2007 Annual Scientific Report - Revision history

Tkapur: /* 1. Introduction */

2007-06-07T13:42:13Z

1. Introduction

Gerig: /* Fiber Tract Extraction and Analysis */

2007-06-06T14:56:14Z

Fiber Tract Extraction and Analysis

Tkapur at 17:27, 5 June 2007

2007-06-05T17:27:42Z

Tkapur at 17:27, 5 June 2007

2007-06-05T17:27:25Z

Tkapur: /* Logistics */

2007-06-05T17:26:16Z

Logistics

Tkapur at 17:25, 5 June 2007

2007-06-05T17:25:43Z

Tkapur: /* Notes for Editor for Final Draft */

2007-05-22T20:20:52Z

Notes for Editor for Final Draft

Tkapur: /* Logistics */

2007-05-22T20:20:40Z

Logistics

Whitaker: /* Response to EAB Report */

2007-05-22T19:10:03Z

Response to EAB Report

Gerig: /* Summary of NA-MIC Clinical DWI Applications */

2007-05-21T16:35:42Z

Summary of NA-MIC Clinical DWI Applications

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 Below, in the next section (Section 2) we summarize our progress over the last year using the same four central themes to organize the progress report. These four themes include: Diffusion Image analysis (Section 2.1), Structural analysis (Section 2.2), Functional MRI analysis (Section 2.3), and the NA-MIC toolkit (Section 2.4). Section 3 highlights four important accomplishments of the third year: advanced algorithm development in Shape and DTI analysis, the newly architected open source application platform, Slicer 3, and our outreach and technology transfer efforts. Section 4 summarizes the impact and value of our work to the biocomputing community at three different levels: within the center, within the NIH-funded research community, and externally to a national and international community. The final section of this report, Section 5, provides a timeline of Center activities.
-In addition, the end of the first three years of the center marks a transition from the first set of DBPs that were focused entirely on Schizophrenia to a new set that span a wider range of biological problems.  The new DBPs continue to include neuropsychiatric disorders such as Systemic Lupus Erythematosis (MIND Institute, University of New Mexico), Schizophrenia (Harvard), and Autism (University of North Carolina, Chapel Hill), along with a adopting a direction that is new but synergistic for NA-MIC: Prostate Interventions (Johns Hopkins University).  Funding for the second round of DBPs starts in the next cycle, but the PIs were able to attend the recent All-hands meeting and start developing plans for their future research in NA-MIC.
+In addition, the end of the first three years of the center marks a transition from the first set of DBPs that were focused entirely on Schizophrenia to a new set that span a wider range of biological problems.  The new DBPs continue to include neuropsychiatric disorders such as Systemic Lupus Erythematosis (MIND Institute, University of New Mexico), Velocardiofacial Syndrome (Harvard), and Autism (University of North Carolina, Chapel Hill), along with a adopting a direction that is new but synergistic for NA-MIC: Prostate Interventions (Johns Hopkins University).  Funding for the second round of DBPs starts in the next cycle, but the PIs were able to attend the recent All-hands meeting and start developing plans for their future research in NA-MIC.
 Finally, we note that Core 3.1 (Shenton and Saykin), are in the process of applying for a Collaborative R01 to expand current research with NA-MIC, which ends on July 31, 2007. Both Drs. Shenton and Saykin have worked for three years in driving tool development for shape measures, DTI tools, and path analysis measures for fMRI as part of the driving biological project in NA-MIC, and they now plan to expand this research in a Collaborative R01 by working closely with Drs. Westin, Miller, Pieper, and Wells, to design, assess, implement, and apply tools that will enable the integration of MRI, DTI, and fMRI in individual subjects, as well as to develop an atlas of functional networks and circuits that are based on a DTI atlas (i.e., structural connectivity), which will be integrated with a network of functional connectivity that will be identified from fMRI probes of attention, memory, emotion, and semantic processing. We mention this here because this will be, to our knowledge, the first DBP to apply for further funding to continue critical work begun with NA-MIC.

