Difference between revisions of "2011 Summer Project Week Plastimatch for EMSegmenter"

From NAMIC Wiki
Jump to: navigation, search
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
(8 intermediate revisions by 2 users not shown)
Line 2: Line 2:
 
<gallery>
 
<gallery>
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
 
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]]
Image:notfound.png|Interesting picture to be added...
 
 
</gallery>
 
</gallery>
  
'''Full Title of Project'''
+
'''Integrating Plastimatch into the EMSegmenter'''
  
 
==Key Investigators==
 
==Key Investigators==
 
* University of Pennsylvania: Dominique Belhachemi
 
* University of Pennsylvania: Dominique Belhachemi
 
* University of Pennsylvania: Kilian Pohl
 
* University of Pennsylvania: Kilian Pohl
 +
* University of Pennsylvania: Daniel Haehn
 
* MGH: Greg Sharp
 
* MGH: Greg Sharp
  
Line 17: Line 17:
  
 
<h3>Objective</h3>
 
<h3>Objective</h3>
 
+
During the EMSegmenter's pre-processing we have to register our internal atlas to the subject scan. Currently we support two registration tools:<br>
The EMSegmenter module supports two registration tools right now:<br>
 
 
1. BRAINSFit<br>
 
1. BRAINSFit<br>
 
2. CMTK<br>
 
2. CMTK<br>
Line 44: Line 43:
  
 
<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
 
<!-- Fill this out before Friday's summary presentations - list what you did and how well it worked. -->
 
+
We added plastimatch to the EMSegmenter GUI and integrated some base code to call plastimatch.<br>
 +
Fixed compiler issue on i386 for stand-alone plastimatch and Slicer's plastimatch extension.<br>
 +
Now we have a nighly plastimatch-slicer extension for Linux 32 bit.<br>
 +
We had to add an option to plastimatch's reformat command to specify the target grid. <br>
 +
<br>
 +
Open: Find the right parameter for our CT use cases.
  
 
</div>
 
</div>
Line 53: Line 57:
 
==References==
 
==References==
  
http://plastimatch.org/
+
http://plastimatch.org/ <br>
http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks
+
https://www.slicer.org/wiki/EMSegmenter-Tasks
 
<!-- Add links here to background material: where can we download the data?  where is the source code repository?  what papers or web sites will help someone quickly learn what the outstanding issues are? -->
 
<!-- Add links here to background material: where can we download the data?  where is the source code repository?  what papers or web sites will help someone quickly learn what the outstanding issues are? -->
  
Line 61: Line 65:
 
<!-- List here how you plan to deliver your results to user communities -->
 
<!-- List here how you plan to deliver your results to user communities -->
  
This work will be delivered to the NAMIC Kit as a
+
This work will be delivered to the NAMIC Kit as part of the EMSegmenter module.
 
 
<!-- #NITRIC distribution -->
 
#Slicer Module
 
##Built-in:
 
##Extension -- commandline: 
 
##Extension -- loadable:
 

Latest revision as of 16:58, 10 July 2017

Home < 2011 Summer Project Week Plastimatch for EMSegmenter

Integrating Plastimatch into the EMSegmenter

Key Investigators

  • University of Pennsylvania: Dominique Belhachemi
  • University of Pennsylvania: Kilian Pohl
  • University of Pennsylvania: Daniel Haehn
  • MGH: Greg Sharp


Objective

During the EMSegmenter's pre-processing we have to register our internal atlas to the subject scan. Currently we support two registration tools:
1. BRAINSFit
2. CMTK

We would like to add "plastimatch" to this list.


Approach, Plan

Investigating the commandline interface of plastimatch.
Find the right parameter for our use cases.


Progress

We added plastimatch to the EMSegmenter GUI and integrated some base code to call plastimatch.
Fixed compiler issue on i386 for stand-alone plastimatch and Slicer's plastimatch extension.
Now we have a nighly plastimatch-slicer extension for Linux 32 bit.
We had to add an option to plastimatch's reformat command to specify the target grid.

Open: Find the right parameter for our CT use cases.

References

http://plastimatch.org/
https://www.slicer.org/wiki/EMSegmenter-Tasks

Delivery Mechanism

This work will be delivered to the NAMIC Kit as part of the EMSegmenter module.