View source for BRAINSFit prostate registration

=Goal=

We are developing registration module in Slicer version 4 (which is using ITKv4) for deformable registration of prostate MRI.

We want to develop a prostate registration tool in Slicer4/ITKv4. This Slicer4/ITKv4 registration tool should be functional, accurate and fast (i.e., comparable with the functionality we had in Slicer3/ITKv3, which has been evaluated previously [1]). We worked on implementing BRAINSFit registration in SimpleITK but due to several issues (see [http://www.na-mic.org/Wiki/index.php/BRAINSFit_prostate_registration#Standing_SimpleITK_issues here]) we are considering a C++ implementation that uses ITKv3 libraries and can be integrated in the latest Slicer versions.

=Details on the registration approach=
Registration is applied to align preprocedural and intraoperational MR T2 image volumes. We are using masks the prostate for both image data sets. Registration is done using MMI metric with rigid, affine and B-spline stages applied in sequence. In Slicer3/BRAINSFit we use gradient descent for rigid/affine, and LBFGS for B-spline.

=Parameters we are using to call BRAINSFit in Slicer 3.6 and Slicer 4.4=

{| class="wikitable"
|-
! Parameter                                          !! Slicer 3.6 !! Slicer 4.4                     
|-
| --fixedVolume     || dir || dir 
|-
| --movingVolume           || dir || dir 
|-
| --outputVolume || dir || dir 
|-
| --bsplineTransform     || dir || dir 
|-
| --movingBinaryVolume           || dir || dir 

|-
| --fixedBinaryVolume   || dir || dir 

|-
| --useCenterOfROIAlign                   || True || style="background:#cef2e0;"| &#160; not an option

|-
| --initializeTransformMode                   || style="background:#cef2e0;"| &#160; not an option || useCenterOfROIAlign

|-
| --samplingPercentage                   || style="background:#cef2e0;"| &#160; not an option || 0.002

|-
| --useRigid             || True || True

|-
| --useAffine                   || True || True

|-
| --useROIBSpline                   || True || True

|-
| --useScaleVersor3D           || True || True

|-
| --useScaleSkewVersor3D            || True || True

|-
| --useBSpline             || style="background:#cef2e0;"| &#160; not an option  || True

|-
| --splineGridSize                 || 3,3,3 || 3,3,3

|-
| --numberOfIterations                  || 1500 || 1500

|-
| --maskProcessing               || ROI || ROI

|-
| --outputVolumePixelType                || float || float

|-
| --backgroundFillValue              || 0 || 0

|-
| --maskInferiorCutOffFromCenter                 || 1000 || 1000

|-
| --interpolationMode                   || Linear || Linear

|-
| --minimumStepSize                || 0.005 || style="background:#cef2e0;"| &#160; not an option 

|-
| --minimumStepLength                ||  style="background:#cef2e0;"| &#160; not an option  || 0.005

|-
| --translationScale                  || 1000 || 1000

|-
| --reproportionScale                 || 1 || 1

|-
| --skewScale                 || 1 || 1

|-
| --numberOfHistogramBins                || 50 || 50

|-
| --numberOfMatchPoints              || 10 || 10

|-
| --numberOfSamples            || 100000 ||  style="background:#cef2e0;"| &#160; not an option

|-
| --fixedVolumeTimeIndex             || 0 || 0

|-
| --movingVolumeTimeIndex              || 0 || 0

|-
| --medianFilterSize           || 0,0,0 || 0,0,0

|-
| --ROIAutoDilateSize              || 0 || 0

|-
| --relaxationFactor              || 0.5 || 0.5

|-
| --maximumStepSize              || 0.2 ||  style="background:#cef2e0;"| &#160; not an option 

|-
| --maximumStepLength              ||  style="background:#cef2e0;"| &#160; not an option  || 0.2

|-
| --failureExitCode             || -1 || -1

|-
| --debugNumberOfThreads             || -1 ||  style="background:#cef2e0;"| &#160; not an option 

|-
| --numberOfThreads            ||  style="background:#cef2e0;"| &#160; not an option  || -1

|-
| --debugLevel          || 0 || 0 

|-
| --costFunctionConvergenceFactor            || 1.00E+09 || 1.00E+09

|-
| --projectedGradientTolerance          || 1.00E-05 || 1.00E-05

|-
| --maxBSplineDisplacement            || 0 || 0

|-
| --maximumNumberOfEvaluations             ||  style="background:#cef2e0;"| &#160; not an option  || 900

|-
| --maximumNumberOfCorrections            ||  style="background:#cef2e0;"| &#160; not an option  || 25