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- Back to [[2007_Progress_Report]]
+Back to [[2007_Progress_Report]]
 [[media:2007 NAMIC Progress Report No EAB.pdf|An electronic copy of this report that was mailed to NIH on May 31, 2007(pdf)]]
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 ==== Fiber Tract Extraction and Analysis ====
-* Since last year, all of the algorithms for fiber tractography and anisotropy estimation have been implemented in both the “Fiber Viewer” and “Slicer” packages, and now the resulting methods are being applied to clinical studies. The FiberViewer tool such as its application in a large clinical UNC DTI study are published in medical image analysis such as archive journals. Utah recently extended the tractography-based concept with a new approach based on solving a PDE, thus replacing the tractography-based extraction of fiber bundles by a fully volumetric process. Characterization of bundles is then approached by a new regression method (IPMI'07). In a similar spirit, the BWH/MIT/UNC groups applied diffusion measures along a specific fiber bundle of inerest, parametrized by arc-length, to the cingulum bundle. Georgia Tech develops a method called "Finsler Active Contour DWI", a mathematically more sophisticated approach to standard tractography methods that makes use of Finsler geometry and solves a new anisotropic energy function for extraction of 3D curves from tensor data. Preliminary applications to the cinculum bundle in the PNL schizophrenia dataset of our Core-3 partner are very promising.
+* Since last year, all of the algorithms for fiber tractography and anisotropy estimation have been implemented in both the “Fiber Viewer” and “Slicer” packages, and now the resulting methods are being applied to clinical studies. The FiberViewer tool such as its application in a large clinical UNC DTI study are published in medical image analysis such as archive journals. Utah recently extended the tractography-based concept with a new approach based on solving a PDE, thus replacing the tractography-based extraction of fiber bundles by a fully volumetric process. Characterization of bundles is then approached by a new regression method (IPMI'07). In a similar spirit, the BWH/MIT/UNC groups applied diffusion measures along a specific fiber bundle of interest, parametrized by arc-length, to the cingulum bundle. Georgia Tech develops a method called "Finsler Active Contour DWI", a mathematically more sophisticated approach to standard tractography methods that makes use of Finsler geometry and solves a new anisotropic energy function for extraction of 3D curves from tensor data. Preliminary applications to the cinculum bundle in the PNL schizophrenia dataset of our Core-3 partner are very promising.
 * In addition to clinical studies, teams have been working on other methods to define and estimate brain connectivity. The most important developments in this regard included volumentric connectivity and stochastic tractography measures. For volumentric connectivity, a PDE-based approach to white matter connectivity from DTI has been developed, that is founded on the principal of minimal paths through the tensor volume. This method computes a volumetric representation of a white matter tract given two endpoint regions. In addition, statistical methods for quantifying the full tensor data along these pathways have been also developed. Directional PDE-based flows have been proposed and implemented for a similar purpose. Further, an approach called "stochastic tractography," has been developed to calculate probability of two regions being connected by the fiber tract. This should be especialy useful when tract has to go through the regions characterized by low diffusion anisotropy.

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   Back to [[2007_Progress_Report]]
-[[media:2007 NAMIC Progress Report No EAB.pdf|An electronic copy of the report that was mailed to NIH (pdf)]]
+[[media:2007 NAMIC Progress Report No EAB.pdf|An electronic copy of this report that was mailed to NIH on May 31, 2007(pdf)]]
 == 1. Introduction ==

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−

		+	[[media:2007 NAMIC Progress Report No EAB.pdf\|An electronic copy of the report that was mailed to NIH (pdf)]]

