Difference between revisions of "2014 Project Week:TBISegmentation"

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Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
Image:Active_4D.png| Interactive process
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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
 
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==Key Investigators==
 
==Key Investigators==
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<h3>Progress</h3>
 
<h3>Progress</h3>
*  
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* Ran the command line tool with Andrei step by step to show how it works and test it.
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* Meeting with Jack and Andrei to discuss sharing the current command line tool with them.
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* Joined the TBI DBP meeting to discuss how to integrate the current command line tool into Slicer 3D.
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** Stephen and Steve recommended to do a Python scripting module and talk to Jean-Christophe.
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** 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].
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** Tried to understand the Slicer4Python tutorial and followed it step by step (still working on).
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** Talked to other Slicer developers to ask for help and suggestions.
 
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Latest revision as of 06:12, 10 January 2014

Home < 2014 Project Week:TBISegmentation


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