Difference between revisions of "2014 Project Week:TBISegmentation"

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<gallery>
 
<gallery>
 
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
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Image:AcSeg_initial_box.jpg| Initial bounding box
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Image:AcSeg_selftraining.jpg| Self training update
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Image:AcSeg_activelearning.jpg| Active learning update
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Image:AcSeg_final_alphamap.jpg| Final alpha map
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Image:AcSeg_final_seg_normal_tissue_classes.jpg| Segmentation of normal tissue classes
 
</gallery>
 
</gallery>
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==Key Investigators==
 
==Key Investigators==
 
* GE: Marcel Prastawa
 
* GE: Marcel Prastawa
 
* Utah: Bo Wang, Guido Gerig
 
* Utah: Bo Wang, Guido Gerig
−
* UCLA: Andrei Irimia, Jack Van Horn
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* USC: Andrei Irimia, Jack Van Horn
  
  
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<h3>Objective</h3>
 
<h3>Objective</h3>
−
* Developing a pipeline using Slicer modules for the input of the TBI segmentation algorithm.  
+
* Develop a pipeline combining our TBI segmentation algorithm with other Slicer modules.
−
* We intend to spend some time on user study about human experts manual segmentation.  
+
* Study and gain understanding of the manual process for segmenting TBI.
−
* Testing the algorithm and getting feedback from USC team.  
+
* Test the algorithm with users from USC.  
  
 
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</div>
 
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<div style="width: 27%; float: left; padding-right: 3%;">
 
<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
−
* Testing to use Slicer registration module for intra and inter time points coregistration
+
* Wrap existing code into a Slicer extension.
−
* Testing to use Slicer registration module for initial atlas alignment
+
* Determine approaches for user interaction for semi-automatic segmentation.
−
* Testing to use Slicer skull stripping module to generate initial brain mask  
+
* Test and evaluate Slicer modules for TBI processing:
−
* Conducting user studies about human experts manual segmentation
+
** Intra and inter time points coregistration.
 +
** Initial atlas alignment using affine transformation.
 +
** Skull stripping to obtain initial brain mask.
 
</div>
 
</div>
 
<div style="width: 27%; float: left; padding-right: 3%;">
 
<div style="width: 27%; float: left; padding-right: 3%;">
 
<h3>Progress</h3>
 
<h3>Progress</h3>
−
*  
+
* Ran the command line tool with Andrei step by step to show how it works and test it.
 +
* Meeting with Jack and Andrei to discuss sharing the current command line tool with them.
 +
* Joined the TBI DBP meeting to discuss how to integrate the current command line tool into Slicer 3D.
 +
** Stephen and Steve recommended to do a Python scripting module and talk to Jean-Christophe.
 +
** Talked to Jean-Christophe and he pointed me a tutorial [http://www.na-mic.org/Wiki/index.php/2013_Project_Week_Breakout_Session:Slicer4Python the wiki of breakout session Slicer4Python].
 +
** Tried to understand the Slicer4Python tutorial and followed it step by step (still working on).
 +
** Talked to other Slicer developers to ask for help and suggestions.
 
</div>
 
</div>
 
</div>
 
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 +
== Reference ==
 +
* [http://www.nitrc.org/projects/parser_4d 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration) Code Repo]
 +
* [http://www.cs.utah.edu/~bowang/projects/active4D/4D_Active_Cut.html 4D Active Cut]
 +
* [http://link.springer.com/chapter/10.1007/978-3-319-02126-3_4 Modeling 4D changes in TBI]

Latest revision as of 06:12, 10 January 2014

Home < 2014 Project Week:TBISegmentation

  • Initial bounding box

  • Self training update

  • Active learning update

  • Final alpha map

  • Segmentation of normal tissue classes


Key Investigators

  • GE: Marcel Prastawa
  • Utah: Bo Wang, Guido Gerig
  • USC: Andrei Irimia, Jack Van Horn


Project Description

Objective

  • Develop a pipeline combining our TBI segmentation algorithm with other Slicer modules.
  • Study and gain understanding of the manual process for segmenting TBI.
  • Test the algorithm with users from USC.

Approach, Plan

  • Wrap existing code into a Slicer extension.
  • Determine approaches for user interaction for semi-automatic segmentation.
  • Test and evaluate Slicer modules for TBI processing:
    • Intra and inter time points coregistration.
    • Initial atlas alignment using affine transformation.
    • Skull stripping to obtain initial brain mask.

Progress

  • Ran the command line tool with Andrei step by step to show how it works and test it.
  • Meeting with Jack and Andrei to discuss sharing the current command line tool with them.
  • Joined the TBI DBP meeting to discuss how to integrate the current command line tool into Slicer 3D.
    • Stephen and Steve recommended to do a Python scripting module and talk to Jean-Christophe.
    • Talked to Jean-Christophe and he pointed me a tutorial the wiki of breakout session Slicer4Python.
    • Tried to understand the Slicer4Python tutorial and followed it step by step (still working on).
    • Talked to other Slicer developers to ask for help and suggestions.

Reference

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