	== 1. Introduction ==		== 1. Introduction ==

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	• Training for outside researchers in the use of the NA-MIC Kit. The dissemination and training sessions include a web-based feedback mechanism for attendees.		• Training for outside researchers in the use of the NA-MIC Kit. The dissemination and training sessions include a web-based feedback mechanism for attendees.
−
−	~~= Logistics =~~
−	~~==Notes for Editor for Final Draft==~~
−	#disorders or diseases should not be capitalized (because they are not proper nouns), unless they are named after a person. Currently, this inconsistent in the text (schizophrenia is sometime upper case and sometimes lower case).
−	~~#Check upper and lower case in sub headings (e.g. "Hippocampal and frontal memory circuitry abnormalities in schizophrenia:" under fMRI).~~
−
−	~~== Schedule and process for preparation of this report ==~~
−
−	* March 30 - Assign section/theme leads (Ron). Last year: introduction (marty), structural analysis (allen, martin), dti (guido, marty/marek), fmri (polina, andy), namic kit(bill), timeline (ross), highlights (will), impact (bill).
−	*April 7,10 - tcons with Marty, Ross, Will, Tina to finalize the layout, process, and timeline of report.
−	* April 13 - update projects list using last year's [[NA-MIC_Collaborations]] and [[2007_Project_Half_Week#Projects\|projects pursued at the half week in SLC]]. Remind investigators to update individual pages. (Tina)
−	* April 23- complete project description pages in updated list: [[NA-MIC_Collaborations]] (all project owners).
−	* April 30 - complete section summaries, introduction, highlights, impact, timeline (owners of these topics)
−	* May 8 - submit wiki report to NA-MIC editor, Ann (Tina)
−	* May 17 - submit Edited report to Rachana in pdf format (Ann)
−	* May 25 - submit final report, if changes are needed (Ann)
−	* May 29 - ship final package to NIH (Rachana)
−
−	~~== Guidelines from NIH Program Officer ==~~
−	~~===NIH Reviewer Comments on Yr2 APR (July 2006)===~~
−	~~The following additional guidelines were provided by the NIH progress review committee after they reviewed the 2006 report:~~
−
−	~~1. Comment on obstacles and challenges encountered during the year.~~
−
−	~~2. Comment on outcomes of DBPs.~~
−
−	~~3. Create a context for the report in the Introduction.~~
−
−	~~4. Comment on how all the themes as a whole are moving forward.~~
−
−	~~5. Full citations should be given within the report as footnotes or in a bibliography, not just as hyperlinks.~~
−
−	~~6. Explain time-lines with text including reasons for delays. Link timelines to papers and citations.~~
−
−	~~7. Define terms used in the timeline to describe the amount of progress being made, especially with respect to software development.~~
−
−	~~8. Put priority weights on completed tasks within timeline. Note if a task is a stepping stone or a final goal.~~
−
−	~~9. Make sure the projects presented in the annual report are also listed in the project pages of the NAMIC Wiki and vice versa.~~
−
−	~~10. In the budget pages, please elaborate on the number and locations for travel.~~
−
−	~~===Feb 2006===~~
−	~~The following guidelines were provided by Grace Peng, NA-MIC program officer, in Feb 2006.~~
−
−	~~The key is to synthesize all the individual elements into bigger picture stories that really speak of each area’s impact to the community.~~
−
−	~~The specialized scientific report should have the following format:~~
−
−	~~# Introductory page describing the new grouping of NAMIC project themes.~~
−	~~# A description of progress in each NAMIC project theme (not to exceed 2 pages each), tying together relevant activities from participating subcomponents and referencing cores in parentheses.~~
−	# A table of NAMIC timelines (from original proposal), graphically depicting completed tasks/goals in years 1,2, and 3 and tasks/goals to be completed in years 4-5. Changes to the original timelines should be described.
−	~~# A description of 3 highlights selected from all NAMIC projects to showcase NAMIC.~~
−	~~# A discussion of NAMIC’s impact and value to the biocomputing community this year.~~

← Older revision		Revision as of 17:25, 5 June 2007
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−	~~For reference:~~

−	*[[2006_Progress_Report]]
−
−	*[[Media:2005_NAMIC_Specialized_ProgReport.pdf\|2005 Annual Scientific Report]]

	== 1. Introduction ==		== 1. Introduction ==

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 = Logistics =
 ==Notes for Editor for Final Draft==
-#disorders or diseases should not be capitalized (because they are not proper nouns), unless they are named after a
+#disorders or diseases should not be capitalized (because they are not proper nouns), unless they are named after a person. Currently, this inconsistent in the text (schizophrenia is sometime upper case and sometimes lower case).
 #Check upper and lower case in sub headings (e.g. "Hippocampal and frontal memory circuitry abnormalities in schizophrenia:" under fMRI).

