Difference between revisions of "Summer project week 2010 Workflows SOA"

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<gallery>
 
<gallery>
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2010.png|[[2010_Summer_Project_Week#Projects|Projects List]]
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Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
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Image:SlicerWF_PECS_SUMMARY.png|Summary of Segmentation Workflow for Social Cognition Study for MS Patients.
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Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
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Image:SlicerWF_BPEL_Description.png|Simple Workflow Description Screenshot. BPEL Notation
 
</gallery>
 
</gallery>
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−
==Instructions for Use of this Template==
 
−
#Please create a new wiki page with an appropriate title for your project using the convention Project/<Project Name>
 
−
#Copy the entire text of this page into the page created above
 
−
#Link the created page into the list of projects for the project event
 
−
#Delete this section from the created page
 
−
#Send an email to tkapur at bwh.harvard.edu if you are stuck
 
  
 
==Key Investigators==
 
==Key Investigators==
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* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
+
* BWH: Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis
−
* Utah: Tom Fletcher, Ross Whitaker
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* PECS Univeristy (Hungary): Andrea Mike
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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<h3>Objective</h3>
 
<h3>Objective</h3>
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We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.
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Supplement 3D Slicer and Extensible Neuroimaging Archive Toolkit (XNAT) with workflow management system. Provide integration and interoperability between 3D Slicer, XNAT Services and 3-rd party image processing applications and high performance computing systems. Implement it as within currently developed Structural Planning and Implementation in Neurological Exploration (SPINE) System.
  
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
  
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Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below.  The main challenge to this approach is <foo>.
+
Our approach for analyzing diffusion tensors is summarized in the Main Project Page reference below.   
  
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Our plan for the project week is to first try out <bar>,...
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Our plan for the project week is to present live demo for use case instances, show examples of integration Slicer3, XNAT and Cluster Computing using Service Oriented Architecture (SOA) and Workflow approach.
 +
We also planning to quest for demanded by end-users modules that need improvement in Slicer3 (such as Brainmask Extraction), setup automation for upgraded EM Segmentation Module. We will provide on-demand tutorial for composing workflows of Slicer3 modules.
  
 
</div>
 
</div>
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<h3>Progress</h3>
 
<h3>Progress</h3>
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Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.
+
'''Prior to Project Week''': Interaction with XNAT data repository and Cluster Computing had been implemented. Several use cases had been deployed:
−
 
+
* Emphysema Assessment: Integration of Slicer Extension, Cluster Computing, XNAT Image Repository
 +
* Image Preprocessing Workflow for EM Segmentation: Integration of Slicer Internal Modules, XNAT Image Repository
 +
* Registration and Resampling to Common Space of Multi-Modality (PET/CT) Images for Longitudinal Studies: Integration of Slicer CLI and GUI Modules. (See [[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] for details).
 +
* Complex Image Processing using Slicer3 and 3-rd Party Modules: Segmentation for Social Cognition Study for MS Patients (PECS University, Hungary [[File:SlicerWF_NAC_PECS_Workflow.pdf]] )
 +
'''During Project Week''':
 +
* Adaptation of updated BRAINSFit module (Slicer 3.7 June builds) to registration pipelines
 +
* Tuning Workflow for Registration and Resampling to Common Space of Multi-Modality (PET/CT) Images for Longitudinal Studies
 +
* Training on Java SPECTRE skull stripping / brainmask extraction module (MIPAV version, Slicer CLI Pending release)
 +
* Training on updated EM Segmenter (Slicer 3.6)
 +
* Discussion of Grid Wizard (GWE) integration with workflow instances
  
 
</div>
 
</div>
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==Delivery Mechanism==
 
==Delivery Mechanism==
  
−
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
+
This work will be delivered to the NA-MIC Kit as a
  
−
#ITK Module
+
#ITK Module No
 
#Slicer Module
 
#Slicer Module
−
##Built-in
+
##Built-in No
−
##Extension -- commandline
+
##Extension -- commandline Yes (Workflow Invocation Stubs)
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##Extension -- loadable
+
##Extension -- loadable No
−
#Other (Please specify)
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#Other --  Web Service Libraries, Workflow Composite Applications deployable on GlassFish Application Server, Rich Clients for Orchestrating Workflows and Slicer GUI
  
 
==References==
 
==References==
−
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
+
* '''Main Project Page:''' [http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerWF SlicerWF Page]
−
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
+
* '''Use Case Presentations:''' [http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerWF#Presentations SlicerWF Presentations]
−
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
+
* '''Integration with Slicer GUI:''' [[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]]
−
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .
 
