Difference between revisions of "Projects:RegistrationLibrary:RegLib C06"
From NAMIC Wiki
Line 5: | Line 5: | ||
== <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 == | ||
− | {| style="color:#bbbbbb | + | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" |
− | |[[Image:RegLib_C06_BreastCancer_PreRx.png| | + | |[[Image:RegLib_C06_BreastCancer_PreRx.png|150px|lleft|this is the fixed reference image. All images are aligned into this space]] |
− | |[[Image: | + | |[[Image:RegArrow_NonRigid.png|100px|lleft]] |
− | |[[Image:RegLib_C06_BreastCancer_PostRx.png| | + | |[[Image:RegLib_C06_BreastCancer_PostRx.png|150px|lleft|this is the DTI Baseline scan, to be registered with the T2]] |
− | |||
− | |||
− | |||
|- | |- | ||
− | | | + | |fixed image/target<br>pre Rx MRI |
| | | | ||
− | | | + | |moving image<br>post Rx MRI |
− | |||
− | |||
− | |||
− | |||
|} | |} | ||
+ | |||
+ | === 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 === | ===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). | ||
Line 28: | Line 27: | ||
===Input Data=== | ===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 === | === Methods === | ||
Line 35: | Line 35: | ||
#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) | ||
− | #run affine registration ('' | + | #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 | ||
Line 43: | Line 43: | ||
##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) | ||
− | #run Bspline non-rigid registration (''Deformable BSpline registration'' module) | + | #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 C06Back to ARRA main page
Back to Registration main page
Back to Registration Use-case Inventory
Contents
v3.6.1
Registration Library Case #6: Breast MRI Treatment Assessment
![]() |
![]() |
![]() |
fixed image/target pre Rx MRI |
moving image post Rx MRI |
Modules
- Slicer 3.6.1 recommended 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
- Extract left 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 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
Download
- download entire package (Data,Presets, Solution, zip file 85 MB)
- download registration parameter presets file (.mrml file 20 kB)
- download guided tutorial (PowerPoint, 2.6 MB)
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)