2014 Project Week:TBISegmentation - Revision history

Bowang at 06:12, 10 January 2014

2014-01-10T06:12:19Z

2014-01-10T06:08:06Z

2014-01-10T05:51:24Z

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 <h3>Progress</h3>
 * Ran the command line tool with Andrei step by step to show how it works and test it.
 * 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].
 ** Talked to other Slicer developers to ask for help and suggestions.
 </div>

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 Image:AcSeg_final_seg_normal_tissue_classes.jpg| Segmentation of normal tissue classes
 </gallery>
 ==Key Investigators==
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 <div style="width: 27%; float: left; padding-right: 3%;">
 <h3>Progress</h3>
+* Ran the command line tool with Andrei step by step to show how it works and test it.
 </div>
 </div>

@@ Line 8: / Line 8: @@
 Image:AcSeg_final_seg_normal_tissue_classes.jpg| Segmentation of normal tissue classes
 </gallery>
 ==Key Investigators==

@@ Line 2: / Line 2: @@
 <gallery>
 Image:PW-SLC2014.png|[[2014_Winter_Project_Week#Projects|Projects List]]
-Image:Active_4D.png| Interactive process
+Image:AcSeg_initial_box.jpg| Initial bounding box
 </gallery>
 ==Key Investigators==

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 <h3>Objective</h3>
 * Develop a pipeline combining our TBI segmentation algorithm with other Slicer modules.
-* Study and gain understanding of the manual process for segmenting TBI
+* Study and gain understanding of the manual process for segmenting TBI.
 * Test the algorithm with users from USC.
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 == Reference ==
-* [http://www.nitrc.org/projects/parser_4d 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration)]
+* [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]

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 <div style="width: 27%; float: left; padding-right: 3%;">
 <h3>Approach, Plan</h3>
-* Wrap existing code into a Slicer extension
+* Wrap existing code into a Slicer extension.
-* Determine approaches for user interaction for semi-automatic segmentation segmentation.
+* Determine approaches for user interaction for semi-automatic segmentation.
 * Test and evaluate Slicer modules for TBI processing:
-** Intra and inter time points coregistration
+** Intra and inter time points coregistration.
-** Initial atlas alignment using affine transformation
+** Initial atlas alignment using affine transformation.
-** Skull stripping to obtain initial brain mask
+** Skull stripping to obtain initial brain mask.
 </div>
 <div style="width: 27%; float: left; padding-right: 3%;">
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 == Reference ==
 * [http://www.nitrc.org/projects/parser_4d 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration)]

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 * GE: Marcel Prastawa
 * Utah: Bo Wang, Guido Gerig
-* UCLA: Andrei Irimia, Jack Van Horn
+* USC: Andrei Irimia, Jack Van Horn