  
 
</div>
 
</div>
−
 
−
 
−
'''Main Project Page:''' <br>
 
−
[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerWF SlicerWF Page]
 
−
<br><br>
 
−
'''Use Case Presentations:''' <br>
 
−
[http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerWF#Presentations SlicerWF Presentations]
 
−
<br><br>
 
−
'''Plans for 2010 Summer Project Week:'''
 
−
 
−
* Use Case Scenarios. Live Demo
 
−
** Emphysema Assessment: Integration of Slicer Extension, Cluster Computing, XNAT Image Repository
 
−
** Image Preprocessing Workflow for EM Segmentation: Integration of Slicer Internal Modules, XNAT Image Repository
 
−
** Registration and Resampling to Common Space of Multi-Modality (PET/CT) Images for Longitudinal Studies: Integration of Slicer CLI and GUI Modules. (See [[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] for details).
 
−
* Complex Image Processing using Slicer3 and 3-rd Party Modules
 
−
** Use Case Presentation: Segmentation for Social Cognition Study for MS Patients (PECS University, Hungary [[File:SlicerWF_NAC_PECS_Workflow.pdf]] )
 
−
* Quest for Existing Slicer3 Functionality Extensions
 
−
** Slicer Wizards for Integration with Web Services and Workflow Instances
 
−
** Brain Mask Extraction
 
−
** White Matter Lesion Segmentation
 
−
* (On Demand) Tutorial Demo for Composing Workflow Applications
 

Latest revision as of 15:33, 25 June 2010

Home < Summer project week 2010 Workflows SOA

  • Summary of Segmentation Workflow for Social Cognition Study for MS Patients.

  • Simple Workflow Description Screenshot. BPEL Notation

Key Investigators

  • BWH: Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis
  • PECS Univeristy (Hungary): Andrea Mike

Objective

Supplement 3D Slicer and Extensible Neuroimaging Archive Toolkit (XNAT) with workflow management system. Provide integration and interoperability between 3D Slicer, XNAT Services and 3-rd party image processing applications and high performance computing systems. Implement it as within currently developed Structural Planning and Implementation in Neurological Exploration (SPINE) System.




Approach, Plan

Our approach for analyzing diffusion tensors is summarized in the Main Project Page reference below.

Our plan for the project week is to present live demo for use case instances, show examples of integration Slicer3, XNAT and Cluster Computing using Service Oriented Architecture (SOA) and Workflow approach. We also planning to quest for demanded by end-users modules that need improvement in Slicer3 (such as Brainmask Extraction), setup automation for upgraded EM Segmentation Module. We will provide on-demand tutorial for composing workflows of Slicer3 modules.

Progress

Prior to Project Week: Interaction with XNAT data repository and Cluster Computing had been implemented. Several use cases had been deployed:

  • Emphysema Assessment: Integration of Slicer Extension, Cluster Computing, XNAT Image Repository
  • Image Preprocessing Workflow for EM Segmentation: Integration of Slicer Internal Modules, XNAT Image Repository
  • Registration and Resampling to Common Space of Multi-Modality (PET/CT) Images for Longitudinal Studies: Integration of Slicer CLI and GUI Modules. (See Slicer Wizard for PET/CT workflow for details).
  • Complex Image Processing using Slicer3 and 3-rd Party Modules: Segmentation for Social Cognition Study for MS Patients (PECS University, Hungary File:SlicerWF NAC PECS Workflow.pdf )

During Project Week:

  • Adaptation of updated BRAINSFit module (Slicer 3.7 June builds) to registration pipelines
  • Tuning Workflow for Registration and Resampling to Common Space of Multi-Modality (PET/CT) Images for Longitudinal Studies
  • Training on Java SPECTRE skull stripping / brainmask extraction module (MIPAV version, Slicer CLI Pending release)
  • Training on updated EM Segmenter (Slicer 3.6)
  • Discussion of Grid Wizard (GWE) integration with workflow instances

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a

  1. ITK Module No
  2. Slicer Module
    1. Built-in No
    2. Extension -- commandline Yes (Workflow Invocation Stubs)
    3. Extension -- loadable No
  3. Other -- Web Service Libraries, Workflow Composite Applications deployable on GlassFish Application Server, Rich Clients for Orchestrating Workflows and Slicer GUI

References

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