and required to decide whether a subsequent word is a member of the category (e.g., vehicle-bus). To control for phonological processing, other items require a match-mismatch decision between pseudo-words constructed from reordered semantic items (e.g., yodb-rea).
-'''Progress:''' It was decided that the basic underlaying access and storage of data is provided through the Dart 2 database. This is the current bottleneck and progress will resume as soon as Dart 2 has been released.
+'''Progress:''' To date, 6 patients with schizophrenia and 3 healthy controls have been studied with this task. Data will be available in year three.
 '''Key Investigators:'''
-* GE: Jim Miller, Dan Blezek
+* Dartmouth: Andrew Saykin, Robert Roth, Laura Flashman, John West, Thomas McAllister
-* UNC: Martin Styner
+* Harvard: Martha Shenton, Marek Kubicki
-'''Links:'''
+'''Links'''
-* [[NAMIC_Wiki:Community_ShapeAnalysis|Documentation of preliminary discussions for the framework]]
+* [[DBP:Marek_Kubicki_visit_Dartmouth_December_20_2005|December 20, 2005: Marek Kubicki visit to Dartmouth]]
-* [[Engineering:Project:Feature_Analysis_Framework|Programming week Summer 05 results]]
+* [[DBP:Andy_Saykin_visit_BWH_December_14_2005|December 14, 2005: Andy Saykin and Group visit to Brigham and Women's Hospital]]