Difference between revisions of "2011 Summer Project Week Plastimatch for EMSegmenter"
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<gallery> | <gallery> | ||
Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]] | Image:PW-MIT2011.png|[[2011_Summer_Project_Week#Projects|Projects List]] | ||
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</gallery> | </gallery> | ||
| − | ''' | + | '''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: Daniel Haehn | ||
| + | * MGH: Greg Sharp | ||
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<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> | ||
| + | 1. BRAINSFit<br> | ||
| + | 2. CMTK<br> | ||
| + | We would like to add "plastimatch" to this list. | ||
<!-- What you plan to achieve during project week goes here --> | <!-- What you plan to achieve during project week goes here --> | ||
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<h3>Approach, Plan</h3> | <h3>Approach, Plan</h3> | ||
| + | Investigating the commandline interface of plastimatch.<br> | ||
| + | Find the right parameter for our use cases. | ||
<!-- What specific things you will be doing during the week: writing code? trying code on specific datasets? talking with other attendees? All of the above? --> | <!-- What specific things you will be doing during the week: writing code? trying code on specific datasets? talking with other attendees? All of the above? --> | ||
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<!-- 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> | ||
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==References== | ==References== | ||
| − | http://plastimatch.org/ | + | http://plastimatch.org/ <br> |
| − | + | 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? --> | ||
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<!-- 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 | + | This work will be delivered to the NAMIC Kit as part of the EMSegmenter module. |
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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.