← Older revision		Revision as of 20:20, 22 May 2007
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	= Logistics =		= Logistics =
		+	==Notes for Editor for Final Draft==
		+	#disorders or diseases should not be capitalized (because they are not proper nouns), unless they are named after a
		+	person. Currently, this inconsistent in the text (schizophrenia is sometime upper case and sometimes lower case).
		+	#Check upper and lower case in sub headings (e.g. "Hippocampal and frontal memory circuitry abnormalities in schizophrenia:" under fMRI).

	== Schedule and process for preparation of this report ==		== Schedule and process for preparation of this report ==

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 ''
-NA-MIC: The Center intends to continue its effort in validation and verification of its software implementations. Center researchers have also come up with original techniques for validation, e.g., the Laplacian method for comparing the accuracy of segmentations which was developed at Georgia Tech,
+NA-MIC: The Center is proactive in the validation and verification of its software implementations, and our record is quite good in this regard. Center researchers have come up with original techniques for validation, e.g., the Laplacian method for comparing the accuracy of segmentations which was developed at Georgia Tech,
-and has been incorporated into ITK. These validation techniques have been used to drive new original algorithmic as well. In addition, work within the Center has continued to compare manual measures of brain structure, i.e., the caudate, as a gold standard for automated measures of caudate in the same subjects. In DTI, validation methodology work includes access of NAMIC researchers to high-resolution DTI of a volunteer with 10 repeated datasets (UNC), to be used for reproducibility studies of quantitative DTI analysis methods. Joint work by Utah and UNC explores number of gradient directions versus errors of FA and MD measures as functions of spatial direction. The theoretical analysis has been recently confirmed by an in vivo experiment (UNC, ISMRM conference presentation and MICCAI’07 submission). We are also co-organizing a workshop at MICCAI 2007 whose goal is to compare automatic and semi-automatic segmentation methodologies (existing and new) against manual segmentations for the liver in CT and the caudate in MRI. These kinds of validation efforts will continue to grow within NAMIC and distributed to
+and has been incorporated into ITK. These validation techniques have been used to drive new original algorithmic as well. In addition, work within the Center has continued to compare manual measures of brain structure, i.e., the caudate, as a gold standard for automated measures of caudate in the same subjects. In DTI, validation methodology work includes access of NAMIC researchers to high-resolution DTI of a volunteer with 10 repeated datasets (UNC), to be used for reproducibility studies of quantitative DTI analysis methods. Joint work by Utah and UNC explores number of gradient directions versus errors of FA and MD measures as functions of spatial direction. The theoretical analysis has been recently confirmed by an in vivo experiment (UNC, ISMRM conference presentation and MICCAI’07 submission). We are also co-organizing a workshop at MICCAI 2007 whose goal is to compare automatic and semi-automatic segmentation methodologies (existing and new) against manual segmentations for the liver in CT and the caudate in MRI. Recent submissions to IPMI (to appear) and MICCAI (under review) from a Utah/UNC collaboration, make explicit comparisons between different methods for shape analysis.  These kinds of validation efforts will continue to grow within NAMIC and distributed to
 the general medical imaging community.

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 ==== Summary of NA-MIC Clinical DWI Applications ====
-The current reporting period is clearly characerized by a significant increase of application of tools to clinical DWI data provided by the Core-3 DBP groups.
+The current reporting period is clearly characerized by a significant increase of application of tools to clinical DWI data provided by the Core-3 DBP groups. Main reasons are two-fold, first there are several new tools that are ready to be applied to a set of image datasets, and second there are new high-resolution DTI data from 3-Tesla scanners that are more appropriate for the new tools than older data using highly non-isotropic voxel data.
 * Application of NA-MIC DTI tools jointly with the Core-3 partners include the ongoing study of inferior frontotemporal connections (BWH/MIT) by applying fiber tractography to extract the uncinate fasciculus and occipito-frontal fasciculus in a study of 27 chronic schizophrenics and 34 controls. The same group studies corpus callosum clustering in the new 3Tesla dataset provided by PNL (24 subjects, 12 chronic schizophrenics and 12 matched control subjects). Preliminary results show reduced FA and reduced volume in two different clusters.