Difference between revisions of "Projects:RegistrationLibrary:RegLib C06b"
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[[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br> | [[Projects:RegistrationDocumentation:UseCaseInventory|Back to Registration Use-case Inventory]] <br> | ||
− | == <small>v3.6. | + | == <small>v3.6.3</small>[[Image:Slicer_cvers_banner.png|70px|This case is complete and up to date for version 3.6.3]] Registration Library Case #6B: '''RSNA 2011 DEMO''' Breast MRI Treatment Assessment == |
{| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | {| style="color:#bbbbbb; " cellpadding="10" cellspacing="0" border="0" | ||
− | |[[Image: | + | |[[Image:RegLib_C06b_Thumb1.png|150px|lleft|this is the fixed reference image: PreRx Breast MRI with large tumor mass]] |
|[[Image:RegArrow_NonRigid.png|100px|lleft]] | |[[Image:RegArrow_NonRigid.png|100px|lleft]] | ||
− | |[[Image: | + | |[[Image:RegLib_C06b_Thumb2.png|150px|lleft|this is the moving image, to be registered with the reference above: PostRx Breast MRI with tumor largely absent]] |
|- | |- | ||
|fixed image/target<br>pre Rx MRI | |fixed image/target<br>pre Rx MRI | ||
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=== Modules === | === Modules === | ||
− | *'''Slicer 3.6. | + | *'''Slicer 3.6.3 recommended modules: [https://www.slicer.org/wiki/Modules:BRAINSFit Modules:BRAINSFit]''' |
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===Objective / Background === | ===Objective / Background === | ||
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===Download === | ===Download === | ||
*Data: | *Data: | ||
− | **'''[[Media: | + | **'''[[Media:RegLib_C06B_Data.zip|RegLib_C06B_Data.zip <small> (Data,Presets, Solution, zip file 85 MB) </small>]]''' |
*Presets | *Presets | ||
− | **'''[[Media: | + | **'''[[Media:RegLib_C06B_Presets.mrml|Registration parameter presets file <small> (.mrml file 20 kB) </small>]]''' |
**[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]] | **[[Projects:RegistrationDocumentation:ParameterPresetsTutorial|Link to User Guide: How to Load/Save Registration Parameter Presets]] | ||
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=== Methods === | === Methods === | ||
*'''Phase 1''': affine alignment | *'''Phase 1''': affine alignment | ||
− | #Go to the [ | + | #Go to the [https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit'''] module |
##select Presets "Xf1_Affine" or set the parameters as given below: | ##select Presets "Xf1_Affine" or set the parameters as given below: | ||
##fixed image: "PreRx_left", moving image: "PostRx_left" | ##fixed image: "PreRx_left", moving image: "PostRx_left" | ||
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###reduce "Number of Samples" to 20,000 | ###reduce "Number of Samples" to 20,000 | ||
##leave rest at defaults | ##leave rest at defaults | ||
− | ##Click Apply. Execution time ~ | + | ##Click Apply. Execution time ~ 4 seconds |
*'''Phase 2''': BSpline alignment | *'''Phase 2''': BSpline alignment | ||
− | #Go to the [ | + | #Go to the [https://www.slicer.org/wiki/Modules:BRAINSFit '''BRAINSfit'''] module |
##select Presets "Xf2_BSpline1" or set the parameters as given below: | ##select Presets "Xf2_BSpline1" or set the parameters as given below: | ||
##fixed image: "PreRx_left", moving image: "PostRx_left" | ##fixed image: "PreRx_left", moving image: "PostRx_left" | ||
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###set ''Number of Grid Subdivisions'' to 7,7,5 | ###set ''Number of Grid Subdivisions'' to 7,7,5 | ||
###set ''Maximum B-Spline Displacement'' to 10 [mm] | ###set ''Maximum B-Spline Displacement'' to 10 [mm] | ||
− | ##Click Apply. Execution time ~ | + | ##Click Apply. Execution time ~ 60 seconds |
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=== Registration Results=== | === Registration Results=== | ||
− | [[Image: | + | [[Image:RegLib_C06b_unregistered.gif||300px|unregistered]] unregistered <br> |
− | [[Image: | + | [[Image:RegLib_C06b_Affine.gif|300px|affine registered]] affine <br> |
− | [[Image: | + | [[Image:RegLib_C06b_BSpline1.gif|300px|Bspline registered]] BSpline 9x9x4 max 15mm <br> |
+ | [[Image:RegLib_C06b_DeformationField.png|300px|Bspline registered]] Deformation field for BSpline 9x9x4 max 10mm <br> | ||
