Difference between revisions of "Projects:RegistrationLibrary:RegLib C06"

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== <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]]  Registration Library  Case #6: Breast MRI Treatment Assessment ==
 
== <small>v3.6.1</small> [[Image:Slicer3-6Announcement-v1.png‎|150px]]  Registration Library  Case #6: Breast MRI Treatment Assessment ==
  
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{| style="color:#bbbbbb; background-color:#333333;" cellpadding="10" cellspacing="0" border="0"
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{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0"
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|[[Image:RegLib_C06_BreastCancer_PreRx.png|200px|lleft|this is the fixed reference image. All images are aligned into this space]]  
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|[[Image:RegLib_C06_BreastCancer_PreRx.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]]  
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|[[Image:Arrow_left_gray.jpg|100px|lleft]]  
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|[[Image:RegArrow_NonRigid.png|100px|lleft]]  
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|[[Image:RegLib_C06_BreastCancer_PostRx.png|200px|lleft|this is the moving image. The transform is calculated by matching this to the reference image]]
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|[[Image:RegLib_C06_BreastCancer_PostRx.png|150px|lleft|this is the DTI Baseline scan, to be registered with the T2]]
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|align="left"|LEGEND<br>
 
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[[Image:Button_red_fixed.jpg|20px|lleft]] this indicates the reference image that is fixed and does not move. All other images are aligned into this space and resolution<br>
 
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[[Image:Button_green_moving.jpg|20px|lleft]]  this indicates the moving image that determines the registration transform.  <br>
 
 
|-
 
|-
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|[[Image:Button_red_fixed.jpg|40px|lleft]]  axial
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|fixed image/target<br>pre Rx MRI
 
|
 
|
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|[[Image:Button_green_moving.jpg|40px|lleft]] T1 SPGR
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|moving image<br>post Rx MRI
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|-
 
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|0.44 x 0.44 x 5 mm<br> 784 x 784 x 30<br>RAS
 
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|
 
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|0.68 x 0.68 x 1.5 mm<br> 515 x 515 x 93<br>RAS
 
 
|}
 
|}
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=== Modules  ===
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*'''Slicer 3.6.1 recommended modules:
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** [http://www.slicer.org/slicerWiki/index.php/Modules:RegisterImagesMultiRes-Documentation-3.6 Robust Multiresolution Affine]'''
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** [http://www.slicer.org/slicerWiki/index.php/Modules:DeformableB-SplineRegistration-Documentation-3.6 Fast Nonrigid BSpline]'''
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===Objective / Background ===
 
===Objective / Background ===
 
We seek to align the post-treatment (PostRx) scan with the pre-treatment scan to compare local effects (left side only).
 
We seek to align the post-treatment (PostRx) scan with the pre-treatment scan to compare local effects (left side only).
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===Input Data===
 
===Input Data===
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*[[Image:Button_red_fixed_white.jpg|20px]]reference/fixed : T1 SPGR , 0.9375 x 0.9375 x 1.4 mm voxel size, axial, RAS orientation.
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*reference/fixed : 0.44 x 0.44 x 5 mm , 784 x 784 x 30
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*[[Image:Button_green_moving_white.jpg|20px]] moving: T1 SPGR , 0.9375 x 0.9375 x 1.2 mm voxel size, sagittal, RAS orientation.
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*moving: 0.68 x 0.68 x 1.5 mm, 515 x 515 x 93
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=== Methods ===
 
=== Methods ===
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#Extract right breast image of PreRx scan (''ExtractSubvolumeROI'' module)
 
#Extract right breast image of PreRx scan (''ExtractSubvolumeROI'' module)
 
#run MRI Bias field inhomogeneity correction on PreRx scan (''MRI Bias Field Correction'' module)
 
#run MRI Bias field inhomogeneity correction on PreRx scan (''MRI Bias Field Correction'' module)
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#run affine registration (''RegisterImages Multires'' module)
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#run affine registration (''Robust Multiresolution Affine'' module)
 
##Fixed Image: PreRx_left_BiasCorr
 
##Fixed Image: PreRx_left_BiasCorr
 
##Moving Image: PostRx_left
 
##Moving Image: PostRx_left
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##Step Size (voxels):5
 
##Step Size (voxels):5
 
#Evaluate quality of Affine registration: drag PostRx_left inside the abovecreated Xform node (''Data'' module)
 
#Evaluate quality of Affine registration: drag PostRx_left inside the abovecreated Xform node (''Data'' module)
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#run Bspline non-rigid registration (''Deformable BSpline registration'' module)
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#run Bspline non-rigid registration (''Fast Deformable BSpline registration'' module)
 
##Iterations: 50
 
##Iterations: 50
 
##Grid Size: 5
 
##Grid Size: 5

Revision as of 17:03, 28 September 2010

Home < Projects:RegistrationLibrary:RegLib C06

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v3.6.1 Slicer3-6Announcement-v1.png Registration Library Case #6: Breast MRI Treatment Assessment

this is the fixed reference image. All images are aligned into this space lleft this is the DTI Baseline scan, to be registered with the T2
fixed image/target
pre Rx MRI 		moving image
post Rx MRI

Modules

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

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

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

Registration Results

unregistered affine registered Bspline registered

Download

Link to User Guide: How to Load/Save Registration Parameter Presets


Discussion: Registration Challenges

  • soft tissue deformations during image acquisition cause large differences in appearance
  • 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)
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