Difference between revisions of "2013 Project Week:BRAINSFit new features"

From NAMIC Wiki
Jump to: navigation, search
 
(2 intermediate revisions by the same user not shown)
Line 2: Line 2:
 
<gallery>
 
<gallery>
 
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
 
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
 +
Image:SLC2013-Prostate_BRAINS_fixed.png|Reference test image
 +
Image:SLC2013-Prostate_BRAINS_moving.png|Registered moving image
 
</gallery>
 
</gallery>
  
Line 7: Line 9:
  
 
* BWH: Andrey Fedorov
 
* BWH: Andrey Fedorov
* Iowa: Hans Johnson
+
* Iowa: Hans Johnson, David Welch
 
==Project Description==
 
==Project Description==
  
Line 25: Line 27:
 
<div style="width: 27%; float: left; padding-right: 3%;">
 
<div style="width: 27%; float: left; padding-right: 3%;">
 
<h3>Progress</h3>
 
<h3>Progress</h3>
 
+
* all features that we intended to integrate were implemented and merged with the BRAINS main repository (https://github.com/BRAINSia/BRAINSStandAlone/pull/160)
 +
** in the process, several minor bugs were resolved
 +
* test added and is passing on BRAINS dashboard
 +
* Note: BRAINS is using ITK3 registration framework implemented in ITK4; it is currently not possible to evaluate the new registration framework of ITK4 with BRAINS
 +
* Testing on 10 clinical datasets was performed using BRAINS+ITK4
 +
** computation time is comparable with our in-house BRAINS implementation + ITK3
 +
** registration was successful in 8 out of 10 cases, based on visual inspection; further investigation is needed for the failed cases and larger scale validation
 
</div>
 
</div>
 
</div>
 
</div>
Line 31: Line 39:
 
==References==
 
==References==
 
* https://github.com/BRAINSia/BRAINSStandAlone
 
* https://github.com/BRAINSia/BRAINSStandAlone
* http://www.na-mic.org/Wiki/index.php/Image_Registration_for_MRg_Prostate_Biopsy
 
 
* http://www.na-mic.org/Wiki/index.php/Image_Registration_for_MRg_Prostate_Biopsy
 
* http://www.na-mic.org/Wiki/index.php/Image_Registration_for_MRg_Prostate_Biopsy

Latest revision as of 23:14, 10 January 2013

Home < 2013 Project Week:BRAINSFit new features

Key Investigators

  • BWH: Andrey Fedorov
  • Iowa: Hans Johnson, David Welch

Project Description

Objective

  • integrate, test and document new capabilities, which proved to be very helpful for prostate MRI registration, into BRAINSFit registration module

Approach, Plan

  • specific features include:
    • initializer based on the center of mask for the registration ROIs
    • initialization of the B-spline transform support region restricted to the bounding box of the ROIs union
    • ability to perform registration with only fixed ROI available

These features have been implemented earlier in a fork of ITK3-based BRAINSFit. We would like to merge these modifications with the main repository of BRAINS and test the capabilities with ITK4 on prostate MRI datasets.

Progress

  • all features that we intended to integrate were implemented and merged with the BRAINS main repository (https://github.com/BRAINSia/BRAINSStandAlone/pull/160)
    • in the process, several minor bugs were resolved
  • test added and is passing on BRAINS dashboard
  • Note: BRAINS is using ITK3 registration framework implemented in ITK4; it is currently not possible to evaluate the new registration framework of ITK4 with BRAINS
  • Testing on 10 clinical datasets was performed using BRAINS+ITK4
    • computation time is comparable with our in-house BRAINS implementation + ITK3
    • registration was successful in 8 out of 10 cases, based on visual inspection; further investigation is needed for the failed cases and larger scale validation

References