+ | [[Image:RegLib_C06b_BSpline2.gif|300px|Bspline registered]] BSpline 7x7x5 max 10mm <br> | ||
+ | |||
+ | ---- | ||
+ | After N4 bias correction and histogram equalization: <br> | ||
+ | [[Image:RegLib_C06b_unregistered_n4h.gif||300px|unregistered]] unregistered <br> | ||
+ | [[Image:RegLib_C06b_Affine_n4h.gif|300px|affine registered]] affine <br> | ||
+ | [[Image:RegLib_C06b_BSpline1_n4h.gif|300px|Bspline registered]] BSpline 7x7x5 max 10mm<br> | ||
+ | [[Image:RegLib_C06b_BSpline1_deformation.gif|300px|Bspline1 deformation only]] Deformation of Post image from unmasked BSpline 7x7x5 max 10mm <br> | ||
+ | ---- | ||
+ | [[Image:RegLib_C06b_BSpline1_n4h_mask.gif|300px|Bspline registered '''+ tumor mask''']] BSpline 7x7x5 max 10mm '''+ tumor mask'''<br> | ||
+ | [[Image:RegLib_C06b_BSpline1_deformation_masked.gif|300px|Bspline1 deformation only]] Deformation of Post image from '''masked''' BSpline 7x7x5 max 10mm <br> | ||
+ | ---- | ||
+ | '''EXPERIMENTAL: BRAINSDemonsWarp'''<br> | ||
+ | [[Image:Demons_Defaults.png|200px|]] Demons: defaults<br> | ||
+ | [[Image:Demons_Demons.png|200px|]] Demons: cost fn: Demons<br> | ||
+ | [[Image: Demons_FastSymm.png|200px|]] Demons: cost fn: FastSymm <br> | ||
+ | [[Image: Demons_LogDemons.png|200px|]] Demons: cost fn: LogDemons <br> | ||
+ | [[Image: Demons_SymmetricLogDemons.png|200px|]] Demons: cost fn: SymmetricLogDemons <br> | ||
+ | [[Image: Demons_SymmetricLogDemons_Masked.png|200px|]] Demons: cost fn: SymmetricLogDemons_Masked <br> | ||
Latest revision as of 17:51, 10 July 2017
Home < Projects:RegistrationLibrary:RegLib C06bBack to ARRA main page
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Back to Registration Use-case Inventory
Contents
v3.6.3
Registration Library Case #6B: RSNA 2011 DEMO Breast MRI Treatment Assessment
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fixed image/target pre Rx MRI |
moving image post Rx MRI |
Modules
- Slicer 3.6.3 recommended modules: Modules:BRAINSFit
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:
- Presets
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
- Phase 1: affine alignment
- Go to the BRAINSfit module
- select Presets "Xf1_Affine" or set the parameters as given below:
- fixed image: "PreRx_left", moving image: "PostRx_left"
- Initialize with previous transform: select "Off"
- Initialize Transform Mode: check box for use MomentsAlign
- Registration Phases: check boxes for Include Rigid ..." and Include Affine registration phase
- Output: under Slicer Linear Transform, select new and rename to "Xf1_Affine" or similar
- Registration Parameters: this first phase is for initial alignment, we optimize/push for speed
- reduce "Number of Iterations" to 200
- reduce "Number of Samples" to 20,000
- leave rest at defaults
- Click Apply. Execution time ~ 4 seconds
- Phase 2: BSpline alignment
- Go to the BRAINSfit module
- select Presets "Xf2_BSpline1" or set the parameters as given below:
- fixed image: "PreRx_left", moving image: "PostRx_left"
- Initialize with previous transform: select "Xf1_Affine" from phase 1 above
- Initialize Transform Mode: check box for Off
- only check box for Include BSpline registration phase" , all other boxes off.
- Registration Parameters: set "Number of Samples" to 200,000 at least
- Output:
- Slicer BSpline Transform, select new and rename to "Xf2_BSpline" or similar
- Output Image Volume: select new and rename to "PostRx_left_Xf2" or similar
- Output Image Pixel Type: check box for "ushort"
- Registration Parameters:
- set "Number of Samples" to 100,000
- set Number of Grid Subdivisions to 7,7,5
- set Maximum B-Spline Displacement to 10 [mm]
- Click Apply. Execution time ~ 60 seconds
Registration Results
unregistered
affine
BSpline 9x9x4 max 15mm
Deformation field for BSpline 9x9x4 max 10mm
BSpline 7x7x5 max 10mm
After N4 bias correction and histogram equalization:
unregistered
affine
BSpline 7x7x5 max 10mm
Deformation of Post image from unmasked BSpline 7x7x5 max 10mm
BSpline 7x7x5 max 10mm + tumor mask
Deformation of Post image from masked BSpline 7x7x5 max 10mm
EXPERIMENTAL: BRAINSDemonsWarp
Demons: defaults
Demons: cost fn: Demons
Demons: cost fn: FastSymm
Demons: cost fn: LogDemons
Demons: cost fn: SymmetricLogDemons
Demons: cost fn: SymmetricLogDemons_Masked
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)