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Meier: /* Versions */

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== v3.6.1 [[Image:Slicer3-6Announcement-v1.png‎|150px]] Registration Library Case #6: Breast MRI Treatment Assessment ==

{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
|[[Image:RegLib_C06_BreastCancer_PreRx.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]
|[[Image:RegArrow_NonRigid.png|100px|lleft]]
|[[Image:RegLib_C06_BreastCancer_PostRx.png|150px|lleft|this is the DTI Baseline scan, to be registered with the T2]]
|-
|fixed image/target pre Rx MRI
|
|moving image post Rx MRI
|}
=== Versions ===
<big>[[Projects:RegistrationLibrary:RegLib_C06B|'''For the Slicer 4.1 version of this tutorial see here''']]</big>

=== Modules ===
*'''Slicer 3.6.1 recommended modules:
** [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]'''
** [http://www.slicer.org/slicerWiki/index.php/Modules:DeformableB-SplineRegistration-Documentation-3.6 Fast Nonrigid BSpline]'''

===Objective / Background ===
We seek to align the post-treatment (PostRx) scan with the pre-treatment scan to compare local effects (left side only).

=== Keywords ===
MRI, breast cancer, intra-subject, treatment assessment, change detection, non-rigid registration

===Download ===
*Data:
**'''[[Media:RegLib_C06_BreastCancer_Data.zip|RegLib_C06_BreastCancer_Data.zip (Data,Presets, Solution, zip file 85 MB) ]]'''
*Presets
**'''[[Media:RegLib_C06_BreastCancer_ParameterPresets.mrml|Registration parameter presets file (.mrml file 20 kB) ]]'''
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]]
*Documentation
**'''[[Media:RegLib_C06_BreastCancer_Tutorial.ppt|download guided tutorial (PowerPoint, 2.6 MB) ]]'''
**'''[[Media:RegLib_C06_BreastCancer_Tutorial.ppt|download guided tutorial (PDF, 1 MB) ]]'''

===Input Data===
*reference/fixed : 0.44 x 0.44 x 5 mm , 784 x 784 x 30
*moving: 0.68 x 0.68 x 1.5 mm, 515 x 515 x 93

=== Methods ===
#Extract left breast image of PreRx scan (''ExtractSubvolumeROI'' module)
#Extract left breast image of PostRx scan (''ExtractSubvolumeROI'' module)
#run MRI Bias field inhomogeneity correction on PreRx scan (''MRI Bias Field Correction'' module)
#run affine registration (''Robust Multiresolution Affine'' module)
##Fixed Image: PreRx_left_BiasCorr
##Moving Image: PostRx_left
##Resample Image: none
##Output transform: Create new linear transform, rename to: ''Xform_Aff0_MRes''
##Fixed Image Mask: none
##Step Size (voxels):5
#Evaluate quality of Affine registration: drag PostRx_left inside the abovecreated Xform node (''Data'' module)
#run Bspline non-rigid registration (''Fast Deformable BSpline registration'' module)
##Iterations: 50
##Grid Size: 5
##Histogram Bins: 100
##Spatial Samples: 80000
##Constrain Deformation: no
##Initial Transform: XForm_Aff0_MRes
##Fixed Image: PreRx_left_BiasCorr
##Moving Image: PostRx_left
##Output Transform: Create New BSpline Transform, rename to: Xform_BSpline1_Aff0Init
##Output Volume: Create New Volume, rename to: PostRx_left_BSpline1
##Apply.

=== Registration Results===
[[Image:RegLib_C06_LeftUnreg_AnimGif.gif||300px|unregistered]]
[[Image:RegLib_C06_LeftAffreg_AnimGif.gif|300px|affine registered]]
[[Image:RegLib_C06_LeftBSplreg_AnimGif.gif|300px|Bspline registered]]



=== Discussion: Registration Challenges ===
*soft tissue deformations during image acquisition cause large differences in appearance
*the large tumor recession represents a significant pre/post difference in image content that will influence unmasked intensity-driven registration, which becomes a problem for the non-rigid portion of registration, particularly at higher DOF, because the registration will try to "recreate" the tumor area from the postRx image in order to match the content.
*contrast enhancement and pathology and treatment changes cause additional differences in image content
*the surface coils used cause strong differences in intensity inhomogeneity.
*we have strongly anisotropic voxel sizes with much less through-plane resolution
*resolution and FOV change between the two scans

=== Discussion: Key Strategies ===
*because of the strong changes in shape and position, we break the problem down and register each breast separately.
*we perform a bias-field correction on both images before registration
*we use the Multires version of RegisterImages for an initial affine alignment
*the nonlinear portion is then addressed with a BSpline or DiffeomorphicDemons algorithm
*because accuracy is more important than speed here, we increase the sampling rate (i.e. the number of points sampled for the BSpline registration)

@@ Line 19: / Line 19: @@
 === Modules  ===
 *'''Slicer 3.6.1 recommended modules:
-** [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]'''
+** [https://www.slicer.org/wiki/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]'''
-** [http://www.slicer.org/slicerWiki/index.php/Modules:DeformableB-SplineRegistration-Documentation-3.6 Fast Nonrigid BSpline]'''
+** [https://www.slicer.org/wiki/Modules:DeformableB-SplineRegistration-Documentation-3.6 Fast Nonrigid BSpline]'''
 ===Objective / Background ===

@@ Line 15: / Line 15: @@
 |}
 === Versions ===
-<big>[[Projects:RegistrationLibrary:RegLib_C06B|'''For the Slicer 4.1 version of this tutorial see here''']]</big>
+<big>[[Projects:RegistrationLibrary:RegLib_C06|'''For the Slicer 4.1 version of this tutorial see here''']]</big>
 === Modules  ===

Projects:RegistrationLibrary:RegLib C06B - Revision history

Grundlett: Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/"

Meier: /* Versions */

Meier: Created page with 'Back to ARRA main page Back to Registration main page [[Projects:RegistrationDocumentation:UseCaseInv…'

Meier: Created page with 'Back to ARRA main page
Back to Registration main page
[[Projects:RegistrationDocumentation:UseCaseInv…'