|-
| --metricSamplingStrategy             ||  style="background:#cef2e0;"| &#160; not an option || Random

|-
| --costMetric             ||  style="background:#cef2e0;"| &#160; not an option  || MMI 

|-
| --removeIntensityOutliers            ||  style="background:#cef2e0;"| &#160; not an option  || 0 


|-
| --ROIAutoClosingSize             ||  style="background:#cef2e0;"| &#160; not an option  || 9


|-
| --useExplicitPDFDerivativesMode            || AUTO ||  style="background:#cef2e0;"| &#160; not an option 

|-
| --useCachingOfBSplineWeightsMode            || ON || style="background:#cef2e0;"| &#160; not an option 

|}

=Results using the above parameters=
We used [http://www.slicer.org/publications/item/view/2147 this sample data] with Reader 1 segmentations to visually evaluate differences in the registration results. 
All three results of BRAINSFit with ITKv3 in Slicer 3.6 look reasonable. Using BRAINSFit with ITKv4 in Slicer 4.4 creates a reasonable result for Case 7, but look strongly distorted towards the edges of the bounding box in Case 8 and 9. 

{|
| Case 7
|[[Image:pat7-ref.png‎ |thumb|300px|Reference intraop volume]] 
|[[Image:pat7-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]] 
|[[Image:pat7-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]] 
|}

{|
| Case 8
|[[Image:pat8-ref.png‎ |thumb|300px|Reference intraop volume]] 
|[[Image:pat8-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]] 
|[[Image:pat8-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]] 
|}

{|
| Case 9
|[[Image:pat9-ref.png‎ |thumb|300px|Reference intraop volume]] 
|[[Image:pat9-3_6.png|thumb|300px|Reg Result Slicer 3.6 with ITKv3]] 
|[[Image:pat9-4_4.png|thumb|300px|Reg Result Slicer 4.4 with ITKv4]] 
|}

=Current status=

SimpleITK registration code on github: [https://github.com/PeterBehringer/SimpleITKtraining/blob/master/BRAINSFit_to_sitk_MMI.py here]

'''Latest update: Mai 9, 2015'''

==Things that are working==
* exhaustive search based initialization procedure implemented and produces good results (cross-correlation metric) in SimpleITK

==Things that are implemented, but are not working==
* SimpleITK code for rigid registration
** the voxel sampling exception can be avoided by cropping the images sharply around the masks. 
{|
|
|[[Image:FixedVolume.png|thumb|300px|Fixed Volume as Reference]] 
|[[Image:AfterInit.png|thumb|300px|SimpleITK result after Initialization]] 
|[[Image:AfterRigid.png|thumb|300px|SimpleITK result after rigid registration]] 
|[[Image:BRAINSFitOut.png|thumb|300px|BRAINSFit result after rigid without using masks and --useCenterOfGeometryAlign]]
|}
** The rigid registration result is too much rotated and translated. Also the number of iteration steps varies with every computation. Reason might be that seed is set randomized and not set as done in BRAINSFit [https://github.com/BRAINSia/BRAINSTools/blob/af0ff12b8b751f9423061d42178268acab5f85f4/BRAINSCommonLib/BRAINSFitHelper.h#L375 here]. There is no option at the [http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageRegistrationMethod.html SimpleITK::ImageRegistrationMethod] to set a metric seed.

==Things that are not implemented, but need to be implemented==
* SimpleITK code for affine registration
** setting affineOptimizer [https://github.com/BRAINSia/BRAINSTools/blob/19fa37dfbdee37deff4ccee412bb601f7a787bda/BRAINSCommonLib/genericRegistrationHelper.hxx#L158-L187 here]
** setting RegistrationMethod [https://github.com/BRAINSia/BRAINSTools/blob/19fa37dfbdee37deff4ccee412bb601f7a787bda/BRAINSCommonLib/genericRegistrationHelper.hxx#L289-L353 here]
* SimpleITK code for BSpline registration (started [https://github.com/PeterBehringer/SimpleITKtraining/blob/master/simpleITK_to_sitk_BSpline.py here])

=Unresolved issues out of our direct control=
==Standing SimpleITK issues==
* no API for consistent initialization of the metric seed
*

==Standing ITKv4 issues==
* capability to sample voxels only within the mask (see topic under review on Gerrit: http://review.source.kitware.com/#/c/19684/)
*

==Standing Slicer4 issues==
=References=
[1] Fedorov A, Tuncali K, Fennessy FM, Tokuda J, Hata N, et al. (2012) Image registration for targeted MRI-guided transperineal prostate biopsy. J Magn Reson Imaging 36: 987–992. Available: http://dx.doi.org/10.1002/jmri.23688.