Difference between revisions of "2014 Project Week:TBISegmentation"

From NAMIC Wiki
Jump to: navigation, search
 
(One intermediate revision by the same user not shown)
Line 8: Line 8:
 
Image:AcSeg_final_seg_normal_tissue_classes.jpg| Segmentation of normal tissue classes
 
Image:AcSeg_final_seg_normal_tissue_classes.jpg| Segmentation of normal tissue classes
 
</gallery>
 
</gallery>
 +
  
 
==Key Investigators==
 
==Key Investigators==
Line 36: Line 37:
 
<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>
 
</div>

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